Contacts of the strand formed by residues 51 - 59 (chain B) in PDB entry 1CVJ
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 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 4.8 3.4 - - - +
18B LEU* 5.2 2.9 - - - +
19B HIS 4.8 1.7 + - - -
20B PRO* 3.3 38.1 + - - +
22B VAL 5.3 2.7 + - - -
42B VAL* 4.2 15.0 - - - +
43B CYS 3.8 8.2 + - - -
44B ARG* 4.0 3.4 - - - -
49B ARG 3.1 5.9 + - - -
50B ARG* 1.3 91.8 - - - +
52B LEU* 1.3 64.6 + - - +
53B GLY* 3.0 15.3 + - - -
54B TYR 4.6 0.9 + - - -
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Residues in contact with LEU 52 (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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43B CYS* 2.8 15.7 + - + +
44B ARG* 3.5 25.6 - - - +
45B ASP* 3.5 23.6 - - + +
50B ARG* 4.0 2.9 - - + +
51B SER* 1.3 78.6 + - - +
53B GLY* 1.3 60.7 + - - +
54B TYR* 3.4 24.6 - - + -
4N A 4.6 9.6 + - - +
5N A 3.9 52.0 - - + +
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Residues in contact with GLY 53 (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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14B TYR* 4.8 0.2 + - - -
17B ASP* 2.7 29.6 + - - -
18B LEU* 2.8 29.3 + - - -
20B PRO* 5.9 0.4 - - - +
51B SER* 3.0 11.4 + - - -
52B LEU* 1.3 77.6 - - - +
54B TYR* 1.3 60.3 + - - +
4N A 5.3 3.4 + - - -
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Residues in contact with TYR 54 (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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14B TYR* 3.4 37.2 - + + +
15B VAL 3.2 7.9 - - - -
16B GLY* 3.4 7.0 - - - -
18B LEU* 3.5 7.5 - - - +
42B VAL* 3.9 2.6 - - - +
43B CYS* 3.1 45.7 + - + +
51B SER* 4.6 0.6 + - - -
52B LEU* 3.4 31.6 - - + -
53B GLY* 1.3 79.6 - - - +
55B ALA* 1.3 68.6 + - - +
56B TYR* 4.1 10.3 - + - -
4N A 3.6 36.2 - - - +
5N A 2.9 23.8 + - + +
6N A 2.9 25.2 + - - -
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Residues in contact with ALA 55 (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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14B TYR* 3.6 4.5 - - - -
15B VAL* 3.0 35.9 + - + +
18B LEU* 3.9 1.8 - - + -
27B LEU* 3.6 27.1 - - + -
41B ARG 2.7 20.9 - - - +
42B VAL* 3.5 10.8 - - + +
43B CYS* 4.3 1.8 - - - +
54B TYR* 1.3 84.3 - - - +
56B TYR* 1.3 65.5 + - - +
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Residues in contact with TYR 56 (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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13B LEU 3.2 12.1 - - - +
14B TYR* 4.6 3.8 - - + -
39B SER 3.9 0.5 - - - +
40B ILE* 3.2 7.3 - - - +
41B ARG* 2.6 39.4 + - + +
43B CYS* 3.8 23.1 - - - -
54B TYR* 4.1 7.5 - + - -
55B ALA* 1.3 76.5 - - - +
57B VAL* 1.3 62.2 + - - +
58B ASN* 4.0 0.9 - - - +
87B SER* 3.3 26.0 - - - -
89B ARG* 3.6 10.6 - - + +
4N A 3.6 23.1 + + - -
6N A 2.9 98.2 + + + +
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Residues in contact with VAL 57 (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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12B SER* 3.8 0.5 - - - -
13B LEU* 2.9 42.9 + - + +
15B VAL* 4.1 21.3 - - + -
27B LEU* 4.8 3.1 - - + -
31B PHE* 4.0 30.3 - - + -
37B ILE* 4.6 2.0 - - + -
40B ILE* 3.1 36.3 - - + -
56B TYR* 1.3 76.7 - - - +
58B ASN* 1.3 61.7 + - - +
59B PHE* 3.6 30.2 + - + -
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Residues in contact with ASN 58 (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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11B ALA 3.9 4.0 - - - +
12B SER* 2.4 35.6 + - - +
37B ILE* 3.3 6.5 - - - +
38B LEU* 2.6 42.5 + - + -
39B SER* 2.7 46.6 + - - +
56B TYR* 4.5 2.5 - - - +
57B VAL* 1.3 75.4 - - - +
59B PHE* 1.3 55.1 - - - +
6N A 2.8 36.3 + - - +
992N A 4.0 8.5 + - - -
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Residues in contact with PHE 59 (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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11B ALA* 3.1 20.9 + - - +
13B LEU* 3.6 7.9 - - + -
31B PHE* 3.3 38.1 - + + -
34B ALA* 3.8 10.5 - - + -
35B GLY 3.9 5.2 - - - -
36B PRO 3.7 15.3 - - - -
37B ILE* 3.9 11.4 - - + -
38B LEU* 4.0 11.0 - - - +
57B VAL* 3.6 21.1 - - + -
58B ASN* 1.3 76.3 - - - +
60B GLN* 1.3 65.6 + - - +
61B GLN 3.5 17.3 - - - +
64B ASP* 3.8 12.1 - - + -
65B ALA* 3.3 26.7 - - + -
68B ALA* 3.4 34.1 - - + -
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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