Contacts of the strand formed by residues 5 - 21 (chain A) in PDB entry 1SJB
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 GLY 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.7 4.7 - - - +
4A SER* 1.3 80.9 - - - +
6A VAL* 1.3 67.5 + - - +
37A VAL 2.9 25.8 + - - -
76A LEU* 3.8 7.4 - - - +
365A TRP* 3.4 18.1 - - - -
366A ILE 3.0 13.9 - - - -
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Residues in contact with VAL 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 LEU* 4.0 16.6 - - + -
5A GLY* 1.3 80.6 - - - +
7A GLU* 1.3 65.0 + - - +
34A LEU* 4.1 26.2 - - + -
35A ARG 3.4 13.5 - - - +
36A ALA* 4.5 8.3 - - + +
72A ILE* 3.7 44.9 - - + -
103A LEU* 4.4 11.4 - - + -
364A VAL 3.5 1.9 - - - +
365A TRP* 3.6 6.0 - - - -
366A ILE* 2.8 36.0 + - - +
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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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6A VAL* 1.3 76.8 - - - +
8A LEU* 1.3 64.0 + - - +
9A ARG* 2.7 33.9 + - - +
33A LEU 3.7 0.7 - - - +
34A LEU* 3.5 6.1 - - - -
35A ARG* 2.3 85.7 + - + +
44A TRP* 4.2 1.7 - - - -
363A LYS* 3.1 35.4 + - + +
364A VAL 3.2 10.8 - - - +
365A TRP* 4.3 9.2 - - + -
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Residues in contact with LEU 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 VAL 4.0 0.8 + - - -
7A GLU* 1.3 72.4 - - - +
9A ARG* 1.3 62.2 + - - +
10A ARG* 5.3 3.3 + - + +
32A LEU* 2.8 42.6 - - + -
33A LEU 3.8 1.1 - - - -
34A LEU* 3.3 24.9 - - + -
64A GLU* 4.2 26.9 - - + +
67A LEU* 4.3 12.1 - - + -
68A ARG* 4.8 3.6 - - - +
72A ILE* 4.1 11.4 - - + -
362A ALA 3.7 0.9 - - - +
363A LYS* 3.1 5.0 + - - -
364A VAL* 2.7 49.3 + - + +
366A ILE* 4.0 17.0 - - + -
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Residues in contact with ARG 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 GLU* 2.7 45.8 + - - +
8A LEU* 1.3 74.9 - - - +
10A ARG* 1.3 66.5 + - - +
11A VAL* 4.6 2.5 - - + -
32A LEU* 3.3 11.0 - - - +
33A LEU* 3.2 38.6 + - + +
35A ARG* 4.7 1.8 - - - +
44A TRP* 4.3 11.1 - - + -
356A LEU* 3.2 39.2 - - - +
357A ASP* 2.5 31.9 + - - -
360A THR* 3.0 23.0 + - + +
362A ALA 3.0 4.0 - - - -
363A LYS* 3.7 34.2 - - + +
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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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8A LEU* 5.3 3.3 + - + +
9A ARG* 1.3 77.2 - - - +
11A VAL* 1.3 58.0 + - - +
31A LEU 3.7 6.5 - - - +
32A LEU* 4.5 8.1 - - + -
61A ASP* 5.1 7.6 + - - -
64A GLU* 2.9 42.9 + - - +
68A ARG* 3.9 10.5 - - - +
360A THR* 3.2 5.2 - - - +
361A THR* 2.4 49.6 + - - +
362A ALA* 2.6 38.5 + - - +
363A LYS 4.9 3.2 + - - +
364A VAL* 5.4 6.1 - - - +
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Residues in contact with VAL 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 ARG* 4.6 5.8 - - + -
10A ARG* 1.3 80.3 - - - +
12A GLN* 1.3 64.1 + - - +
13A MET* 3.6 15.3 - - + -
30A GLU* 3.3 6.9 - - - +
31A LEU* 2.8 52.2 + - + +
33A LEU* 4.0 20.0 - - + -
328A ILE* 5.3 0.4 - - + -
356A LEU* 3.7 28.7 - - + -
359A VAL* 3.3 30.7 - - + -
360A THR* 4.1 4.0 - - - +
361A THR* 4.6 1.8 - - - -
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Residues in contact with GLN 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 VAL* 1.3 71.3 - - - +
13A MET* 1.3 60.0 - - - +
14A PRO* 4.0 6.5 - - - +
28A VAL* 3.8 25.1 - - + +
29A ARG 3.6 2.0 - - - -
30A GLU* 3.4 36.9 - - + +
359A VAL* 2.8 31.0 + - - +
361A THR* 4.0 21.2 - - + +
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Residues in contact with MET 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 VAL* 3.6 18.4 - - + -
12A GLN* 1.3 78.8 - - - +
14A PRO* 1.3 67.2 - - + +
15A LEU* 4.1 0.3 - - - +
28A VAL* 3.8 2.4 - - - +
29A ARG* 2.7 42.9 + - + +
31A LEU* 3.8 15.3 - - + -
295A THR* 4.0 7.4 - - + -
324A TYR* 3.7 42.6 - - + +
326A THR 3.5 24.5 - - - +
327A ASP* 4.2 5.2 - - - +
328A ILE* 3.6 29.8 - - + +
359A VAL* 3.8 11.4 - - + -
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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 GLN* 4.0 7.0 - - - +
13A MET* 1.3 90.1 - - + +
15A LEU* 1.3 67.0 + - - +
16A VAL 3.7 0.5 + - - -
27A SER 4.7 0.2 - - - +
28A VAL* 3.9 19.3 - - + -
323A PHE 3.7 1.6 - - - +
324A TYR* 3.5 17.8 - - - -
325A LYS 5.1 1.7 + - - -
359A VAL* 5.2 5.6 - - + -
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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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13A MET 4.1 0.2 - - - +
14A PRO* 1.3 77.4 - - - +
16A VAL* 1.3 66.9 + - - +
17A ALA* 3.2 11.1 + - - +
18A PRO* 4.7 2.8 - - - +
19A PHE* 3.9 20.2 - - + +
26A GLN* 3.2 41.1 - - + +
27A SER* 2.6 24.7 + - - +
29A ARG* 4.0 19.1 - - + +
293A ILE* 4.3 11.2 - - + -
323A PHE* 3.6 17.7 - - + +
324A TYR* 3.7 25.6 - - + -
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Residues in contact with VAL 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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14A PRO 3.7 0.8 + - - -
15A LEU* 1.3 72.5 - - - +
17A ALA* 1.3 65.5 + - + +
18A PRO* 4.7 1.2 - - - +
321A ASP 3.7 13.5 - - - +
322A ARG 4.2 8.7 - - - +
323A PHE* 2.7 37.9 + - - +
324A TYR 3.6 17.0 - - - -
325A LYS* 3.6 11.0 - - + +
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Residues in contact with ALA 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 13.8 - - - +
16A VAL* 1.3 87.0 - - + +
18A PRO* 1.3 76.9 - - + +
19A PHE* 3.4 4.2 + - - +
152A TYR* 6.0 0.9 - - - +
322A ARG* 4.7 15.5 + - - +
323A PHE* 5.4 0.5 - - - +
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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* 4.6 3.8 - - - +
16A VAL 4.7 1.6 - - - +
17A ALA* 1.3 88.3 - - + +
19A PHE* 1.3 61.9 + - - +
20A ARG* 4.0 1.7 + - - +
25A THR* 3.8 19.6 - - + +
26A GLN 3.0 12.6 - - - +
27A SER* 4.0 19.7 - - - +
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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* 3.9 18.8 - - + -
17A ALA 3.4 2.4 + - - +
18A PRO* 1.3 74.0 - - - +
20A ARG* 1.3 60.7 + - - +
21A THR* 3.9 23.7 + - + +
24A GLY 3.3 2.9 - - - +
25A THR* 3.1 2.9 - - - -
26A GLN* 2.4 48.0 + - + +
135A SER* 3.4 24.5 - - - -
137A GLY* 3.2 34.5 - - - -
163A LYS* 4.2 6.7 - - + -
293A ILE* 4.1 19.7 - - + -
322A ARG* 3.4 27.1 - - - -
323A PHE* 4.3 8.1 - + + -
1000A OSB 3.8 22.0 - + + -
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Residues in contact with ARG 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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18A PRO 4.0 2.6 + - - +
19A PHE* 1.3 77.2 - - - +
21A THR* 1.3 70.1 + - - +
24A GLY* 3.1 5.2 - - - +
25A THR* 3.2 26.2 - - + +
137A GLY* 3.5 7.7 - - - -
138A ILE* 2.8 73.6 + - + +
139A MET 4.2 5.4 + - - -
140A ASP* 3.7 22.4 + - - +
163A LYS* 4.0 1.4 - - - +
165A GLU* 3.4 25.1 + - - -
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Residues in contact with THR 21 (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* 3.9 27.8 - - + +
20A ARG* 1.3 84.5 - - - +
22A SER* 1.3 62.6 + - - +
23A PHE* 3.0 58.5 + - + -
24A GLY* 2.6 18.7 + - - +
138A ILE* 3.4 14.6 - - - +
163A LYS* 4.2 19.1 - - - +
165A GLU* 3.6 3.5 - - - +
191A ASN* 4.2 5.8 - - - -
1000A OSB 4.8 2.5 - - + -
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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