Contacts of the helix formed by residues 342 - 361 (chain A) in PDB entry 4K71
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 SER 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A TYR* 1.3 74.8 - - - +
343A VAL* 1.3 63.6 + - - +
344A VAL 3.9 2.0 - - - -
345A LEU* 3.2 26.4 + - - +
346A LEU* 3.1 20.1 + - - +
446A MET* 4.6 3.0 - - - -
447A PRO* 3.6 25.2 - - - +
450A GLU* 3.8 18.0 - - - +
451A ASP* 3.3 30.3 - - - -
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 3.3 34.1 - - + +
217A ALA* 4.0 15.7 - - + -
218A ARG* 3.9 37.2 - - + +
221A GLN* 4.1 11.7 - - - +
341A TYR 3.5 0.6 + - - +
342A SER* 1.3 71.1 - - - +
344A VAL* 1.3 59.1 + - + +
346A LEU* 3.1 9.3 + - - +
347A LEU* 2.8 45.0 + - + +
451A ASP* 3.8 11.7 + - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER* 4.3 0.2 - - - +
343A VAL* 1.3 79.6 - - + +
345A LEU* 1.3 56.5 + - - +
347A LEU* 4.5 4.7 - - - -
348A ARG* 3.0 36.9 + - - +
450A GLU* 4.0 27.8 - - + +
451A ASP* 3.1 21.3 - - - +
454A SER* 4.0 21.1 - - - +
481A LEU 5.3 1.1 - - - +
482A VAL* 3.2 44.6 - - + +
485A ARG* 6.4 0.7 - - + -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.8 33.7 - - + -
342A SER* 3.2 22.3 + - - +
343A VAL 3.2 0.2 - - - -
344A VAL* 1.3 79.0 - - - +
346A LEU* 1.3 63.5 + - - +
348A ARG* 3.2 25.3 + - - +
349A LEU* 2.9 37.9 + - + +
380A LEU 3.6 27.6 - - - +
381A VAL* 4.3 9.4 - - + -
384A PRO* 4.9 3.6 - - + -
446A MET* 3.6 30.7 - - + -
450A GLU* 5.1 1.5 - - + +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA* 4.2 12.3 - - + -
221A GLN* 3.9 25.6 - - - +
330A PHE* 5.4 0.7 - - - -
331A LEU* 3.6 17.6 - - + +
334A TYR* 3.4 34.3 - - + +
335A ALA* 3.8 33.7 - - + +
338A HIS* 4.6 1.6 - - + +
341A TYR* 4.0 18.6 - - + -
342A SER 3.1 15.5 + - - +
343A VAL* 3.1 10.4 + - - +
345A LEU* 1.3 76.7 - - - +
347A LEU* 1.3 57.2 + - - +
349A LEU* 3.2 7.0 + - + +
350A ALA 3.0 23.7 + - - -
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ALA 4.9 4.5 - - - +
213A ALA* 3.5 42.2 - - + +
214A TRP* 4.0 16.8 - - + +
217A ALA* 4.7 1.6 - - + -
331A LEU* 3.7 12.8 - - + -
343A VAL* 2.8 37.0 + - + +
344A VAL* 3.9 4.9 - - - +
346A LEU* 1.3 75.5 - - - +
348A ARG* 1.3 57.4 + - - +
350A ALA* 3.4 4.8 + - + +
351A LYS* 2.9 29.6 + - - +
481A LEU* 6.5 1.1 - - + -
482A VAL* 3.7 29.1 - - + +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 3.0 29.7 + - - +
345A LEU* 3.4 20.1 - - + +
347A LEU* 1.3 77.8 - - - +
349A LEU* 1.3 51.6 + - + +
351A LYS* 3.5 6.7 + - + +
352A THR* 2.7 39.5 + - - +
380A LEU* 5.0 19.0 + - + -
383A GLU* 4.9 2.0 + - - -
384A PRO* 4.0 12.9 - - - +
450A GLU* 2.9 33.3 + - - +
482A VAL* 3.0 29.9 + - + +
483A ASN* 3.2 28.1 + - - +
485A ARG* 4.0 11.5 - - - +
486A PRO* 3.6 21.7 - - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PHE* 4.3 6.5 - - + -
334A TYR* 3.9 33.4 - - + +
341A TYR* 4.1 17.5 - - + -
345A LEU* 2.9 30.8 + - + +
346A LEU* 3.2 8.7 + - - +
348A ARG* 1.3 75.9 - - - +
350A ALA* 1.3 64.7 + - - +
352A THR* 3.2 4.7 + - - -
353A TYR* 2.9 24.1 + - - +
377A PHE* 3.7 49.9 - - + +
380A LEU* 4.0 22.0 - - + -
381A VAL* 4.4 4.9 - - + -
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LEU* 4.1 12.4 - - + +
330A PHE* 3.8 21.6 - - + -
331A LEU* 3.6 35.2 - - + -
346A LEU 3.0 8.2 + - - +
347A LEU* 3.7 6.5 - - + +
349A LEU* 1.3 75.4 - - - +
351A LYS* 1.3 58.2 + - - +
353A TYR* 3.4 2.5 + - - +
354A GLU* 2.8 28.8 + - - +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU 2.9 18.2 + - - +
348A ARG* 3.6 7.9 - - + +
350A ALA* 1.3 78.4 - - - +
352A THR* 1.3 57.1 + - - +
354A GLU* 3.1 17.2 + - - +
355A THR* 2.8 42.0 + - - +
479A GLU 5.0 1.6 + - - -
480A SER* 3.0 34.6 + - - +
482A VAL* 5.2 9.9 - - + -
483A ASN* 3.9 18.6 - - - +
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Residues in contact with THR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 2.7 20.2 + - - +
349A LEU* 3.4 9.9 - - - -
351A LYS* 1.3 78.8 - - - +
353A TYR* 1.3 57.6 + - - +
355A THR* 3.3 6.6 + - - +
356A THR* 3.0 31.8 + - - -
373A VAL* 5.5 0.2 - - + -
376A GLU* 3.1 42.4 - - + +
377A PHE* 4.3 6.3 - - + -
380A LEU* 3.3 23.2 - - + +
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Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PHE* 2.7 55.1 + + + +
315A VAL* 4.1 2.1 - - - +
326A PHE* 3.6 13.3 - + - -
327A LEU* 3.6 21.5 - - + -
330A PHE* 3.9 38.1 - + + -
349A LEU 2.9 16.0 + - - +
350A ALA 3.7 3.4 - - - +
352A THR* 1.3 74.4 - - - +
354A GLU* 1.3 64.3 + - - +
356A THR* 3.3 3.5 + - - -
357A LEU* 3.0 52.8 + - + +
370A TYR* 6.1 0.2 - - + -
373A VAL* 3.8 36.1 - - + -
374A PHE* 4.5 2.2 - + - -
377A PHE* 4.3 4.0 - - + -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TYR* 3.6 15.4 + - - +
323A LYS* 5.4 2.3 - - - +
324A ASP* 4.5 9.0 - - - +
327A LEU* 2.9 39.6 - - + +
350A ALA 2.8 15.3 + - - +
351A LYS* 3.1 21.5 + - - +
353A TYR* 1.3 76.5 - - - +
355A THR* 1.3 62.3 + - - +
357A LEU* 3.2 5.3 + - - +
358A GLU* 3.0 27.1 + - + +
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LYS* 2.8 29.4 + - - +
352A THR* 3.8 6.9 - - - -
354A GLU* 1.3 74.7 + - - +
356A THR* 1.3 62.0 + - - +
358A GLU* 3.4 9.5 + - + +
359A LYS* 3.2 23.1 + - + +
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Residues in contact with THR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A THR 3.0 14.5 + - - -
353A TYR 3.5 7.9 - - - -
355A THR* 1.3 78.2 - - - +
357A LEU* 1.3 58.5 + - + +
359A LYS* 3.4 4.0 + - - +
360A CYS* 2.9 37.0 + - - +
369A CYS 5.1 1.1 - - - +
370A TYR* 3.7 28.5 - - + -
373A VAL* 3.7 21.2 - - + +
376A GLU* 2.8 26.1 + - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 3.8 21.8 - - + -
319A TYR* 3.8 42.5 - - + -
326A PHE* 4.3 2.7 - - + -
327A LEU* 5.2 0.4 - - + -
353A TYR* 3.0 54.1 + - + +
354A GLU 3.2 3.8 + - - +
356A THR* 1.3 73.7 - - + +
358A GLU* 1.3 66.3 + - - +
360A CYS* 4.4 0.4 - - - +
361A CYS* 2.9 33.7 + - - +
370A TYR* 3.4 37.9 - - + -
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TYR* 2.7 28.7 + - - +
323A LYS* 2.6 34.7 + - - +
354A GLU* 3.0 16.8 + - + +
355A THR* 3.6 12.6 - - + +
356A THR 3.3 0.2 - - - -
357A LEU* 1.3 78.9 - - - +
359A LYS* 1.3 59.7 + - - +
361A CYS* 5.1 0.7 - - - +
362A ALA* 4.4 10.9 + - - +
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A THR* 3.2 12.0 + - + +
356A THR* 3.8 6.7 - - - +
358A GLU* 1.3 80.2 - - - +
360A CYS* 1.3 64.6 + - - +
362A ALA* 3.4 14.6 + - - +
363A ALA* 3.8 6.9 + - - +
369A CYS* 4.5 18.6 - - - -
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Residues in contact with CYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A THR* 2.9 26.5 + - - +
357A LEU 4.4 0.2 - - - +
359A LYS* 1.3 78.0 - - - +
361A CYS* 1.3 58.0 + - - +
362A ALA 3.1 5.4 - - - -
363A ALA* 2.9 17.7 + - - +
366A PRO* 3.3 18.4 - - - +
369A CYS* 2.1 64.2 - - + -
370A TYR* 3.5 23.3 - - + -
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Residues in contact with CYS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A CYS* 2.1 59.9 - - + +
319A TYR* 4.7 9.4 - - + -
357A LEU* 2.9 35.9 + - - +
358A GLU 5.2 0.7 - - - +
360A CYS* 1.3 74.5 - - - +
362A ALA* 1.3 57.0 + - - +
363A ALA 3.4 1.4 - - - +
366A PRO* 3.9 7.8 - - - +
370A TYR* 4.3 6.3 - - - -
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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
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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) + - + + + + + -
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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