Contacts of the helix formed by residues 346 - 368 (chain A) in PDB entry 4P3N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 346 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 3.4 56.3 - - + +
332A LEU 2.8 17.4 + - - +
333A TYR* 4.6 2.9 - - - +
334A PHE* 3.9 28.3 - - + -
344A PHE 3.7 1.0 + - - -
345A PHE* 1.3 73.1 - - - +
347A PRO* 1.3 68.9 - - + +
348A LYS 3.2 1.1 - - - +
349A GLY 3.0 3.3 + - - -
350A ALA* 2.7 30.9 + - - +
419B MET* 3.6 27.6 - - + +
422B HIS* 4.6 12.6 - - + +
425B ARG* 5.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 1.3 93.6 - - + +
348A LYS* 1.3 60.1 + - + +
350A ALA* 3.5 1.7 - - - +
351A TYR* 2.9 26.5 + - - +
647A MET* 4.7 7.6 - - + +
370B GLN* 3.7 48.5 - - + +
371B GLU 3.3 14.3 - - - +
372B VAL* 3.7 16.6 - - + -
419B MET* 4.6 1.8 - - + -
432B LEU* 6.2 0.2 - - + -
434B LEU* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN 3.6 7.2 - - - +
331A GLU* 3.8 15.0 - - + +
332A LEU* 3.6 10.8 - - + -
346A LEU* 3.0 1.4 + - - +
347A PRO* 1.3 75.4 - - + +
349A GLY* 1.3 65.8 + - - +
351A TYR* 3.0 8.1 + - - +
352A ILE* 3.0 24.8 + - - +
618A PRO* 3.5 29.9 + - + +
619A ARG* 3.5 57.4 - - - +
647A MET* 4.7 8.4 - - + +
649A ASP* 3.7 18.4 + - - -
670A TYR* 4.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.6 30.1 + - - +
333A TYR* 5.3 0.9 - - - -
345A PHE* 3.9 17.7 - - - -
346A LEU 3.0 5.8 + - - -
348A LYS* 1.3 78.0 - - - +
350A ALA* 1.3 56.8 + - - +
352A ILE* 3.1 9.9 + - - +
353A TYR* 2.9 27.7 + - - +
601A ILE* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 3.9 6.1 - - - +
346A LEU 2.7 17.9 + - - +
347A PRO 3.5 2.5 - - - +
349A GLY* 1.3 70.8 - - - +
351A TYR* 1.3 58.9 + - - +
353A TYR* 3.2 8.7 - - - +
354A ASN* 2.9 39.4 + - - +
371B GLU* 3.2 29.2 - - + +
372B VAL* 3.8 17.3 - - - -
373B VAL* 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO 2.9 13.9 + - - +
348A LYS 3.0 10.1 + - - +
350A ALA* 1.3 77.1 - - - +
352A ILE* 1.3 59.4 + - - +
354A ASN* 3.5 5.1 + - + +
355A ALA* 2.9 39.9 + - + +
615A TRP 3.3 18.8 + - - -
616A LEU 4.0 6.7 - - - -
617A SER 3.4 24.9 - - - -
618A PRO* 3.9 9.6 - - + -
620A GLN* 3.1 25.3 + - - -
645A LYS 4.9 9.9 + - - -
647A MET* 3.8 35.7 - - + -
712A LYS* 5.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 4.0 26.0 - - + -
348A LYS 3.0 10.9 + - - +
349A GLY* 3.1 10.1 + - - +
351A TYR* 1.3 77.9 - - + +
353A TYR* 1.3 63.6 + - - +
355A ALA* 3.2 6.1 + - - +
356A LEU* 2.9 27.5 + - + +
601A ILE* 3.9 26.9 - - + -
612A TRP* 3.7 42.6 - - + -
616A LEU* 3.7 29.8 - - + +
618A PRO* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 3.6 44.4 - + - -
349A GLY 2.9 10.8 + - - +
350A ALA* 3.2 14.4 - - - +
352A ILE* 1.3 75.3 - - - +
354A ASN* 1.3 70.1 + - - +
356A LEU* 3.1 7.1 + - - +
357A ILE* 3.0 51.5 + - + +
457A ARG* 3.2 13.7 + - - -
459A GLN* 3.3 25.4 - - - +
597A VAL* 3.7 24.5 - - + +
598A GLU* 2.8 24.8 + - - -
601A ILE* 3.9 8.9 - - + +
373B VAL* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA* 2.9 22.8 + - - +
351A TYR* 4.1 4.8 - - + +
353A TYR* 1.3 88.0 - - - +
355A ALA* 1.3 57.3 + - - +
357A ILE* 3.8 12.5 - - - +
358A GLU* 2.9 31.2 + - - +
361B ARG* 3.6 26.4 + - - +
371B GLU* 3.6 34.6 + - - +
373B VAL* 5.1 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TYR* 2.9 31.3 + - + +
352A ILE* 3.4 5.6 - - - +
354A ASN* 1.3 74.3 - - - +
356A LEU* 1.3 60.0 + - - +
358A GLU* 3.4 6.1 + - - +
359A PHE* 2.9 28.4 + - - +
615A TRP* 4.1 21.2 - - + +
616A LEU* 4.1 15.7 - - + -
715A ARG* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 2.9 19.1 + - + +
353A TYR 3.5 6.3 - - - +
355A ALA* 1.3 73.3 - - - +
357A ILE* 1.3 65.6 + - - +
359A PHE* 3.1 8.2 + - + +
360A ILE* 3.0 27.8 + - - +
490A PHE* 3.8 30.7 - - + -
594A LEU* 4.6 11.7 - - + -
597A VAL* 4.2 17.9 - - + +
600A MET* 4.3 16.4 - - + -
601A ILE* 3.6 31.9 - - + +
604A LEU* 4.2 7.9 - - + -
615A TRP* 4.3 5.2 - - + -
616A LEU* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A TYR* 3.0 46.5 + - + +
354A ASN* 3.9 12.3 - - - +
356A LEU* 1.3 75.7 - - - +
358A GLU* 1.3 58.5 + - - +
360A ILE* 3.3 4.7 + - - +
361A ARG* 2.9 59.7 + - - +
437A PHE* 3.8 30.7 - - + -
459A GLN* 3.9 12.6 - - - +
594A LEU* 6.0 0.2 - - - -
597A VAL* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASN 2.9 19.0 + - - +
355A ALA* 3.7 7.2 - - - +
356A LEU 3.2 0.2 - - - -
357A ILE* 1.3 73.1 - - - +
359A PHE* 1.3 60.9 + - - +
361A ARG* 3.3 14.6 + - - +
362A SER* 2.9 29.6 + - - -
365A ARG* 2.6 36.1 + - - -
715A ARG* 4.6 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA 2.9 14.5 + - - +
356A LEU* 3.3 11.9 - - + +
358A GLU* 1.3 76.3 - - - +
360A ILE* 1.3 68.2 - - + +
362A SER* 2.6 21.9 + - - -
363A GLU* 3.0 24.0 + - + +
485A THR* 5.4 1.1 - - + -
486A VAL* 3.7 42.6 - - + -
489A VAL* 3.6 35.7 - - + -
490A PHE* 4.4 12.3 - + - -
594A LEU* 5.9 0.4 - - + -
615A TRP* 4.1 15.0 - + + -
715A ARG* 3.3 48.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU 3.0 18.0 + - - +
357A ILE* 3.6 6.7 - - - +
359A PHE* 1.3 79.9 - - + +
361A ARG* 1.3 56.2 + - - +
363A GLU* 3.3 6.7 + - - +
364A TYR* 2.9 61.1 + - + +
437A PHE* 3.7 14.1 - - + -
461A ASP* 4.0 12.3 - - + +
482A PHE* 5.0 5.6 - - + -
486A VAL* 4.3 23.1 - - + -
591A ARG* 5.9 0.4 - - - +
593A ILE* 5.0 4.0 - - + -
594A LEU* 3.5 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ILE* 2.9 34.5 + - - +
358A GLU* 3.6 16.5 + - - +
360A ILE* 1.3 73.8 - - - +
362A SER* 1.3 61.6 + - - +
364A TYR* 3.0 10.0 + - + +
365A ARG* 2.9 51.6 + - + +
371A GLU* 2.8 39.0 + - - +
437A PHE* 3.5 26.8 - - + +
354B ASN* 3.5 28.0 + - - +
361B ARG* 5.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU* 2.9 16.0 + - - -
359A PHE* 2.6 23.0 + - - -
361A ARG* 1.3 76.8 - - - +
363A GLU* 1.3 65.1 + - - +
365A ARG* 3.2 27.8 + - - +
366A LYS* 3.7 26.6 + - - +
715A ARG* 3.6 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.0 22.8 + - + +
360A ILE* 3.7 6.5 - - - +
362A SER* 1.3 88.9 + - - +
364A TYR* 1.3 62.9 + - - +
366A LYS* 3.3 32.6 + - - +
367A ARG* 3.3 64.2 + - - +
482A PHE* 3.4 26.2 - - + -
485A THR* 4.1 19.2 - - + +
486A VAL* 4.9 4.9 - - + -
715A ARG* 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 2.9 39.8 + - + +
361A ARG* 3.0 16.3 + - + +
363A GLU* 1.3 76.3 - - - +
365A ARG* 1.3 66.4 + - + +
367A ARG 3.3 0.5 + - - -
368A GLY 3.2 5.4 + - - -
369A PHE* 3.0 63.6 + + + +
371A GLU* 5.3 5.2 - - + +
435A ALA* 3.4 28.5 - - + +
436A ASP 5.5 0.2 - - - -
437A PHE* 3.8 16.8 - + - -
461A ASP* 4.1 4.0 - - - +
462A ASP 4.1 15.3 + - - -
463A ALA* 4.2 0.2 - - - +
482A PHE* 3.6 28.3 - + - -
591A ARG* 3.7 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU* 2.6 37.6 + - - -
361A ARG* 2.9 30.6 + - - +
362A SER* 3.2 33.7 + - - +
363A GLU 3.3 0.2 - - - -
364A TYR* 1.3 78.5 - - + +
366A LYS* 1.3 61.7 + - + +
368A GLY* 4.1 5.0 + - - -
369A PHE 4.9 3.8 - - - +
642B HIS* 2.9 34.3 + - + +
645B LYS* 4.6 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 3.7 19.3 + - - +
363A GLU* 3.3 38.1 + - - +
364A TYR 3.2 0.6 - - - -
365A ARG* 1.3 80.1 - - + +
367A ARG* 1.3 64.3 + - + +
368A GLY 3.4 0.8 + - - -
642B HIS* 4.8 4.5 + - - -
643B ASP* 5.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU* 3.3 44.5 + - - +
364A TYR 3.3 0.6 + - - -
366A LYS* 1.3 82.4 - - + +
368A GLY* 1.3 61.1 + - - +
369A PHE* 3.5 21.4 - - + -
433A ARG* 3.9 13.5 + - - -
478A GLY* 4.1 3.8 + - - -
481A ASP* 2.5 28.7 + - - +
482A PHE* 3.5 43.7 - - - +
485A THR* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A TYR 3.2 3.4 + - - -
365A ARG 4.1 4.5 + - - -
366A LYS 3.4 4.0 + - - -
367A ARG* 1.3 80.3 - - - +
369A PHE* 1.3 64.5 + - - +
370A GLN* 4.0 8.0 + - - +
433A ARG* 3.4 27.5 + - - +
642B HIS* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il