Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 2WJ7
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 VAL 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.6 2.4 - - - +
31A LEU* 3.1 38.0 + - + +
32A GLY 3.4 2.6 - - - -
33A ASP* 1.3 88.1 - - + +
35A ILE* 1.3 73.8 - - - +
36A GLU* 3.6 7.4 + - + +
58A LYS* 3.8 28.9 - - + -
59A TYR 3.2 14.8 - - - +
60A ARG* 5.2 6.5 - - + -
61A ILE* 3.6 3.3 - - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.2 15.3 - - + -
14A VAL* 6.4 1.1 - - + -
28A VAL* 4.3 16.8 - - + -
29A LYS 3.7 4.0 - - - +
30A VAL* 4.5 7.4 - - + +
34A VAL* 1.3 71.9 - - - +
36A GLU* 1.3 62.0 + - - +
37A VAL* 4.3 9.9 - - + -
57A ARG 3.5 0.7 - - - +
58A LYS* 3.1 6.6 - - - -
59A TYR* 2.9 62.0 + - + +
60A ARG 5.4 0.7 - - - +
61A ILE* 3.9 25.9 - - + +
62A PRO* 5.9 0.2 - - + -
70A ILE* 3.9 18.8 - - + -
82A VAL* 4.0 32.3 - - + -
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Residues in contact with GLU 36 (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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27A LYS 3.6 1.4 - - - +
28A VAL* 3.4 6.9 - - - +
29A LYS* 2.9 42.4 + - + +
31A LEU* 3.0 38.5 - - + +
34A VAL* 4.4 11.2 - - + +
35A ILE* 1.3 75.6 - - - +
37A VAL* 1.3 61.4 + - - +
38A HIS* 4.1 0.7 - - + -
56A HIS* 3.5 20.7 + - + -
57A ARG 3.3 3.8 - - - -
58A LYS* 3.8 28.5 + - + +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.1 10.5 - - + -
26A LEU* 5.0 3.4 - - + -
27A LYS 3.6 7.0 - - - +
28A VAL* 4.6 9.9 - - + -
35A ILE* 4.0 10.3 + - + -
36A GLU* 1.3 76.6 - - - +
38A HIS* 1.3 66.5 + - - +
55A PHE* 3.8 22.5 - - + -
56A HIS* 3.2 5.3 + - - -
57A ARG* 2.9 41.4 + - + -
59A TYR* 4.3 23.1 - - + -
80A LEU* 3.9 25.4 - - + -
82A VAL* 4.8 6.3 - - + -
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Residues in contact with HIS 38 (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 GLU 3.8 1.9 - - - +
26A LEU* 3.3 7.0 - - - +
27A LYS* 2.9 44.5 + - + +
36A GLU 4.1 0.4 - - - -
37A VAL* 1.3 76.9 - - - +
39A GLY* 1.3 60.6 + - - +
40A LYS* 3.8 16.0 - - + +
54A GLU* 2.8 41.8 + - + -
55A PHE* 3.1 19.1 + - - -
56A HIS* 3.8 25.3 - + + +
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Residues in contact with GLY 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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21A PHE* 3.8 8.7 - - - -
25A GLU 3.2 9.2 - - - -
26A LEU* 3.9 5.6 - - - -
38A HIS* 1.3 77.4 - - - +
40A LYS* 1.4 59.1 + - - -
54A GLU* 3.3 5.7 - - - +
55A PHE* 2.9 54.0 + - - +
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Residues in contact with LYS 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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21A PHE* 3.9 2.6 - - - -
25A GLU* 3.1 31.6 + - - +
38A HIS* 3.8 19.4 + - + +
39A GLY* 1.4 73.7 - - - +
41A HIS* 1.3 69.3 + - - +
42A GLU* 5.0 1.1 - - - +
53A ARG 3.5 7.0 - - - +
54A GLU* 3.9 21.5 - - + +
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Residues in contact with HIS 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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20A HIS 3.6 11.2 + - - -
21A PHE* 3.8 16.6 - - + -
25A GLU* 3.7 26.7 - - - +
40A LYS* 1.3 81.5 - - - +
42A GLU* 1.3 76.7 + - - +
44A ARG* 3.7 26.2 + - - +
51A ILE 3.0 20.7 + - - -
52A SER* 3.3 5.6 - - - -
53A ARG* 2.7 70.4 + - + +
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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
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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