Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 1WVY
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 GLN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.8 20.8 - - + +
30A CYS 3.3 17.9 + - - -
31A ARG* 3.9 24.7 + - - +
36A GLY 4.3 5.4 - - - +
37A LEU* 1.3 75.4 - - - +
39A TYR* 1.3 70.2 + - - +
95A LEU* 3.5 28.2 + - + +
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Residues in contact with TYR 39 (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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13A TYR* 3.9 15.7 - + - -
29A LYS* 3.6 9.0 - - - +
30A CYS* 2.8 35.8 + - - +
32A GLU* 3.5 22.5 + - - -
37A LEU* 3.8 36.3 - - + +
38A GLN* 1.3 78.8 - - - +
40A ALA* 1.3 59.8 + - - +
41A ALA 3.8 0.7 - - - -
80A HIS* 3.2 42.4 + + + -
92A ILE* 3.7 21.3 - - + -
93A LEU 3.6 17.7 - - - +
94A GLU* 4.3 9.2 - - + -
95A LEU* 3.7 9.3 - - - +
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Residues in contact with ALA 40 (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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19A LEU* 4.5 8.5 - - + -
27A VAL* 5.5 2.7 - - + -
28A LYS 3.8 4.9 - - - -
30A CYS* 4.6 0.9 - - - -
39A TYR* 1.3 71.2 - - - +
41A ALA* 1.3 63.1 + - - +
42A LYS* 3.5 0.7 + - - +
93A LEU* 2.7 42.7 + - - +
94A GLU 3.8 1.6 - - - +
95A LEU* 3.8 6.0 - - + +
1001A STU 3.3 46.0 - - + +
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Residues in contact with ALA 41 (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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9A VAL* 5.8 1.6 - - + -
15A THR* 5.7 0.4 - - - +
27A VAL* 3.1 3.4 - - - -
28A LYS* 2.7 42.7 + - + +
30A CYS* 3.6 24.2 - - + -
39A TYR 3.8 2.2 - - - -
40A ALA* 1.3 70.3 - - - +
42A LYS* 1.3 60.3 + - - +
43A PHE* 3.7 22.0 - - + -
90A ILE* 4.0 4.3 - - + -
91A LEU 3.5 5.8 - - - -
92A ILE* 3.8 16.4 - - + -
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Residues in contact with LYS 42 (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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25A ALA* 3.7 16.8 - - + -
27A VAL* 3.7 20.4 - - + -
40A ALA 3.5 0.8 + - - +
41A ALA* 1.3 70.5 - - - +
43A PHE* 1.3 61.9 + - - +
44A ILE* 3.6 30.5 + - + +
64A GLU* 2.8 28.7 + - - +
89A VAL 3.7 0.9 - - - +
90A ILE* 3.4 3.3 - - - -
91A LEU* 2.9 45.9 + - + +
93A LEU* 4.1 14.6 - - + -
161A ASP* 3.3 19.2 + - - -
163A GLY* 4.7 3.2 - - - +
1001A STU 3.5 24.6 - - + -
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Residues in contact with PHE 43 (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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9A VAL* 5.2 8.3 - - + -
10A ASP* 5.8 2.2 - - - -
15A THR* 4.1 19.3 - - + -
25A ALA* 3.1 7.0 - - - +
26A VAL* 2.9 61.0 + - + +
28A LYS* 3.7 29.2 - - + -
41A ALA* 3.7 27.1 - - + -
42A LYS* 1.3 71.7 - - - +
44A ILE* 1.3 60.4 + - - +
45A LYS 4.0 1.1 + - - -
85A ASN* 5.9 0.4 - - - -
88A ASP* 4.1 18.2 - - + +
89A VAL 4.2 2.2 - - - -
90A ILE* 3.5 35.2 - - + +
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Residues in contact with ILE 44 (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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24A PHE 3.7 6.3 - - - +
25A ALA* 4.1 2.0 - - + -
42A LYS* 3.6 30.1 - - + +
43A PHE* 1.3 74.6 - - - +
45A LYS* 1.3 64.3 + - - +
46A LYS* 3.4 0.9 + - - +
56A VAL* 3.9 35.2 - - + -
61A ILE* 4.1 20.2 - - + -
64A GLU* 3.2 27.1 - - - +
88A ASP* 3.5 2.7 - - - +
89A VAL* 3.0 40.8 + - + +
91A LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 45 (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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24A PHE* 3.3 13.9 + - - +
43A PHE 4.0 1.8 + - - -
44A ILE* 1.3 74.3 - - - +
46A LYS* 1.3 69.0 + - - +
48A ARG* 6.3 0.4 - - - +
54A ARG* 4.4 22.6 - - - +
55A GLY* 3.4 13.3 - - - +
56A VAL* 3.0 24.4 + - - +
87A THR* 4.0 9.2 - - - +
88A ASP* 3.1 21.9 + - - +
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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