Contacts of the strand formed by residues 37 - 45 (chain A) in PDB entry 2VZ6
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.3 5.2 - - - -
32A LYS* 2.7 35.8 + - - +
35A ALA* 3.1 14.2 + - + +
36A GLY* 1.3 81.2 - - - +
38A GLU* 1.3 87.1 + - - +
39A TYR* 3.5 34.1 - - + +
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Residues in contact with GLU 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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29A ARG* 3.0 30.7 + - - +
30A CYS 3.2 11.0 - - - +
31A VAL* 4.1 9.8 - - + +
37A GLN* 1.3 95.9 + - - +
39A TYR* 1.3 74.3 + - - +
91A LEU* 3.6 28.6 + - + +
93A THR* 5.1 5.5 - - - +
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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 21.1 - + - -
29A ARG* 3.6 8.7 - - - +
30A CYS* 2.8 34.7 + - - +
32A LYS* 3.9 27.6 + - + +
35A ALA* 5.9 0.3 - - - +
37A GLN* 3.5 40.3 - - + +
38A GLU* 1.3 78.2 - - - +
40A ALA* 1.3 56.9 + - - +
76A HIS* 3.9 31.3 + + + +
88A ILE* 3.4 21.5 - - + -
89A PHE 3.2 21.8 - - - +
90A ASP* 4.6 3.4 - - - -
91A LEU* 3.8 11.8 - - - +
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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* 4.2 1.6 - - + -
27A VAL* 4.0 12.3 - - + -
28A ARG 3.5 4.7 - - - -
39A TYR* 1.3 75.3 - - - +
41A ALA* 1.3 60.1 + - - +
42A LYS 3.8 0.4 + - - -
87A LEU 3.6 1.7 - - - +
88A ILE* 3.5 1.6 - - - -
89A PHE* 2.8 35.2 + - - -
90A ASP 4.0 2.5 - - - +
91A LEU* 4.0 8.4 - - + +
600A FEF 3.3 44.9 - - + +
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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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-3A PHE* 4.4 3.4 - - + -
15A LEU* 4.2 11.0 - - + -
26A VAL 3.6 0.2 - - - +
27A VAL* 3.3 4.7 - - - -
28A ARG 2.8 37.0 + - - +
30A CYS* 3.9 11.8 - - - -
39A TYR 4.1 0.6 - - - -
40A ALA* 1.3 71.9 - - - +
42A LYS* 1.3 60.7 + - - +
43A ILE* 3.5 18.0 + - + +
86A TYR* 5.0 1.1 - - + -
87A LEU 3.4 4.7 - - - -
88A ILE* 3.5 23.1 - - + -
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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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24A PHE* 6.0 2.0 - - - +
25A SER* 3.8 30.3 - - - +
26A VAL 3.5 5.2 - - - +
27A VAL* 4.2 15.8 - - + +
40A ALA 3.8 2.0 + - - -
41A ALA* 1.3 69.0 - - - +
43A ILE* 1.3 60.6 + - - +
44A ILE* 3.9 15.2 - - + +
60A GLU* 2.6 35.3 + - - +
85A HIS 3.5 2.1 - - - +
86A TYR* 3.5 3.5 - - - -
87A LEU* 2.8 49.5 + - + +
89A PHE* 3.9 18.7 - - + -
156A ASP* 2.8 34.4 + - - +
158A GLY* 3.7 7.3 - - - -
600A FEF 5.2 3.8 - - + -
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Residues in contact with ILE 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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15A LEU* 3.6 35.9 - - + -
25A SER* 3.6 3.6 - - - -
26A VAL* 2.7 44.3 + - + +
28A ARG* 3.7 24.2 - - + +
41A ALA* 3.6 16.6 - - + +
42A LYS* 1.3 71.8 - - - +
44A ILE* 1.3 63.0 + - - +
45A ASN 4.1 1.0 + - - -
84A HIS* 3.8 24.2 - - + +
85A HIS 3.5 4.0 - - - +
86A TYR* 3.8 29.2 - - + -
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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 4.3 12.8 - - - +
25A SER* 4.3 13.9 - - - -
42A LYS* 3.9 22.9 - - + +
43A ILE* 1.3 73.9 - - - +
45A ASN* 1.3 67.7 + - - +
46A THR* 3.4 1.1 + - + -
49A LEU* 3.9 33.2 - - + -
57A LEU* 3.7 29.6 - - + -
84A HIS* 3.3 7.3 - - - +
85A HIS* 2.9 57.3 + - + +
87A LEU* 3.9 17.7 - - + -
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Residues in contact with ASN 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 5.0 3.2 + - - -
25A SER* 5.6 0.6 - - - +
43A ILE 4.1 1.8 + - - -
44A ILE* 1.3 71.2 - - - +
46A THR* 1.3 61.8 + - - +
47A LYS* 3.1 35.4 + - - +
48A LYS* 3.4 24.7 + - + +
49A LEU* 3.8 10.7 - - - +
83A GLY 3.5 4.2 - - - +
84A HIS* 3.9 24.1 + - + -
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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