Contacts of the helix formed by residues 353 - 367 (chain A) in PDB entry 4GL5
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 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 3.3 26.7 - - + +
336A ILE* 4.4 11.7 - - + -
339A VAL* 4.7 5.6 - - + -
340A ILE* 4.1 20.4 - - + -
345A ILE* 4.1 18.2 - - + -
349A ASP 4.0 6.1 - - - +
350A ILE* 3.5 24.4 + - + +
351A GLN 3.4 2.0 - - - -
352A LYS* 1.3 72.2 - - - +
354A LYS* 1.3 57.1 + - - +
356A MET* 3.3 33.9 + - + -
357A GLU* 2.9 28.3 + - - +
448A LYS* 4.3 8.3 - - + -
452A VAL* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 3.5 3.5 + - - +
351A GLN 4.1 11.0 - - - +
352A LYS* 2.6 15.1 + - - +
353A LEU* 1.3 72.2 - - - +
355A VAL* 1.3 59.7 + - + +
357A GLU* 3.2 39.9 + - - +
358A ASN* 2.8 47.7 + - - +
421A ASN* 5.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A VAL* 5.3 0.7 - - + +
331A ALA* 4.1 23.3 - - + +
332A ILE* 4.0 24.2 - - + +
335A GLU* 2.8 27.6 + - + +
354A LYS* 1.3 68.3 - - + +
356A MET* 1.3 66.4 + - - +
358A ASN* 3.1 6.3 + - + +
359A PHE* 3.0 18.0 + - - +
415A LEU* 3.5 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 4.4 23.6 - - + -
335A GLU* 3.0 10.8 + - - +
336A ILE* 5.3 0.2 - - - -
353A LEU* 3.3 28.9 + - + +
355A VAL* 1.3 75.9 - - - +
357A GLU* 1.3 66.2 + - - +
359A PHE* 2.9 19.6 + - + +
360A ILE* 2.9 26.5 + - + +
448A LYS* 3.3 32.8 - - + +
451A LEU* 3.8 33.2 - - + -
452A VAL* 3.5 23.8 - - + -
455A LEU* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ILE 4.5 0.2 - - - +
351A GLN* 4.3 9.0 - - - +
353A LEU 2.9 13.2 + - - +
354A LYS* 3.2 41.6 + - - +
355A VAL 3.2 0.2 - - - -
356A MET* 1.3 76.8 - - - +
358A ASN* 1.3 60.6 - - - +
360A ILE* 3.5 7.0 + - - +
361A TYR* 3.1 59.5 + - + -
444A MET* 4.0 5.3 - - + +
448A LYS* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS* 2.8 45.1 + - - +
355A VAL* 3.1 9.8 + - + +
357A GLU* 1.3 75.1 - - - +
359A PHE* 1.3 59.4 + - - +
361A TYR* 3.7 10.1 - - - +
362A GLU* 2.9 31.7 + - - +
415A LEU* 3.8 16.0 + - + +
418A PHE* 2.4 51.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
318A MET* 3.2 45.5 - - + -
321A LEU* 4.1 5.6 - - + -
322A ILE* 3.3 30.1 - - + -
328A VAL* 3.8 20.0 - - + -
332A ILE* 4.1 10.1 - - + -
355A VAL 3.0 12.0 + - - +
356A MET* 2.9 14.3 + - + +
358A ASN* 1.3 74.4 - - - +
360A ILE* 1.3 63.5 - - - +
362A GLU* 3.3 1.0 + - - +
363A SER* 2.9 50.7 + - - -
413A PHE* 3.8 20.4 - + - -
415A LEU* 3.6 13.4 - - + +
451A LEU* 3.7 17.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
318A MET* 3.8 19.9 - - + +
356A MET* 2.9 23.1 + - + +
357A GLU 4.0 3.4 - - - +
359A PHE* 1.3 79.3 - - + +
361A TYR* 1.3 57.4 + - - +
363A SER* 3.3 3.0 + - - -
364A MET* 2.9 39.0 + - - +
444A MET* 4.2 17.9 - - + +
447A MET* 3.8 39.5 - - + -
448A LYS* 3.7 44.6 - - + +
451A LEU* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLU* 3.1 49.1 + - + +
358A ASN* 3.7 10.1 - - - +
359A PHE 3.3 0.2 - - - -
360A ILE* 1.3 80.0 - - - +
362A GLU* 1.3 57.4 + - - +
364A MET* 3.9 14.1 - - + +
365A ARG* 3.1 27.5 + - - +
418A PHE* 3.6 25.5 - + + -
422A VAL* 5.8 2.9 - - + -
427A PHE* 3.4 28.0 - + + -
429A PRO* 5.2 1.8 - - + -
430A PHE* 4.9 4.5 - + - -
444A MET* 3.8 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASN 2.9 19.3 + - - +
359A PHE 4.0 0.7 - - - +
361A TYR* 1.3 74.3 - - - +
363A SER* 1.3 60.7 + - - +
365A ARG* 2.6 47.5 + - - -
366A TYR* 2.9 28.8 + - - +
412A GLU 3.6 1.0 - - - +
413A PHE* 3.6 21.4 - - + -
414A THR 3.3 38.6 + - - +
415A LEU* 3.7 11.9 - - + -
417A ASN* 3.5 4.4 + - - +
418A PHE* 3.0 21.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 6.1 0.9 - - - -
318A MET* 3.4 25.6 - - - -
321A LEU* 3.4 22.2 - - - +
359A PHE* 2.9 39.5 + - - -
360A ILE 3.7 1.3 - - - -
362A GLU* 1.3 78.1 - - - +
364A MET* 1.3 57.5 + - - +
367A GLN* 2.8 36.0 + - - +
413A PHE* 3.6 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 4.6 13.9 - - - +
318A MET* 5.5 2.7 - - - +
360A ILE* 2.9 32.9 + - - +
361A TYR* 3.9 18.6 - - + +
363A SER* 1.3 77.0 - - - +
365A ARG* 1.3 59.9 + - - +
367A GLN 4.7 0.7 - - - -
368A PRO* 3.2 32.0 - - + +
369A VAL 5.8 0.4 - - - +
402A HIS* 4.9 2.9 + - - -
427A PHE* 4.7 1.6 - - + -
429A PRO* 3.4 40.6 - - + +
430A PHE* 3.7 23.1 - - + -
444A MET* 4.9 1.1 - - - -
447A MET* 4.3 2.0 - - - +
600A HEM 4.2 29.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
361A TYR 3.1 18.6 + - - +
362A GLU* 2.6 43.9 + - - +
363A SER 3.2 0.2 - - - -
364A MET* 1.3 78.9 - - - +
366A TYR* 1.3 73.2 + - - +
368A PRO* 3.8 8.1 - - - +
399A GLY 4.9 4.2 - - - +
402A HIS* 3.0 48.8 + - + +
403A ARG* 4.3 7.6 + - - +
407A PHE* 3.5 35.1 - - + -
409A LYS 3.9 0.6 + - - -
410A PRO* 2.9 33.5 + - - +
412A GLU 3.4 12.3 + - - -
417A ASN* 3.8 13.6 - - - +
418A PHE* 3.8 1.1 - - + -
427A PHE* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.5 7.2 - - + -
362A GLU 2.9 17.4 + - - +
363A SER 4.4 0.2 - - - +
365A ARG* 1.3 95.4 - - - +
367A GLN* 1.3 76.8 + - + +
368A PRO* 3.6 5.5 - - - +
403A ARG* 2.7 54.1 + - - +
411A ASN 3.7 20.2 + - - -
412A GLU* 3.9 5.1 - - - -
413A PHE* 3.6 45.5 - + + -
468A VAL* 5.0 1.3 - - + -
469A GLU* 2.6 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 3.5 29.9 - - + +
321A LEU* 4.4 11.2 - - + -
363A SER 2.8 21.6 + - - +
364A MET* 4.7 0.3 - - - -
366A TYR* 1.3 94.8 + - + +
368A PRO* 1.3 66.9 - - - +
369A VAL* 4.8 0.3 - - - +
403A ARG* 5.9 0.2 - - - +
468A VAL* 3.7 31.3 + - + +
469A GLU* 4.8 2.0 - - - +
473A LYS* 3.6 25.9 - - - +
479A LEU* 3.2 30.8 - - - +
----------------------------------------------------------
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