Contacts of the helix formed by residues 358 - 367 (chain A) in PDB entry 2W7P
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 GLY 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ARG* 3.5 9.3 + - - -
356A GLY 3.6 2.4 + - - -
357A ILE* 1.3 75.4 - - - +
359A LYS* 1.3 58.1 + - - -
362A GLU* 3.0 30.8 + - - +
11P T 2.7 29.0 + - - -
12P T 3.5 17.9 - - - -
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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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57A GLU* 4.0 26.0 + - - +
352A ARG* 3.7 23.3 - - - +
358A GLY* 1.3 71.2 - - - +
360A VAL* 1.3 68.6 + - + +
362A GLU* 4.0 2.6 - - - +
363A LYS* 3.4 28.1 + - - +
11P T 3.2 7.4 + - - +
12P T 4.9 0.2 + - - -
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Residues in contact with VAL 360 (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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60A VAL* 3.8 18.8 - - + -
63A ARG* 4.1 4.0 - - - +
359A LYS* 1.3 83.8 - - + +
361A THR* 1.3 56.7 + - - +
362A GLU 3.1 1.9 + - - -
363A LYS* 3.1 4.1 + - - +
364A MET* 2.7 62.4 + - + +
10P A 3.3 43.7 - - + +
11P T 3.0 17.4 + - - +
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Residues in contact with THR 361 (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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356A GLY 5.3 1.2 + - - -
357A ILE* 3.6 34.8 - - + +
358A GLY 4.1 0.8 + - - -
360A VAL* 1.3 79.1 - - - +
362A GLU* 1.3 57.1 + - - +
364A MET* 4.2 9.0 - - - -
365A LEU* 2.9 45.9 + - + +
387A PHE* 6.5 0.2 - - + -
395A PHE* 4.3 13.0 - - + -
10P A 4.1 4.3 + - - -
11P T 3.3 18.0 + - - -
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Residues in contact with GLU 362 (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 ILE* 4.9 8.3 - - + +
352A ARG* 2.5 58.3 + - + +
357A ILE* 4.1 6.9 - - + +
358A GLY 3.0 19.3 + - - +
359A LYS 4.0 2.9 - - - +
361A THR* 1.3 75.0 - - - +
363A LYS* 1.3 67.7 + - + +
365A LEU* 3.9 2.6 - - - +
366A LYS* 3.1 41.2 + - + +
370A ILE 4.9 1.2 - - - +
371A ILE* 5.8 4.3 - - + +
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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
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57A GLU* 4.2 18.8 + - - +
60A VAL* 5.0 7.2 - - + -
61A ASN* 2.7 39.6 + - - +
64A ILE* 4.2 12.1 - - + -
359A LYS* 3.4 21.3 + - - +
360A VAL* 3.1 4.3 + - - +
362A GLU* 1.3 78.1 - - + +
364A MET* 1.3 68.9 + - - +
365A LEU 2.8 2.1 + - - -
366A LYS* 2.9 21.9 + - - +
367A ALA* 3.2 10.2 + - - +
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Residues in contact with MET 364 (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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60A VAL* 4.6 4.3 - - + -
63A ARG* 3.2 60.8 - - + +
64A ILE* 3.4 31.6 - - + +
67A MET* 3.9 13.9 - - + +
360A VAL* 2.7 39.6 + - + +
361A THR* 4.0 8.1 - - - +
363A LYS* 1.3 74.3 - - - +
365A LEU* 1.3 56.0 + - + +
367A ALA* 3.3 9.2 - - - +
368A LEU* 3.2 19.4 - - - +
387A PHE* 4.1 19.1 - - + -
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Residues in contact with LEU 365 (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 ILE* 4.4 23.3 - - + -
357A ILE* 5.0 1.1 - - + -
361A THR* 2.9 36.3 + - + +
362A GLU* 4.0 3.1 - - - +
363A LYS 3.0 0.2 - - - -
364A MET* 1.3 76.1 - - - +
366A LYS* 1.3 57.1 + - - +
367A ALA 2.9 5.6 - - - -
368A LEU* 3.0 21.9 + - + +
370A ILE* 3.1 43.1 + - + +
376A LEU* 4.3 9.9 - - + -
383A LEU* 4.2 1.1 - - + -
387A PHE* 3.7 24.0 - - + -
395A PHE* 3.5 38.1 - - + -
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Residues in contact with LYS 366 (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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362A GLU* 3.1 35.3 + - - +
363A LYS* 2.9 11.1 + - - +
365A LEU* 1.3 73.3 - - - +
367A ALA* 1.3 59.7 + - - +
368A LEU 3.2 0.4 - - - -
369A GLY* 2.9 17.7 + - - -
370A ILE 3.6 15.0 + - - +
371A ILE* 3.6 29.5 - - + +
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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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64A ILE* 4.1 20.2 - - + -
67A MET* 4.1 10.1 - - + -
68A MET* 3.7 26.6 - - + +
363A LYS 3.2 8.2 + - - +
364A MET 3.3 18.4 - - - +
366A LYS* 1.3 79.2 - - - +
368A LEU* 1.3 62.3 + - + +
369A GLY 3.5 0.3 + - - -
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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
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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