Contacts of the strand formed by residues 3 - 20 (chain A) in PDB entry 1JPM
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 71.8 - - - +
4A ILE* 1.3 64.5 + - - +
5A ARG 4.1 2.9 - - - +
6A ILE* 3.9 21.1 - - + -
36A ILE* 3.6 21.5 - - + -
37A THR 3.8 4.0 - - - -
38A TYR* 3.6 23.3 - - + -
74A LEU* 3.6 39.5 - - + +
75A LEU* 4.2 4.0 - - + -
76A GLY* 2.8 29.3 + - - -
77A LYS* 3.0 14.6 + - + +
79A LEU* 4.3 6.7 - - + -
85A ILE* 4.9 2.2 - - + -
107A LEU* 3.9 26.2 - - + -
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Residues in contact with ILE 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* 3.8 13.5 - - + +
3A ILE* 1.3 76.8 - - - +
5A ARG* 1.3 77.0 + - + +
37A THR* 2.9 40.1 + - + +
38A TYR 4.1 1.8 - - - +
39A ASP* 3.8 28.5 - - + -
75A LEU* 3.7 12.8 - - - +
76A GLY 5.0 0.2 - - - +
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Residues in contact with ARG 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 0.2 - - - -
4A ILE* 1.3 94.6 + - + +
6A ILE* 1.3 71.5 + - - +
7A GLU* 3.7 34.7 + - + +
35A ARG 4.4 0.4 - - - -
36A ILE* 3.3 1.7 - - - +
37A THR* 2.8 61.4 + - - +
71A LYS* 6.1 0.4 - - - +
75A LEU* 3.7 5.9 - - - +
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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* 3.9 17.3 - - + -
5A ARG* 1.3 82.6 - - - +
7A GLU* 1.3 65.8 + - - +
8A THR* 5.1 0.2 - - + -
34A VAL* 4.5 14.6 - - + -
35A ARG 3.5 3.6 - - - +
36A ILE* 4.1 13.5 - - + -
66A ILE* 4.2 25.1 - - + -
67A HIS* 4.7 2.8 - - - +
71A LYS* 3.2 58.0 + - + +
74A LEU* 3.9 34.8 - - + -
75A LEU* 4.1 6.7 - - + +
103A VAL* 5.8 2.7 - - + -
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Residues in contact with GLU 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 ARG* 3.7 34.4 + - + +
6A ILE* 1.3 78.4 - - - +
8A THR* 1.3 71.4 + - - +
34A VAL* 3.4 2.9 - - - +
35A ARG* 2.9 69.8 + - - +
37A THR* 4.4 6.8 + - - -
67A HIS* 5.0 3.1 - - - -
71A LYS* 5.8 0.4 - - - +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 5.1 0.2 - - + -
7A GLU* 1.3 81.8 - - - +
9A SER* 1.3 63.4 + - - +
32A VAL* 4.2 7.9 - - + -
33A ILE 3.1 8.5 - - - -
34A VAL* 4.3 6.3 - - + -
35A ARG* 4.5 5.4 + - - +
63A GLU* 3.5 18.2 + - + +
66A ILE* 3.8 37.7 - - + -
67A HIS* 2.6 37.1 + - + +
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Residues in contact with SER 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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8A THR* 1.3 76.0 - - - +
10A ARG* 1.3 69.0 + - - +
11A ILE* 4.9 2.9 - - - +
32A VAL* 3.4 7.1 - - - +
33A ILE* 2.7 45.7 + - - +
35A ARG* 4.3 17.1 + - - -
63A GLU* 4.2 4.5 - - - -
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Residues in contact with ARG 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 SER* 1.3 77.5 - - - +
11A ILE* 1.3 70.7 + - - +
30A GLU* 5.5 2.2 + - - -
31A SER 3.4 3.8 - - - -
32A VAL* 4.8 2.2 - - + -
59A MET* 3.4 44.9 + - + +
60A ASP* 2.7 40.2 + - - +
63A GLU* 2.7 40.8 + - - +
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Residues in contact with ILE 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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9A SER* 4.9 3.8 - - - +
10A ARG* 1.3 80.1 - - - +
12A ALA* 1.3 63.5 + - - +
13A VAL* 4.3 6.7 - - + -
29A ALA 5.0 1.3 - - - +
30A GLU* 3.4 5.2 - - - +
31A SER* 3.1 38.8 + - - +
33A ILE* 3.7 34.5 - - + -
59A MET* 4.6 1.9 - - - +
300A THR* 3.7 28.7 - - + -
332A VAL* 4.2 17.9 - - + -
333A PHE* 4.2 3.8 - - + -
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Residues in contact with ALA 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 ILE* 1.3 75.9 - - - +
13A VAL* 1.3 63.3 + - - +
14A PRO* 3.7 8.0 - - - +
28A THR* 3.9 24.0 - - + +
29A ALA 3.5 5.6 - - - -
30A GLU* 4.7 7.4 - - + -
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Residues in contact with VAL 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 ILE* 4.3 9.4 - - + -
12A ALA* 1.3 75.7 - - - +
14A PRO* 1.3 72.4 - - + +
15A LEU 3.3 0.3 + - - -
28A THR* 4.0 0.9 - - - -
29A ALA* 2.7 41.1 + - + +
300A THR* 4.2 15.3 - - + -
328A LEU* 3.6 26.8 - - + +
330A THR* 3.3 29.8 - - - +
332A VAL* 3.9 34.8 - - + -
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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 ALA 3.7 8.0 - - - +
13A VAL* 1.3 88.0 - - + +
15A LEU* 1.3 61.7 + - - +
27A TYR 3.5 9.6 - - - +
28A THR* 4.0 11.8 - - + -
328A LEU* 3.9 2.1 - - - -
329A LYS* 3.1 58.0 + - + +
330A THR* 5.3 5.2 - - - +
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Residues in contact with LEU 15 (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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14A PRO* 1.3 76.4 - - - +
16A THR* 1.3 61.2 + - - +
17A LYS 3.1 17.9 + - - +
18A PRO* 4.4 5.5 - - - +
19A PHE* 3.5 36.1 - - + -
26A VAL* 4.0 7.0 - - + +
27A TYR 2.8 30.4 + - - +
28A THR 4.1 8.5 - - - +
29A ALA* 4.0 17.0 - - + +
298A ILE* 4.1 13.0 - - + -
327A MET* 3.7 13.5 - - + +
328A LEU* 3.9 21.8 - - + +
329A LYS* 3.3 15.9 - - - -
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Residues in contact with THR 16 (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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15A LEU* 1.3 73.2 - - - +
17A LYS* 1.3 76.4 + - - +
18A PRO* 4.1 4.0 - - - +
326A LEU 4.7 4.0 + - - +
327A MET* 3.1 32.7 + - - +
328A LEU 3.6 22.4 - - - +
329A LYS* 3.7 19.1 - - + +
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Residues in contact with LYS 17 (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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15A LEU* 3.1 10.0 - - - +
16A THR* 1.3 95.9 + - - +
18A PRO* 1.3 70.9 - - - +
19A PHE* 3.5 9.9 + - - +
134A TYR* 5.7 2.0 + - - -
135A THR 5.3 0.8 + - - -
137A SER* 3.1 33.9 + - - +
147A ASP* 4.9 5.7 + - - -
151A TYR* 3.3 24.2 + - - -
327A MET* 4.7 13.0 + - - -
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Residues in contact with PRO 18 (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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15A LEU* 4.4 12.5 - - + +
16A THR 4.1 4.3 - - - +
17A LYS* 1.3 90.6 - - - +
19A PHE* 1.3 58.3 + - - +
25A THR* 6.2 1.1 - - - -
26A VAL 3.0 19.5 - - - +
27A TYR* 4.0 33.4 - - + -
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Residues in contact with PHE 19 (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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15A LEU* 3.5 28.9 - - + -
17A LYS 4.2 6.7 - - - +
18A PRO* 1.3 75.3 - - - +
20A LYS* 1.3 70.8 + - - +
21A THR* 4.1 9.4 - - + -
25A THR* 3.6 1.8 - - - -
26A VAL* 2.6 67.3 + - + +
298A ILE* 3.7 31.4 - - + -
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Residues in contact with LYS 20 (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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19A PHE* 1.3 86.7 - - - +
21A THR* 1.3 67.6 + - - +
24A ARG 3.5 6.3 - - - +
25A THR* 4.4 17.5 - - - -
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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