Contacts of the strand formed by residues 25 - 32 (chain C) in PDB entry 2VKM
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 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C THR* 3.1 3.9 - - - -
20C VAL* 2.9 46.2 + - + +
23C PRO* 3.9 7.2 + - + +
24C PRO* 1.3 75.5 - - - +
26C THR* 1.3 64.2 + - - +
27C LEU* 3.7 4.2 + - + -
51C TYR 3.8 5.1 - - - +
52C TYR* 3.6 16.3 - - - -
53C GLN* 2.9 55.2 + - - +
56C LEU* 4.2 20.5 + - + +
57C SER* 4.2 8.1 - - - -
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.6 40.0 + - + +
18C MET 3.5 4.7 - - - +
19C THR* 3.9 13.2 - - + +
24C PRO* 4.0 3.4 + - - +
25C GLN* 1.3 73.1 - - - +
27C LEU* 1.3 76.7 + - - +
50C ARG* 3.5 32.6 + - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.6 2.9 - - - +
18C MET* 2.8 35.6 + - + +
20C VAL* 3.9 25.8 - - + -
25C GLN* 4.2 7.6 - - + +
26C THR* 1.3 83.3 - - - +
28C ASN* 1.3 62.1 + - - +
29C ILE* 3.8 14.1 + - + +
40C VAL* 3.9 30.1 - - + -
41C GLY 5.0 0.9 - - - +
50C ARG* 3.8 20.0 - - + +
51C TYR* 4.1 21.3 - - - +
52C TYR* 4.2 12.1 - - + +
116C GLU* 3.7 21.5 - - + +
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Residues in contact with ASN 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ARG* 3.7 11.0 + - - +
15C TYR* 3.5 27.0 - - + -
16C VAL 3.7 2.0 - - - -
17C GLU* 3.9 23.8 + - - +
27C LEU* 1.3 74.5 + - - +
29C ILE* 1.3 60.7 + - - +
50C ARG* 3.1 20.3 + - - +
114C ASN* 3.2 41.3 + - - +
115C TRP* 3.5 3.0 - - - -
116C GLU* 2.7 39.5 + - - +
117C GLY 3.4 3.8 + - - -
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 3.5 4.7 - - - +
16C VAL* 2.8 41.8 + - + +
18C MET* 3.6 33.9 - - + -
20C VAL* 6.2 1.1 - - + -
27C LEU* 4.0 15.3 - - + +
28C ASN* 1.3 80.7 - - - +
30C LEU* 1.3 63.1 + - - +
31C VAL 3.5 0.5 + - - -
38C PHE* 4.0 8.7 - - + -
40C VAL* 3.6 29.6 - - + -
117C GLY* 3.6 10.1 - - - +
118C ILE 3.4 8.5 - - - +
119C LEU* 3.3 39.9 - - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY* 3.7 22.4 - - - -
14C TYR 3.5 11.4 - - - +
15C TYR* 3.8 4.9 - - - +
29C ILE* 1.3 71.2 - - - +
31C VAL* 1.3 71.8 + - - +
32C ASP* 3.5 14.3 + - + -
115C TRP* 3.4 43.1 - - + +
117C GLY 2.9 17.8 + - - +
118C ILE* 3.5 6.8 - - + -
119C LEU* 2.7 32.6 + - - +
229C SER 5.2 0.7 - - - +
230C GLY* 4.5 7.0 - - - -
1386C BSD 3.8 34.5 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.2 17.0 - - + -
14C TYR* 2.9 18.6 + - + +
16C VAL* 3.8 28.3 - - + -
29C ILE 4.2 1.6 - - - +
30C LEU* 1.3 75.9 - - - +
32C ASP* 1.3 57.7 + - - +
119C LEU* 4.2 7.0 - - + -
121C LEU* 3.4 25.8 - - + -
152C LEU* 3.8 30.7 - - + -
154C LEU* 5.7 1.5 - - + +
174C MET* 3.9 13.7 - - - -
229C SER* 2.8 24.7 + - - +
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Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.5 3.8 + - + -
31C VAL* 1.3 74.6 - - - +
33C THR* 1.3 57.3 + - - +
34C GLY 2.9 20.5 + - - -
35C SER* 2.5 23.8 + - - +
118C ILE* 3.3 27.4 - - + +
119C LEU 2.9 16.3 + - - +
120C GLY* 3.4 2.4 - - - -
121C LEU* 2.8 23.6 + - - -
228C ASP* 3.2 3.5 - - - +
229C SER* 3.4 1.6 - - - -
230C GLY* 3.1 21.7 - - - +
1386C BSD 2.7 22.4 + - - -
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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