Contacts of the strand formed by residues 27 - 31 (chain B) in PDB entry 4WIP
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 ASP 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 3.7 27.7 - - + -
67A VAL* 4.8 0.7 - - - -
68A LYS* 3.2 32.8 - - - +
16B VAL 3.6 1.2 - - - +
17B ILE* 3.3 3.5 - - - -
18B TYR* 3.0 69.9 + - + +
23B GLU* 4.3 8.9 + - - +
25B THR 4.0 0.2 + - - -
26B PRO* 1.3 75.5 - - - +
28B LEU* 1.3 58.6 + - - +
29B VAL* 4.2 0.9 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 3.4 33.0 - - + +
67A VAL* 4.0 20.6 - - + +
68A LYS 2.8 10.7 + - - +
69A GLU* 4.2 18.8 - - + +
70A GLU 2.9 30.2 + - - +
15B LYS* 4.1 25.8 - - + -
16B VAL 3.5 2.9 - - - +
17B ILE* 3.7 25.4 - - + +
27B ASP* 1.3 72.6 - - - +
29B VAL* 1.3 79.7 + - - +
30B LYS* 4.3 8.5 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.3 11.9 - - + -
70A GLU* 3.8 30.1 - - + +
14B THR 3.6 0.2 - - - +
15B LYS* 3.5 1.4 - - - -
16B VAL* 2.7 43.6 + - + +
18B TYR* 3.8 25.8 - - + +
27B ASP* 4.6 0.2 - - + -
28B LEU* 1.3 82.5 - - - +
30B LYS* 1.3 75.0 + - - +
31B ILE* 4.6 5.6 - - + -
43B PHE* 6.2 1.1 - - + -
46B VAL* 4.2 24.7 - - + -
47B LEU* 5.9 1.6 - - + -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 4.5 16.8 + - - -
70A GLU* 5.3 10.4 + - - +
13B GLU* 3.2 39.9 + - - +
14B THR 3.3 6.5 - - - +
15B LYS* 4.3 18.5 - - + +
28B LEU* 4.3 13.7 - - + -
29B VAL* 1.3 85.1 - - - +
31B ILE* 1.3 61.2 + - - +
32B PRO* 4.1 4.5 - - - +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.3 3.5 - - - -
14B THR 2.8 35.6 + - - +
16B VAL* 3.5 28.3 - - + -
29B VAL* 4.5 9.9 - - + +
30B LYS* 1.3 77.2 - - - +
32B PRO* 1.3 68.1 - - + +
33B VAL* 2.9 21.6 + - + +
38B ILE* 4.0 20.0 - - + -
42B ASP* 4.7 7.4 - - + +
43B PHE* 3.9 33.0 - - + -
46B VAL* 4.1 26.5 - - + -
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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