Contacts of the strand formed by residues 4 - 13 (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 VAL 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 6.6 0.4 - - + -
2B LYS 3.6 4.0 + - - +
3B LYS* 1.3 82.1 - - - +
5B VAL* 1.3 63.0 + - - +
6B ALA 3.6 25.1 - - - +
7B VAL* 4.8 4.3 - - + +
58B THR* 3.7 16.2 - - + -
59B ILE 3.7 3.8 - - - +
60B TYR* 3.8 24.5 - - + -
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Residues in contact with VAL 5 (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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3B LYS* 3.7 8.9 + - + -
4B VAL* 1.3 76.8 - - - +
6B ALA* 1.3 62.1 + - - +
30B HIS* 4.1 21.9 + - + +
59B ILE* 2.8 29.2 + - + +
60B TYR 3.5 15.9 - - - +
61B ALA* 3.7 27.8 - - + -
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Residues in contact with ALA 6 (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* 3.6 9.9 - - - +
5B VAL* 1.3 81.5 - - - +
7B VAL* 1.3 60.1 + - - +
8B VAL* 4.0 5.2 - - + -
30B HIS* 3.4 38.4 - - + +
58B THR* 3.5 3.1 - - - -
59B ILE* 2.9 40.0 + - + +
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Residues in contact with VAL 7 (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* 5.3 5.8 - - + -
6B ALA* 1.3 73.1 - - - +
8B VAL* 1.3 64.0 + - - +
9B LYS* 3.7 11.6 + - + +
56B GLU* 3.8 28.7 - - + +
57B ILE 3.4 6.1 - - - +
58B THR* 4.5 12.8 - - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 4.0 13.2 - - + +
30A GLU 5.8 0.2 - - - -
6B ALA* 4.5 9.2 - - + -
7B VAL* 1.3 72.5 - - - +
9B LYS* 1.3 63.3 + - - +
10B LEU* 3.9 16.2 - - + -
26B ALA* 3.7 43.7 - - + +
27B LEU* 4.7 1.6 - - + -
30B HIS* 4.8 3.8 - - + +
55B VAL 3.5 1.7 - - - +
56B GLU* 3.3 3.5 - - - -
57B ILE* 2.7 51.8 + - + +
59B ILE* 3.9 21.8 - - + -
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Residues in contact with LYS 9 (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* 4.0 10.7 - - + +
29A TRP* 3.7 3.8 - - - -
30A GLU* 3.1 65.7 + - + +
7B VAL* 3.7 12.6 + - + +
8B VAL* 1.3 74.2 - - - +
10B LEU* 1.3 63.6 + - - +
55B VAL 3.5 3.8 - - - +
56B GLU* 3.5 40.3 + - + +
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Residues in contact with LEU 10 (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* 4.6 3.0 - - - +
28A LEU 3.3 16.4 - - - +
29A TRP* 3.6 31.4 - - + -
8B VAL* 3.9 11.4 - - + -
9B LYS* 1.3 74.7 - - - +
11B GLN* 1.3 63.3 + - - +
12B LEU* 4.3 12.6 - - + -
22B PRO* 3.8 11.0 - - + -
23B VAL* 4.1 31.0 - - + -
26B ALA* 4.0 3.6 - - + -
27B LEU* 4.5 7.6 - - + -
37B PHE* 4.7 1.1 - - + -
54B PRO* 3.3 4.3 - - - +
55B VAL* 2.8 43.9 + - + +
57B ILE* 3.6 21.1 - - + -
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Residues in contact with GLN 11 (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* 3.5 28.5 + - + +
14A ASP* 5.5 0.6 + - - -
17A LEU* 3.4 28.0 - - - +
21A PHE* 3.6 6.8 - - - -
27A GLY* 3.4 6.4 - - - -
28A LEU* 2.9 63.1 + - + +
10B LEU* 1.3 78.3 - - - +
12B LEU* 1.3 61.7 + - - +
52B ILE* 4.0 19.0 - - + +
53B VAL 3.4 5.4 - - - +
54B PRO* 3.8 25.7 - - + +
73B PRO* 4.9 7.8 - - - +
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Residues in contact with LEU 12 (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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21A PHE* 5.1 0.2 - - - -
26A ARG 4.2 13.2 - - - +
27A GLY* 4.2 6.5 - - - -
10B LEU* 4.3 9.9 - - + -
11B GLN* 1.3 79.3 - - - +
13B PRO* 1.4 66.8 - - + +
17B ALA* 4.0 17.3 - - + -
18B THR 6.0 0.2 - - - +
22B PRO* 4.3 11.4 - - + -
23B VAL* 3.9 32.1 - - + -
37B PHE* 3.9 17.9 - - + -
41B PHE* 3.7 25.1 - - + -
52B ILE* 4.7 3.6 - - - -
53B VAL* 2.7 45.8 + - - +
55B VAL* 4.1 10.5 - - + -
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Residues in contact with PRO 13 (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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21A PHE* 4.4 9.8 - - + -
25A ALA 5.8 0.4 - - - +
26A ARG* 3.4 35.2 - - - +
12B LEU* 1.4 90.0 - - + +
14B ALA* 1.3 66.6 + - - +
15B GLY 3.3 2.9 + - - -
16B LYS* 3.4 47.7 + - + +
17B ALA* 4.1 2.8 + - - +
41B PHE* 3.6 9.2 - - - -
50B ASP 5.3 3.1 - - - +
51B ALA 4.0 5.2 - - - +
52B ILE* 4.5 12.6 - - + -
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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