Contacts of the strand formed by residues 3 - 14 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 1.3 70.8 - - - +
4A ALA* 1.3 61.5 + - - +
5A GLU 3.8 20.6 - - - +
6A ILE* 3.8 16.2 - - + -
37A ILE* 3.7 32.1 - - + -
38A VAL 3.9 3.4 - - - -
39A ALA* 4.5 2.0 - - - +
40A ASP* 4.7 0.3 - - - +
75A LEU* 3.7 31.9 - - + +
76A ILE* 3.8 8.3 - - + +
77A GLY* 2.8 28.1 + - - -
78A ALA* 2.9 26.3 + - + +
80A PRO* 4.1 17.5 - - + -
86A LEU* 4.5 13.0 - - + -
104A ILE* 5.7 0.4 - - + -
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Residues in contact with ALA 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS 3.3 1.6 + - - -
3A ILE* 1.3 74.3 - - - +
5A GLU* 1.3 64.4 + - + +
38A VAL* 2.8 15.5 + - + +
39A ALA 3.9 3.8 - - - +
40A ASP* 3.3 32.5 - - - +
76A ILE* 3.9 10.2 - - - +
369A SER* 3.4 26.4 + - - +
403A MG 3.9 3.3 - - - -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.8 2.5 - - - +
4A ALA* 1.3 88.7 - - + +
6A ILE* 1.3 70.1 + - - +
7A HIS* 2.8 32.4 + - + +
36A LYS 4.4 0.4 - - - -
37A ILE* 3.6 1.2 - - - -
38A VAL* 2.9 50.2 + - + +
76A ILE* 4.2 0.4 - - - -
368A PHE 3.2 8.3 - - - +
369A SER* 3.8 14.6 + - - +
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.8 19.5 - - + -
5A GLU* 1.3 79.5 - - - +
7A HIS* 1.3 67.7 + - - +
8A VAL* 4.7 5.8 - - + -
35A VAL* 3.9 23.8 - - + -
36A LYS 3.4 3.4 - - - +
37A ILE* 4.4 7.2 - - + -
68A LEU* 6.1 1.1 - - + -
72A ALA* 3.9 44.0 - - + +
75A LEU* 3.9 24.9 - - + -
76A ILE* 4.1 4.0 - - + -
104A ILE* 4.4 10.1 - - + -
367A SER* 3.5 1.9 - - - -
368A PHE* 2.8 41.0 + - + -
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Residues in contact with HIS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 2.8 41.2 + - + +
6A ILE* 1.3 77.4 - - - +
8A VAL* 1.3 62.3 + - - +
9A TYR* 3.7 26.8 - - + +
35A VAL* 3.3 6.4 - - - +
36A LYS* 2.8 47.6 + - + +
38A VAL* 4.1 10.7 - - + +
364A PRO* 3.9 11.3 - - + +
366A ALA 3.6 2.5 - - - -
367A SER* 2.8 32.3 + - - -
368A PHE 5.1 1.6 - - - -
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.7 8.1 - - + -
7A HIS* 1.3 77.7 - - - +
9A TYR* 1.3 63.1 + - - +
33A THR* 3.8 24.9 - - + -
34A LEU 3.4 2.9 - - - +
35A VAL* 4.7 4.5 - - + -
65A ARG* 4.2 22.4 - - + +
68A LEU* 4.1 28.9 - - + +
69A ALA 5.4 0.4 - - - +
364A PRO* 3.4 3.6 - - - +
365A VAL* 2.8 29.0 + - + +
366A ALA* 2.8 19.4 + - + +
368A PHE* 4.2 21.1 - - + -
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS* 3.7 30.3 - - + +
8A VAL* 1.3 75.6 - - - +
10A ALA* 1.3 59.3 + - - +
33A THR* 3.3 12.5 - - - +
34A LEU* 2.8 55.8 + - + +
36A LYS* 3.8 10.0 - - + +
46A TRP* 3.5 28.7 - + - -
65A ARG* 4.5 0.6 + - - -
358A GLU* 2.7 37.1 + - + -
361A PHE* 3.8 16.8 - + + +
362A GLY 3.6 24.2 - - - -
363A PRO 4.2 1.6 - - - +
364A PRO* 3.7 29.2 - - + +
365A VAL* 4.3 6.1 - - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 1.3 72.5 - - - +
11A HIS* 1.3 64.0 + - - +
31A GLN* 3.9 8.3 - - - +
32A THR 3.7 5.2 - - - -
65A ARG* 3.5 32.1 - - - +
361A PHE 3.5 17.2 + - - +
363A PRO 5.5 0.8 + - - -
365A VAL* 3.8 24.9 - - + +
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Residues in contact with HIS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 1.3 76.1 + - - +
12A ASP* 1.3 77.1 + - - +
13A LEU* 3.9 10.7 - - + +
31A GLN* 3.6 7.9 - - - +
32A THR* 2.8 44.0 + - + +
34A LEU* 3.7 19.1 - - + -
329A GLN* 4.4 18.5 + - - +
331A TYR* 3.8 30.9 - + - -
360A LEU* 3.6 27.2 + - + +
361A PHE* 3.8 17.7 + + + -
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 1.3 89.1 + - - +
13A LEU* 1.3 70.1 + - - +
14A PRO* 3.6 11.8 - - + +
29A SER* 4.5 9.8 + - - +
30A LEU 3.5 2.6 - - - +
31A GLN* 2.9 36.4 + - - +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 3.9 12.6 - - + +
12A ASP* 1.3 83.1 - - - +
14A PRO* 1.3 66.6 - - - +
15A VAL* 3.5 1.4 + - - +
29A SER* 3.6 3.9 + - - -
30A LEU* 2.6 39.1 + - + +
32A THR* 3.9 26.0 - - + -
50A CYS* 4.2 3.1 - - - -
296A TRP* 4.1 13.6 + - + +
297A GLY* 4.0 13.2 - - - -
327A ILE* 4.0 43.5 - - + -
329A GLN 5.3 0.9 - - - +
331A TYR* 3.8 22.7 - - + +
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Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 3.6 11.4 - - + +
13A LEU* 1.3 88.6 - - + +
15A VAL* 1.3 63.4 + - - +
16A LYS* 3.4 3.3 + - - +
28A TRP 4.1 1.1 - - - +
29A SER* 3.6 17.7 - - - +
326A TYR 3.2 14.4 - - - +
327A ILE* 4.7 4.3 - - - +
328A ALA* 4.9 6.1 + - + +
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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