Contacts of the helix formed by residues 360 - 376 (chain A) in PDB entry 3SUP
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 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A SER* 2.8 14.1 + - - +
358A VAL 3.0 0.6 - - - -
359A PHE* 1.3 80.1 - - - +
361A PRO* 1.3 59.8 - - - +
362A ILE* 4.2 0.5 - - - +
363A LYS* 3.0 22.6 + - - +
364A THR* 2.8 32.1 + - - -
3T C 4.6 5.1 - - - -
4T 2PR 2.4 25.8 + - - -
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Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 3.9 15.0 - - - +
347A MET* 6.0 0.2 - - + -
358A VAL 4.5 1.8 - - - +
359A PHE 3.5 11.0 - - - +
360A SER* 1.3 84.5 - - - +
362A ILE* 1.3 54.3 + - - +
364A THR* 3.9 8.5 - - - +
365A TRP* 2.8 44.2 + - + -
562A LEU* 4.3 14.1 - - + -
565A SER* 3.7 23.1 - - - +
569A ALA* 5.8 0.9 - - - -
4T 2PR 3.6 43.5 - - + +
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Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 3.2 1.2 - - - +
361A PRO* 1.3 78.9 - - - +
363A LYS* 1.3 56.9 + - - +
365A TRP* 4.1 0.2 - - - -
366A ASP* 2.9 32.9 + - + +
569A ALA* 4.0 21.1 - - + -
572A ASN* 3.4 36.8 - - + +
574A TRP* 4.1 17.7 - - + +
575A PHE* 4.1 24.0 - - + +
576A ARG 5.4 0.2 - - - +
3T C 3.5 18.4 - - + +
4T 2PR 3.2 32.1 + - - +
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 2.8 35.3 + - - +
90A LEU* 3.9 21.4 - - + +
353A ILE* 4.0 5.3 - - + +
357A SER* 3.8 27.4 - - - +
360A SER* 3.0 26.6 + - - +
362A ILE* 1.3 75.8 - - - +
364A THR* 1.3 65.7 + - - +
366A ASP* 3.7 8.6 + - + +
367A ALA* 3.1 22.9 + - - +
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 4.1 15.8 - - + +
351A ALA* 3.7 19.2 - - + +
353A ILE* 3.6 15.1 - - + +
357A SER 3.5 10.6 + - - -
358A VAL* 4.1 5.9 - - - -
360A SER 2.8 21.9 + - - -
361A PRO* 3.2 9.9 + - - +
363A LYS* 1.3 78.5 - - - +
365A TRP* 1.3 56.8 + - - +
367A ALA 3.4 0.2 + - - -
368A ILE* 3.1 40.9 + - + +
562A LEU* 3.8 23.6 - - + -
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Residues in contact with TRP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 2.8 32.4 + - + +
362A ILE* 5.5 0.2 - - - -
364A THR* 1.3 69.2 - - - +
366A ASP* 1.3 65.4 + - - +
368A ILE* 3.8 31.6 - - + -
369A ILE* 2.9 37.9 + - + +
474A GLU* 4.0 26.7 - - + -
475A ILE* 4.1 6.5 - - - -
478A VAL* 4.0 13.9 - - + -
562A LEU* 2.8 56.7 + - + +
563A ILE* 3.9 15.5 - - + -
565A SER 4.7 0.4 - - - -
566A LEU* 3.5 54.7 - - + +
569A ALA* 5.7 1.3 - - + -
575A PHE* 4.2 10.5 - - + -
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Residues in contact with ASP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.6 14.2 - - - +
90A LEU* 4.8 2.9 - - - +
362A ILE* 2.9 21.8 + - + +
363A LYS* 3.7 13.9 + - + +
365A TRP* 1.3 77.3 - - - +
367A ALA* 1.3 55.9 + - - +
369A ILE* 4.0 2.8 - - - +
370A PHE* 3.0 30.7 + - - +
380A ILE* 5.1 0.5 - - - +
575A PHE* 4.3 7.7 - - + -
576A ARG* 2.8 56.7 + - - +
577A TYR* 4.0 6.1 + - - -
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Residues in contact with ALA 367 (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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90A LEU* 4.3 16.8 - - + +
351A ALA 3.3 17.3 - - - +
352A LYS 4.5 2.5 - - - +
353A ILE* 3.3 26.9 - - + -
363A LYS 3.1 9.6 + - - +
364A THR 3.8 1.3 - - - +
366A ASP* 1.3 75.0 - - - +
368A ILE* 1.3 64.0 + - - +
370A PHE* 3.9 5.3 - - + +
371A ASN* 2.7 36.6 + - - +
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Residues in contact with ILE 368 (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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350A TYR* 4.1 31.2 - - + +
351A ALA* 3.7 19.3 - - + +
364A THR* 3.1 34.7 + - + +
365A TRP* 3.4 41.5 + - + +
367A ALA* 1.3 76.3 - - - +
369A ILE* 1.3 57.9 + - - +
371A ASN* 3.8 4.3 - - - +
372A SER* 3.0 27.7 + - - -
474A GLU* 3.5 26.2 - - + +
562A LEU* 4.7 6.3 - - + -
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Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 2.9 35.0 + - + +
366A ASP 4.1 0.4 - - - +
368A ILE* 1.3 75.9 - - - +
370A PHE* 1.3 57.1 + - - +
372A SER* 3.3 5.6 + - - -
373A LEU* 2.9 41.3 + - + +
470A VAL* 4.0 19.5 - - + +
471A VAL* 4.4 14.1 - - + -
474A GLU* 4.8 11.4 - - + -
566A LEU* 4.3 14.1 - - + -
575A PHE* 4.2 11.0 - - + -
577A TYR* 3.4 48.0 - - + +
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Residues in contact with PHE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 6.0 0.4 - - - -
85A MET* 3.7 49.1 - - + -
90A LEU* 3.8 13.5 - - + -
91A ALA* 3.9 15.5 - - + -
94A SER* 3.7 22.0 - - - -
366A ASP 3.0 19.5 + - - +
367A ALA* 3.9 2.9 - - - +
368A ILE 3.3 0.2 - - - -
369A ILE* 1.3 78.0 - - - +
371A ASN* 1.3 67.9 + - - +
373A LEU* 3.5 0.9 + - - +
374A LYS* 2.9 53.1 + - + +
378A LYS 6.0 1.6 - - - -
380A ILE* 4.0 28.9 - - + +
577A TYR* 4.8 0.2 + - - -
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Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 5.3 1.6 + - - +
94A SER* 2.6 33.4 + - - -
351A ALA 3.4 17.8 + - - -
352A LYS* 3.6 31.9 + - + +
367A ALA* 2.7 31.8 + - - +
368A ILE* 3.9 4.0 - - - +
370A PHE* 1.3 79.7 - - - +
372A SER* 1.3 65.2 + - - +
374A LYS* 3.6 5.8 + - - +
375A GLU* 3.2 26.4 + - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE 3.0 17.7 + - - -
369A ILE 3.6 4.3 - - - -
370A PHE 3.3 0.4 - - - -
371A ASN* 1.3 76.8 - - - +
373A LEU* 1.3 62.5 + - - +
375A GLU* 3.5 15.7 - - - +
376A GLN* 3.2 20.3 + - - +
470A VAL* 3.6 13.3 - - - +
473A THR* 5.2 2.4 - - - +
474A GLU* 2.6 36.9 + - - -
477A LYS* 4.9 1.0 + - - -
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Residues in contact with LEU 373 (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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52A ILE* 3.4 29.4 - - + -
369A ILE* 2.9 35.5 + - + +
370A PHE 4.0 2.5 - - - +
372A SER* 1.3 76.1 - - - +
374A LYS* 1.3 64.5 + - - +
376A GLN* 2.9 19.9 + - - +
378A LYS* 3.0 54.1 + - + +
380A ILE* 4.0 12.8 - - + +
428A GLU* 5.3 2.2 - - - +
470A VAL* 3.8 30.1 - - + -
577A TYR* 4.0 11.7 - - + +
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Residues in contact with LYS 374 (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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91A ALA 5.1 0.2 - - - -
94A SER* 2.7 46.0 + - - +
95A ASP* 3.3 25.6 + - - +
98A ASN* 4.3 16.3 + - - +
370A PHE* 2.9 42.3 + - + +
371A ASN* 3.9 5.2 - - - +
373A LEU* 1.3 77.1 - - - +
375A GLU* 1.3 57.2 + - - +
377A ASN* 2.9 25.6 + - - +
378A LYS 3.9 10.2 + - - +
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Residues in contact with GLU 375 (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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98A ASN* 3.5 26.5 + - - +
371A ASN 3.2 13.0 + - - +
372A SER* 3.5 15.5 - - - +
373A LEU 3.2 0.4 - - - -
374A LYS* 1.3 77.4 - - - +
376A GLN* 1.3 61.9 + - + +
377A ASN* 3.3 3.9 + - - -
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Residues in contact with GLN 376 (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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48A LYS 5.0 0.5 - - - +
372A SER* 3.2 25.8 + - - +
373A LEU* 2.9 15.6 + - - +
375A GLU* 1.3 79.5 - - + +
377A ASN* 1.3 70.9 + - - +
378A LYS* 3.2 39.1 + - + +
470A VAL* 5.3 1.4 - - - +
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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
------------------------------------------------------------
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