Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 2VN9
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 SER 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.2 4.5 - - - +
23A GLY* 2.6 42.1 + - - +
25A PHE* 1.3 82.4 - - - +
27A VAL* 1.3 64.5 + - - +
28A VAL* 4.7 2.4 - - - +
43A LYS* 3.6 35.2 - - - +
44A ILE 3.3 13.5 - - - -
45A ILE* 4.3 8.1 - - - -
1314A GVD 5.9 1.0 - - - +
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Residues in contact with VAL 27 (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 GLU* 3.4 35.0 - - + +
21A GLY 3.7 3.4 - - - -
22A LYS* 4.3 11.0 - - + +
26A SER* 1.3 78.0 - - - +
28A VAL* 1.3 64.7 + - - +
29A ARG* 3.8 20.2 - - + -
42A ALA 3.6 0.7 - - - +
43A LYS* 3.4 2.4 - - - -
44A ILE* 2.8 41.6 + - + +
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Residues in contact with VAL 28 (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 GLU* 3.5 2.6 - - - -
20A LEU* 2.6 42.0 + - + +
21A GLY 2.8 18.3 + - - +
26A SER* 4.7 4.7 - - - +
27A VAL* 1.3 78.6 - - - +
29A ARG* 1.3 55.4 + - - +
41A ALA* 3.9 25.8 - - + -
42A ALA 3.2 10.8 - - - +
43A LYS* 4.2 20.0 - - + +
1314A GVD 3.7 49.8 - - + +
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Residues in contact with ARG 29 (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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16A LEU* 4.0 34.1 + - + +
17A PHE* 2.7 31.9 + - - +
18A GLU* 3.2 10.2 - - - +
19A GLU* 3.9 11.0 - - - +
20A LEU* 4.1 3.1 - - - -
27A VAL* 3.8 15.9 - - + -
28A VAL* 1.3 76.7 - - - +
30A ARG* 1.3 66.8 + - - +
41A ALA* 3.7 0.2 - - - -
42A ALA* 2.8 35.0 + - - +
44A ILE* 3.4 28.1 - - + +
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Residues in contact with ARG 30 (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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16A LEU* 3.7 0.9 - - - -
17A PHE* 2.7 57.6 + - - +
18A GLU* 2.8 51.0 + - - +
20A LEU* 3.6 20.3 - - + +
29A ARG* 1.3 74.8 - - - +
31A CYS* 1.3 63.2 + - - +
32A MET* 3.8 19.6 - - - +
39A GLU* 2.6 41.1 + - - +
40A TYR 3.5 11.7 - - - +
92A LEU* 4.3 15.7 - - + -
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Residues in contact with CYS 31 (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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0A MET* 5.1 0.2 - - - -
14A TYR* 3.9 22.7 - - + -
15A GLN 3.0 15.5 - - - +
16A LEU* 3.8 17.5 - - + -
17A PHE* 4.0 2.7 - - - -
30A ARG* 1.3 77.6 - - - +
32A MET* 1.3 62.8 + - - +
39A GLU* 3.3 6.4 - - - +
40A TYR* 2.8 57.0 + - - +
42A ALA* 3.9 20.2 - - + -
89A VAL* 4.1 3.6 - - - -
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Residues in contact with MET 32 (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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14A TYR* 3.3 4.0 - - - -
15A GLN* 2.7 39.4 + - + +
17A PHE* 3.5 29.2 - - + -
30A ARG* 3.8 19.7 - - - +
31A CYS* 1.3 77.3 - - - +
33A LYS* 1.3 67.2 + - - +
34A ILE* 3.6 1.1 + - + +
37A GLY* 3.7 31.0 - - - +
38A GLN 3.2 5.4 - - - +
39A GLU* 4.1 14.4 - - + +
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Residues in contact with LYS 33 (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 GLU* 3.5 18.9 + - - +
14A TYR* 3.6 35.9 + - + -
32A MET* 1.3 73.5 - - - +
34A ILE* 1.3 69.6 + - - +
35A PRO 3.7 0.5 - - - -
36A THR* 3.3 23.7 + - + +
37A GLY* 2.9 30.1 + - - -
38A GLN* 2.8 18.9 + - + +
40A TYR* 4.0 21.1 - - + +
77A HIS* 6.6 0.2 - - - -
78A ASP* 5.0 3.7 + - - -
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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