Contacts of the strand formed by residues 5 - 21 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.4 5.6 - - - +
4B SER* 1.3 80.9 - - - +
6B VAL* 1.3 66.5 + - - +
37B VAL* 2.6 35.4 + - - +
76B LEU* 3.9 10.8 - - - -
365B TRP* 3.4 13.2 - - - -
366B ILE 3.1 12.8 - - - -
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Residues in contact with VAL 6 (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 LEU* 4.1 16.4 - - + -
5B GLY* 1.3 81.0 - - - +
7B GLU* 1.3 66.5 + - - +
8B LEU* 4.6 1.3 - - + +
34B LEU* 3.4 32.1 - - + -
35B ARG 3.2 11.4 - - - +
36B ALA* 4.0 14.4 - - + -
72B ILE* 3.9 27.1 - - + +
103B LEU* 4.1 16.4 - - + -
365B TRP* 3.6 5.3 - - - -
366B ILE* 2.7 47.6 + - - +
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Residues in contact with GLU 7 (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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6B VAL* 1.3 75.5 - - - +
8B LEU* 1.3 61.8 + - - +
9B ARG* 2.7 32.7 + - + +
33B LEU 3.4 1.0 - - - +
34B LEU* 3.2 8.3 - - - -
35B ARG* 2.7 80.9 + - + +
44B TRP* 4.5 0.9 - - - -
363B LYS* 3.5 27.4 - - + +
364B VAL 3.1 12.6 - - - +
365B TRP* 3.9 11.7 - - + +
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Residues in contact with LEU 8 (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 GLU* 1.3 74.0 - - - +
9B ARG* 1.3 61.2 - - - +
10B ARG* 5.7 0.4 - - - +
32B LEU* 4.4 11.9 - - + -
33B LEU 3.9 0.7 - - - +
34B LEU* 2.9 39.3 - - + -
64B GLU* 4.2 27.2 - - + +
67B LEU* 4.4 10.8 - - + -
68B ARG* 3.9 19.3 - - + +
72B ILE* 3.9 23.3 - - + -
362B ALA 3.6 0.5 - - - +
363B LYS* 3.1 5.2 - - - -
364B VAL* 2.7 42.8 + - + +
366B ILE* 3.8 20.9 - - + -
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Residues in contact with ARG 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 GLU* 2.7 37.2 + - - +
8B LEU* 1.3 75.5 - - - +
10B ARG* 1.3 63.1 - - - +
11B VAL* 4.0 4.3 - - + -
31B LEU 3.8 0.2 - - - +
32B LEU* 2.9 21.7 - - - +
33B LEU* 3.0 32.6 + - + +
44B TRP* 4.4 10.1 - - + -
356B LEU* 4.0 29.9 - - - +
357B ASP* 2.7 29.7 + - - -
360B THR* 2.7 30.0 + - + +
362B ALA 3.0 10.5 - - - +
363B LYS* 4.0 29.5 - - + +
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Residues in contact with ARG 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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8B LEU 5.7 0.4 - - - +
9B ARG* 1.3 76.5 - - - +
11B VAL* 1.3 57.1 + - - +
30B GLU* 5.9 3.1 - - - +
31B LEU 3.6 6.1 - - - +
32B LEU* 4.2 7.2 - - + -
60B ASN* 6.4 1.8 - - + -
61B ASP* 4.9 11.3 + - - -
64B GLU* 2.4 47.0 + - - +
68B ARG* 3.9 15.0 - - - +
360B THR* 3.2 4.7 - - - +
361B THR* 2.3 51.2 + - - +
362B ALA* 2.7 36.1 + - + +
364B VAL* 5.2 3.2 - - - +
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Residues in contact with VAL 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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9B ARG* 4.4 6.1 - - + -
10B ARG* 1.3 80.6 - - - +
12B GLN* 1.3 65.0 - - - +
13B MET* 3.9 20.6 - - + -
29B ARG 3.9 0.2 - - - +
30B GLU* 3.6 4.3 - - - +
31B LEU* 2.9 47.2 + - + +
33B LEU* 4.2 20.4 - - + -
295B THR* 5.6 0.2 - - + -
328B ILE* 5.3 1.1 - - + -
356B LEU* 3.8 25.6 - - + -
359B VAL* 3.2 29.2 - - + +
360B THR* 4.2 6.7 - - - +
361B THR* 4.8 1.1 - - - -
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Residues in contact with GLN 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 VAL* 1.3 72.3 - - - +
13B MET* 1.3 61.0 + - - +
14B PRO* 3.8 7.9 - - - +
28B VAL* 2.9 34.5 - - + +
29B ARG 3.5 1.3 - - - -
30B GLU* 3.8 31.5 - - + +
359B VAL* 2.9 28.3 + - - +
361B THR* 3.9 23.5 - - + +
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Residues in contact with MET 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 VAL* 3.9 20.1 - - + -
12B GLN* 1.3 77.4 - - - +
14B PRO* 1.3 67.3 - - + +
28B VAL* 4.1 2.9 - - - -
29B ARG* 2.5 46.1 + - - +
31B LEU* 3.9 5.8 - - + +
295B THR* 3.8 23.8 - - + -
324B TYR* 3.5 44.0 - - + +
326B THR 3.6 24.0 - - - +
327B ASP* 4.0 16.4 - - - +
328B ILE* 4.2 15.5 - - + -
359B VAL* 4.0 11.7 - - + -
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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 GLN* 3.8 9.2 - - - +
13B MET* 1.3 92.3 - - + +
15B LEU* 1.3 66.6 + - - +
16B VAL* 3.7 1.2 + - - +
27B SER 4.4 0.7 - - - +
28B VAL* 3.8 21.8 - - + -
323B PHE 3.7 1.0 - - - +
324B TYR* 3.5 16.8 - - - -
325B LYS* 5.1 1.4 + - - +
359B VAL* 5.5 3.8 - - + -
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Residues in contact with LEU 15 (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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14B PRO* 1.3 75.8 - - - +
16B VAL* 1.3 66.5 + - - +
17B ALA* 2.9 23.6 + - - +
18B PRO* 4.6 1.7 - - - +
19B PHE* 4.0 15.7 - - + -
26B GLN* 3.5 38.1 - - + +
27B SER* 2.9 24.0 + - - +
28B VAL* 4.1 2.7 - - - +
29B ARG* 4.2 9.4 - - + +
293B ILE* 4.0 19.3 - - + -
323B PHE* 3.2 16.6 - - + +
324B TYR* 3.8 24.7 - - + -
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Residues in contact with VAL 16 (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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14B PRO 3.7 1.1 + - - +
15B LEU* 1.3 72.2 - - - +
17B ALA* 1.3 69.5 + - + +
18B PRO* 4.6 1.0 - - - +
321B ASP 4.1 8.3 - - - +
322B ARG 3.3 27.4 - - - +
323B PHE* 2.9 11.0 + - - +
324B TYR 3.5 3.4 - - - -
325B LYS* 3.2 42.2 - - + +
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Residues in contact with ALA 17 (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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15B LEU* 2.9 16.9 - - - +
16B VAL* 1.3 89.5 - - + +
18B PRO* 1.3 81.5 - - + +
19B PHE* 3.7 1.4 + - - -
322B ARG* 4.5 15.0 + - - +
323B PHE* 5.3 0.7 - - - -
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Residues in contact with PRO 18 (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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15B LEU* 4.5 3.3 - - + +
16B VAL 4.6 1.1 - - - +
17B ALA* 1.3 93.5 - - + +
19B PHE* 1.3 59.9 + - - +
20B ARG* 4.2 0.9 + - - -
25B THR* 4.5 13.2 - - + -
26B GLN 3.0 17.7 - - - +
27B SER* 4.2 16.6 - - - -
322B ARG* 5.7 0.5 + - - -
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Residues in contact with PHE 19 (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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15B LEU* 4.0 17.5 - - + -
17B ALA 3.7 2.6 + - - +
18B PRO* 1.3 73.6 - - - +
20B ARG* 1.3 62.2 + - - +
21B THR* 3.4 30.6 + - + +
24B GLY 3.6 2.1 - - - +
25B THR* 3.5 1.9 - - - -
26B GLN* 2.6 45.7 + - + +
135B SER* 3.6 17.3 - - - -
137B GLY* 3.6 18.4 - - - -
163B LYS* 4.2 5.8 - - + -
293B ILE* 4.2 15.3 - - + -
322B ARG* 3.6 32.5 - - - -
323B PHE* 4.5 7.2 - + + -
1100B OSB 3.5 38.8 - + + -
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Residues in contact with ARG 20 (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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18B PRO 4.2 1.4 + - - -
19B PHE* 1.3 78.1 - - - +
21B THR* 1.3 73.0 + - - +
24B GLY 3.5 2.7 - - - +
25B THR* 3.7 26.9 + - + +
137B GLY* 3.0 12.0 - - - -
138B ILE* 2.7 62.4 + - + +
139B MET 3.6 21.6 + - - -
140B ASP* 4.3 13.9 + - - +
163B LYS* 3.4 4.2 - - - +
165B GLU* 3.3 23.8 + - - -
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Residues in contact with THR 21 (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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19B PHE* 3.4 33.8 + - + -
20B ARG* 1.3 76.8 + - - +
22B SER* 1.3 66.5 + - - +
23B PHE* 3.2 39.5 + - + -
24B GLY 3.1 15.6 + - - +
138B ILE* 3.1 15.3 - - - +
163B LYS* 3.5 27.6 - - + +
165B GLU* 4.1 1.6 - - - +
191B ASN* 3.9 12.1 - - - +
1100B OSB 4.9 2.0 - - + -
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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