Contacts of the strand formed by residues 3 - 14 (chain B) in PDB entry 4J1O
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 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 1.3 73.4 - - - +
4B ALA* 1.3 61.2 + - - +
5B GLU 3.7 21.3 - - - +
6B ILE* 3.8 16.8 - - + -
37B ILE* 3.7 32.1 - - + -
38B VAL 3.9 3.4 - - - -
39B ALA* 4.5 1.6 - - - +
40B ASP* 4.5 1.1 - - - +
75B LEU* 3.7 27.8 - - + +
76B ILE* 3.8 12.0 - - + +
77B GLY* 2.9 25.8 + - - -
78B ALA* 2.8 28.1 + - + +
80B PRO* 4.0 16.4 - - + -
86B LEU* 4.3 15.0 - - + -
104B ILE* 5.8 0.2 - - + -
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Residues in contact with ALA 4 (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 3.4 1.2 + - - -
3B ILE* 1.3 73.7 - - - +
5B GLU* 1.3 70.0 + - + +
38B VAL* 2.7 16.3 + - + +
39B ALA 3.9 4.9 - - - +
40B ASP* 3.3 31.2 - - - +
76B ILE* 4.0 9.9 - - - +
369B SER* 3.5 22.0 - - - +
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Residues in contact with GLU 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 ILE* 3.7 2.4 - - - +
4B ALA* 1.3 89.8 - - + +
6B ILE* 1.3 69.9 + - - +
7B HIS* 2.8 32.8 + - + +
36B LYS 4.5 0.4 - - - -
37B ILE* 3.6 0.3 - - - -
38B VAL* 2.9 50.5 + - + +
76B ILE* 4.2 0.7 - - - -
368B PHE 3.2 9.2 - - - +
369B SER* 4.3 10.7 - - - -
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.8 20.2 - - + -
5B GLU* 1.3 78.6 - - - +
7B HIS* 1.3 67.4 + - - +
8B VAL* 4.6 7.9 - - + -
35B VAL* 4.1 21.8 - - + -
36B LYS 3.4 2.9 - - - +
37B ILE* 4.4 8.1 - - + -
68B LEU* 6.3 0.7 - - + -
72B ALA* 3.9 33.7 - - + +
75B LEU* 3.8 35.2 - - + -
76B ILE* 4.1 3.6 - - + -
104B ILE* 4.4 10.8 - - + -
367B SER* 3.5 2.4 - - - -
368B PHE* 2.8 38.0 + - + -
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Residues in contact with HIS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 2.8 41.2 + - + +
6B ILE* 1.3 77.6 - - - +
8B VAL* 1.3 63.3 + - - +
9B TYR* 3.6 28.3 - - + +
35B VAL* 3.3 6.6 - - - +
36B LYS* 2.9 45.2 + - + +
38B VAL* 4.1 14.3 - - + +
364B PRO* 3.9 8.5 - - + +
366B ALA 3.6 2.5 - - - -
367B SER* 2.9 33.8 + - - -
368B PHE 5.1 0.7 - - - -
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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
----------------------------------------------------------
6B ILE* 4.6 9.9 - - + -
7B HIS* 1.3 77.6 - - - +
9B TYR* 1.3 58.5 + - - +
33B THR* 3.9 23.3 - - + -
34B LEU 3.5 3.1 - - - +
35B VAL* 4.7 2.7 - - + -
65B ARG* 4.2 12.1 - - + +
68B LEU* 4.0 31.0 - - + -
69B ALA* 5.2 1.1 - - - +
364B PRO* 3.2 4.3 - - - +
365B VAL* 2.8 47.1 + - + +
366B ALA* 2.9 20.9 + - + +
368B PHE* 4.3 17.0 - - + -
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Residues in contact with TYR 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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7B HIS* 3.6 36.5 - - + +
8B VAL* 1.3 78.5 - - - +
10B ALA* 1.3 59.7 + - - +
33B THR* 3.3 11.8 - - - +
34B LEU* 2.9 53.3 + - + +
36B LYS* 3.7 18.5 + - + +
46B TRP* 3.6 31.2 - + - -
65B ARG* 4.7 0.7 - - - -
358B GLU* 4.3 9.4 + - + -
361B PHE* 3.7 21.8 - + + +
362B GLY 3.5 25.1 - - - -
363B PRO 4.3 0.9 - - - -
364B PRO* 3.7 23.7 - - + +
365B VAL* 4.5 4.9 - - - +
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Residues in contact with ALA 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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9B TYR* 1.3 73.4 - - - +
11B HIS* 1.3 61.3 + - - +
65B ARG* 3.4 39.0 - - - +
361B PHE 3.3 18.9 + - - +
363B PRO 5.4 1.6 + - - +
365B VAL* 3.8 22.0 - - + +
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Residues in contact with HIS 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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10B ALA* 1.3 76.1 - - - +
12B ASP* 1.3 80.7 + - - +
13B LEU* 4.1 5.8 - - + +
31B GLN* 3.6 3.2 - - - +
32B THR* 2.8 38.9 + - + +
34B LEU* 3.6 19.7 - - + -
65B ARG* 4.9 0.2 - - - +
329B GLN* 5.5 6.3 + - + +
331B TYR* 3.8 36.7 - + - -
360B LEU* 3.5 34.6 + - + +
361B PHE* 4.0 12.9 + + + -
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Residues in contact with ASP 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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11B HIS* 1.3 98.0 + - - +
13B LEU* 1.3 63.0 + - - +
14B PRO* 4.0 9.4 - - + +
29B SER* 4.8 7.4 + - - +
30B LEU 3.6 3.0 - - - +
31B GLN* 3.6 25.6 - - - +
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Residues in contact with LEU 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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11B HIS* 4.1 10.1 - - + +
12B ASP* 1.3 80.9 - - - +
14B PRO* 1.3 66.8 - - - +
15B VAL 3.7 0.9 + - - -
29B SER* 3.6 2.4 + - - -
30B LEU* 2.7 37.4 + - + +
32B THR* 4.0 27.1 - - + -
50B CYS* 4.4 2.5 - - - -
296B TRP* 4.0 18.1 + - + +
297B GLY* 4.0 22.4 - - - -
327B ILE* 3.9 35.0 - - + -
329B GLN 5.0 1.8 - - - +
331B TYR* 3.9 21.1 - - + +
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Residues in contact with PRO 14 (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 ASP* 4.0 9.2 - - + +
13B LEU* 1.3 88.4 - - - +
15B VAL* 1.3 64.4 + - - +
16B LYS* 3.4 4.3 + - - +
28B TRP 4.4 2.2 - - - +
29B SER* 3.4 20.9 - - - +
326B TYR 3.4 11.8 - - - +
327B ILE* 4.8 3.1 - - - -
328B ALA* 4.9 8.9 + - + +
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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