Contacts of the strand formed by residues 52 - 60 (chain B) in PDB entry 3CJR
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 ILE 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PRO* 6.2 2.2 - - + -
21A PHE* 3.7 62.6 - - + -
11B GLN* 4.0 21.5 - - + +
12B LEU 3.9 4.3 - - - +
13B PRO* 4.5 11.7 - - + -
50B ASP 4.2 9.6 - - - +
51B ALA* 1.3 71.1 - - - +
53B VAL* 1.3 62.1 + - - +
54B PRO* 3.4 1.6 - - - +
72B PRO* 3.1 27.2 - - - +
73B PRO* 3.7 9.9 - - + +
76B TYR* 4.2 26.7 - - + -
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Residues in contact with VAL 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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11B GLN* 3.4 2.1 - - - -
12B LEU* 2.7 43.7 + - - +
14B ALA* 3.8 20.6 - - + -
41B PHE* 3.9 14.3 - - + -
45B THR* 4.0 4.9 - - + -
48B MET* 3.9 25.8 - - + -
51B ALA 3.6 14.6 - - - +
52B ILE* 1.3 72.5 - - - +
54B PRO* 1.3 74.9 - - + +
55B VAL* 3.7 1.2 + - - +
69B THR* 3.8 29.8 - - + -
70B LYS 4.3 5.4 - - - +
72B PRO* 4.5 0.7 - - - -
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Residues in contact with PRO 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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10A LEU* 6.1 0.7 - - + -
10B LEU 3.3 7.9 - - - +
11B GLN* 3.8 26.0 - - + +
52B ILE 3.4 2.5 - - - +
53B VAL* 1.3 85.8 - - + +
55B VAL* 1.3 58.9 + - - +
69B THR* 3.5 2.4 - - - -
70B LYS* 2.9 54.3 + - + +
72B PRO* 3.2 22.4 - - + -
73B PRO* 3.8 19.7 - - + -
114B ASP* 5.6 1.1 - - - +
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Residues in contact with VAL 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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8B VAL 3.5 1.9 - - - +
9B LYS* 3.5 2.1 - - - +
10B LEU* 2.8 57.5 + - + +
12B LEU* 4.1 11.4 - - + -
37B PHE* 4.3 2.0 - - + -
41B PHE* 3.8 30.1 - - + -
53B VAL 4.4 2.0 - - - +
54B PRO* 1.3 76.2 - - - +
56B GLU* 1.3 66.6 + - - +
57B ILE* 4.0 12.8 - - + -
67B PHE* 3.7 33.7 - - + -
68B VAL 3.4 12.6 - - - +
69B THR* 4.3 1.3 - - + -
70B LYS* 5.1 0.4 - - - -
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Residues in contact with GLU 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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7B VAL* 3.8 20.1 - - + +
8B VAL 3.3 3.4 - - - +
9B LYS* 3.5 41.5 + - + +
55B VAL* 1.3 73.2 - - - +
57B ILE* 1.3 63.2 - - - +
58B THR* 3.8 4.6 + - - +
67B PHE* 3.1 4.8 - - - -
68B VAL* 2.9 41.8 + - + +
70B LYS* 3.6 31.5 + - + -
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Residues in contact with ILE 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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7B VAL* 3.4 2.7 - - - -
8B VAL* 2.7 55.3 + - + +
10B LEU* 3.6 33.9 - - + -
27B LEU* 4.2 18.8 - - + -
37B PHE* 3.5 24.7 - - + -
55B VAL* 4.0 15.3 - - + -
56B GLU* 1.3 73.4 - - - +
58B THR* 1.3 64.2 + - - +
59B ILE* 3.7 13.3 + - + -
65B PHE* 4.0 27.4 - - + -
66B THR 3.5 10.5 - - - +
67B PHE* 4.1 2.9 - - + -
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Residues in contact with THR 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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4B VAL* 3.7 28.9 - - + -
6B ALA 3.5 3.6 - - - +
7B VAL* 4.5 13.1 - - + +
56B GLU* 3.8 4.2 + - - +
57B ILE* 1.3 72.0 - - - +
59B ILE* 1.3 61.0 + - - +
60B TYR* 3.6 26.3 - - + +
65B PHE* 3.2 5.4 - - - -
66B THR* 2.8 43.6 + - - +
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Residues in contact with ILE 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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4B VAL* 3.7 3.3 - - - -
5B VAL* 2.8 26.8 + - + -
6B ALA* 2.9 20.5 + - + +
8B VAL* 3.9 26.2 - - + -
27B LEU* 4.2 23.3 - - + -
30B HIS* 3.9 41.1 - - + +
32B ALA* 4.3 12.6 - - + -
57B ILE* 4.0 15.0 - - + +
58B THR* 1.3 76.5 - - - +
60B TYR* 1.3 71.9 + - - +
63B ARG 4.5 2.9 - - - +
64B SER 3.7 9.2 - - - +
65B PHE* 4.3 4.9 - - + -
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Residues in contact with TYR 60 (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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2B LYS* 4.0 35.9 - - + -
3B LYS 3.2 15.3 - - - +
4B VAL* 3.8 17.5 - - + -
5B VAL* 3.5 11.3 - - - +
30B HIS 5.3 0.3 - - - +
58B THR* 3.6 31.8 - - + +
59B ILE* 1.3 74.8 - - - +
61B ALA* 1.3 61.4 + - - +
62B ASP* 3.2 15.9 - - - +
63B ARG* 2.9 21.3 + - - +
64B SER* 2.9 29.8 + - - +
65B PHE 3.9 2.7 - - - -
66B THR* 2.7 40.3 + - + +
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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