Contacts of the strand formed by residues 27 - 33 (chain B) in PDB entry 1V1A
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 LEU 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLN* 4.1 21.3 - - - +
27A LEU* 4.2 18.8 - - + -
28A LEU 3.4 9.4 - - - +
29A GLU* 3.5 27.8 - - + -
30A VAL* 3.8 0.6 - - - +
16B PRO* 4.2 6.1 - - - +
17B GLN* 3.8 34.1 + - - +
25B LYS* 4.7 3.1 - - - +
26B ARG* 1.3 92.4 + - + +
28B LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.8 10.5 - - + -
27A LEU* 3.3 8.6 - - - -
28A LEU* 2.8 38.3 + - + +
30A VAL* 3.8 21.1 - - + -
61A LEU* 6.2 1.3 - - + -
14B LEU* 4.0 35.0 - - + -
15B VAL* 3.4 20.6 - - - +
16B PRO* 4.0 13.9 - - + -
22B LEU* 4.1 11.0 - - + -
25B LYS* 4.5 8.1 - - + -
27B LEU* 1.3 84.1 - - - +
29B GLU* 1.3 65.3 + - - +
30B VAL* 4.2 0.3 - - - +
90B LEU* 4.5 14.1 - - + -
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Residues in contact with GLU 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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26A ARG 3.4 8.7 - - - +
27A LEU* 4.0 9.6 - - + -
13B ALA 3.2 0.9 - - - +
14B LEU* 3.2 6.9 - - - -
15B VAL* 2.7 35.1 + - - +
16B PRO 4.4 6.6 - - - +
17B GLN* 3.5 36.2 + - + +
28B LEU* 1.3 76.1 - - - +
30B VAL* 1.3 61.4 + - - +
31B TYR* 2.7 40.2 + - + +
93B TYR* 5.5 0.3 + - - -
285B ARG* 2.6 37.2 + - - +
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Residues in contact with VAL 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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25A LYS 4.1 10.5 - - - +
26A ARG* 2.9 36.9 + - - +
28A LEU* 3.7 25.6 - - + -
12B VAL* 3.4 31.9 - - + -
13B ALA 3.2 2.7 - - - +
14B LEU* 3.7 17.9 - - + -
28B LEU 4.2 1.3 - - - +
29B GLU* 1.3 76.7 - - - +
31B TYR* 1.3 71.2 + - - +
61B LEU* 5.1 2.2 - - + -
64B MET* 3.8 24.4 - - + +
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Residues in contact with TYR 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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26A ARG* 6.3 0.2 - - - +
12B VAL* 3.4 6.7 - - - +
13B ALA* 2.5 45.1 + - + -
15B VAL* 4.2 22.0 - - + -
29B GLU* 2.7 47.1 + - + -
30B VAL* 1.3 81.5 - - - +
32B VAL* 1.3 65.2 + - - +
64B MET* 5.1 1.3 - - - -
285B ARG* 3.6 16.0 + - + +
286B GLY* 3.6 28.3 - - - -
287B ASP 4.5 1.1 - - - +
289B GLU* 3.1 41.7 - - + +
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Residues in contact with VAL 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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26A ARG* 5.9 2.5 - - - +
11B LEU 3.7 6.5 - - - +
12B VAL* 4.6 1.6 - - + +
31B TYR* 1.3 78.3 - - - +
33B GLY* 1.3 64.4 + - - +
37B VAL* 3.9 23.8 - - + -
64B MET* 4.2 21.3 - - + -
65B VAL* 4.1 33.0 - - + +
68B ARG* 4.0 31.1 - - + +
287B ASP* 3.7 9.5 + - - +
288B HIS* 3.1 30.7 + - + -
289B GLU* 4.8 3.7 + - - +
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Residues in contact with GLY 33 (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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10B PRO* 3.8 0.2 - - - +
11B LEU* 2.6 35.6 + - - +
12B VAL* 4.5 0.4 - - - +
13B ALA* 4.5 1.7 - - - +
31B TYR 3.9 1.0 + - - -
32B VAL* 1.3 74.9 - - - +
34B GLY* 1.3 61.1 + - - -
37B VAL* 3.4 18.4 - - - +
38B ASN* 3.9 7.6 - - - -
89B TYR* 5.2 0.2 - - - -
287B ASP* 3.5 19.3 - - - -
1302B KDG 3.9 1.3 - - - -
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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