Contacts of the strand formed by residues 28 - 32 (chain B) in PDB entry 1VCB
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 GLU 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 2.7 15.0 + - - +
12A THR* 3.5 11.6 + - - +
13A THR* 2.9 28.7 + - - +
20B LYS* 2.7 44.5 + - + -
21B LEU 3.6 3.1 - - - -
22B ILE* 3.6 25.7 - - + +
26B GLY 3.7 10.8 - - - +
27B HIS* 1.3 75.6 - - - +
29B PHE* 1.3 62.1 + - - +
30B ILE* 3.8 4.7 - - + +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR* 3.2 26.0 - - + +
15A PHE* 3.5 25.1 - + + -
93A PHE* 3.5 34.1 - + - -
19B VAL 3.4 3.6 - - - +
20B LYS* 3.4 0.9 - - - -
21B LEU* 3.0 45.0 + - + +
23B SER* 4.5 3.8 - - - -
27B HIS* 3.6 26.5 - - + -
28B GLU* 1.3 72.7 - - - +
30B ILE* 1.3 63.5 + - - +
31B VAL* 3.6 1.9 + - + -
67B SER* 4.2 11.2 - - - -
70B LEU* 3.9 26.9 - - + -
71B SER* 4.1 11.4 - - - -
74B CYS* 4.0 22.0 - - - -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 3.9 22.0 - - + -
13A THR 2.9 6.8 + - - +
14A ILE* 3.7 16.5 - - + +
15A PHE* 3.1 27.0 + - - +
34A ILE* 3.8 20.6 - - + -
35A LEU* 5.0 5.6 - - + -
18B TYR* 3.4 37.0 - - + -
19B VAL 3.2 7.9 - - - +
20B LYS* 4.3 24.2 - - + -
28B GLU 3.8 15.5 - - - +
29B PHE* 1.3 75.5 - - - +
31B VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.1 21.3 - - + +
18B TYR* 3.4 6.6 - - - -
19B VAL* 2.8 38.3 + - + +
21B LEU* 4.3 8.3 - - + -
29B PHE 4.2 7.6 - - - +
30B ILE* 1.3 80.4 - - - +
32B LYS* 1.3 75.0 + - - +
35B HIS* 3.7 21.8 - - + -
36B ALA* 4.4 4.3 - - + +
74B CYS* 3.6 33.2 - - + +
77B PHE* 4.7 10.1 - - + -
78B THR* 5.7 1.1 - - + -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE 4.7 3.2 + - - +
16A THR* 4.4 13.9 + - - +
17A ASP* 2.7 30.2 + - - -
17B MET* 3.5 20.9 - - + +
18B TYR* 3.6 35.6 - - + -
31B VAL* 1.3 80.9 - - - +
33B ARG* 1.3 64.5 + - - +
34B GLU* 3.0 24.2 - - - +
35B HIS* 3.2 33.4 + - + +
36B ALA* 3.1 18.5 + - - +
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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