Contacts of the strand formed by residues 25 - 38 (chain C) 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 THR 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C PRO* 4.7 5.4 - - + -
19C PHE 3.6 14.8 - - - +
20C LYS* 4.2 9.5 - - + +
24C ARG* 1.3 86.2 + - - +
26C VAL* 1.3 64.3 + - - +
27C TYR* 3.1 54.8 + - + +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.8 4.7 - - + +
18C PRO* 2.9 27.9 - - - +
19C PHE* 2.8 54.5 + - + +
21C THR* 3.8 17.3 - - + -
24C ARG* 3.5 32.1 - - + +
25C THR* 1.3 70.1 - - - +
27C TYR* 1.3 59.7 + - - +
28C THR 3.0 26.5 - - - +
29C ALA* 5.3 0.2 - - - -
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Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO* 3.6 4.0 - - - +
15C LEU* 3.0 27.2 + - - +
18C PRO* 4.0 22.0 - - + +
24C ARG* 4.8 1.0 - - - +
25C THR* 3.1 54.5 + - + +
26C VAL* 1.3 74.2 - - - +
28C THR* 1.3 69.9 + - + +
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.8 24.4 - - + +
13C VAL 3.4 11.4 - - - -
14C PRO* 3.9 16.4 - - + -
15C LEU* 4.0 5.2 - - - +
26C VAL* 3.0 22.4 - - - +
27C TYR* 1.3 92.6 - - + +
29C ALA* 1.3 60.9 + - - +
30C GLU* 3.8 13.5 + - - +
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.8 2.1 - - - +
12C ALA* 3.4 1.4 - - - -
13C VAL* 2.7 39.0 + - + +
15C LEU* 3.6 23.1 - - + +
26C VAL* 5.3 0.4 - - - -
28C THR* 1.3 71.0 - - - +
30C GLU* 1.3 63.6 + - - +
31C SER* 5.1 1.0 + - - +
298C ILE* 3.8 22.9 - - + +
299C GLU* 6.2 1.3 - - - -
300C THR* 5.8 3.1 - - + +
328C LEU* 3.9 11.2 - - + -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 5.1 4.2 + - - -
11C ILE 3.1 12.1 - - - +
12C ALA* 4.1 14.3 - - + +
24C ARG* 5.5 8.7 + - - +
28C THR* 3.8 12.9 + - - +
29C ALA* 1.3 74.9 - - - +
31C SER* 1.3 69.5 + - - +
49C PRO* 3.8 3.6 - - - +
50C PRO* 3.3 22.2 - - + +
59C MET* 3.3 30.4 - - + +
298C ILE 4.6 2.9 - - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 3.5 4.3 - - - -
11C ILE* 3.1 46.4 + - - +
29C ALA* 5.1 1.1 + - - +
30C GLU* 1.3 80.3 + - - +
32C VAL* 1.3 64.8 + - - +
33C ILE* 4.4 1.3 - - - -
47C GLU* 2.8 35.8 + - - -
48C ALA 3.8 7.0 - - - -
49C PRO* 3.5 13.2 - - - +
59C MET* 3.8 7.0 - - - +
298C ILE 4.2 3.6 + - - -
299C GLU* 4.6 0.3 - - - -
300C THR* 4.9 1.8 - - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 3.8 31.0 - - + -
9C SER 3.5 5.2 - - - +
10C ARG* 5.1 8.1 - - + -
31C SER* 1.3 73.4 - - - +
33C ILE* 1.3 64.4 + - - +
34C VAL* 3.9 1.8 + - + +
47C GLU* 3.4 4.0 - - - -
48C ALA* 2.9 39.0 + - + +
59C MET* 3.3 38.6 - - + +
62C ILE* 3.9 25.8 - - + -
63C GLU* 4.8 9.9 - - + +
66C ILE* 4.5 5.6 - - + -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLU 3.7 0.3 - - - +
8C THR* 3.0 7.8 - - - -
9C SER* 2.8 50.3 + - - +
11C ILE* 3.7 34.8 - - + -
31C SER* 4.4 1.1 - - - -
32C VAL* 1.3 78.4 - - - +
34C VAL* 1.3 64.7 + - - +
35C ARG* 4.8 3.8 + - + +
45C TRP* 4.0 30.7 - - + -
46C GLY 3.5 7.0 - - - +
47C GLU* 4.1 22.2 - - + -
302C LEU* 4.0 3.6 - - + -
333C PHE* 3.5 28.5 - - + -
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.6 8.5 - - + -
7C GLU 3.3 6.1 - - - +
8C THR* 3.7 11.0 - - + -
32C VAL* 4.5 3.8 - - + +
33C ILE* 1.3 76.7 - - - +
35C ARG* 1.3 69.3 + - - +
36C ILE* 4.0 24.5 - - + -
45C TRP* 3.4 6.1 - - - +
46C GLY 2.8 35.8 + - - +
66C ILE* 3.4 33.2 - - + -
102C ALA* 4.0 24.2 - - + +
103C VAL* 4.8 6.3 - - + +
106C ALA* 4.3 6.5 - - + -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 5.3 4.2 - - - +
5C ARG 3.8 0.9 - - - +
6C ILE* 3.4 2.9 - - - -
7C GLU* 2.9 77.7 + - + +
8C THR 5.6 1.6 + - - -
9C SER* 4.8 19.2 + - - -
33C ILE* 4.8 3.8 + - + +
34C VAL* 1.3 75.0 - - - +
36C ILE* 1.3 62.4 + - - +
37C THR* 4.1 1.7 + - - +
43C VAL* 4.7 8.7 - - + -
44C GLY 3.3 4.5 - - - +
45C TRP* 3.3 55.6 - - + -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 3.8 26.9 - - + -
5C ARG 3.3 3.8 - - - +
6C ILE* 4.3 16.6 - - + -
34C VAL* 4.0 8.5 - - + -
35C ARG* 1.3 76.0 - - - +
37C THR* 1.3 62.0 + - - +
38C TYR* 3.4 30.7 - - + +
43C VAL* 3.4 1.1 - - - -
44C GLY 2.7 36.7 + - - -
74C LEU* 5.2 0.2 - - + -
103C VAL* 3.8 26.2 - - + +
106C ALA* 3.5 27.8 - - + -
107C LEU* 4.0 17.3 - - + +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLY* 3.4 35.8 + - - +
350A PRO* 4.3 2.2 - - + -
3C ILE* 3.8 3.3 - - - +
4C ILE* 2.9 32.6 + - + +
5C ARG* 2.9 36.1 + - - +
7C GLU* 4.5 4.7 + - - -
35C ARG* 4.9 1.7 - - - +
36C ILE* 1.3 74.5 + - - +
38C TYR* 1.3 70.9 + - - +
42C ALA 3.7 9.2 - - - +
43C VAL* 4.0 21.1 - - + +
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLN 3.7 6.8 - - - +
1C MET* 3.9 15.5 - - + -
2C LYS 3.2 9.4 - - - +
3C ILE* 3.7 22.2 - - + -
4C ILE* 4.2 3.6 - - - -
36C ILE* 3.4 26.9 - - + +
37C THR* 1.3 76.6 - - - +
39C ASP* 1.3 58.2 + - - +
40C SER* 3.0 22.5 + - - +
41C GLY* 3.0 13.0 + - - -
42C ALA* 2.9 29.1 + - + +
44C GLY 3.9 5.4 - - - -
79C LEU* 3.4 34.5 - - + -
106C ALA 3.0 19.4 + - - -
107C LEU* 3.3 21.7 + - - +
110C GLY* 3.8 20.4 - - - -
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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