Contacts of the strand formed by residues 5 - 21 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.6 4.1 - - - +
4D SER* 1.3 81.1 - - - +
6D VAL* 1.3 68.9 + - - +
36D ALA* 3.7 0.2 - - - -
37D VAL* 2.9 25.4 + - - -
76D LEU* 3.7 11.7 - - - +
365D TRP* 3.5 14.2 - - - -
366D ILE 3.0 13.7 - - - -
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Residues in contact with VAL 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.5 13.0 - - + -
5D GLY* 1.3 79.5 - - - +
7D GLU* 1.3 68.2 + - - +
8D LEU 3.4 2.5 + - - +
34D LEU* 3.9 18.4 - - + -
35D ARG 3.2 28.9 - - - +
36D ALA* 4.1 7.0 - - + +
72D ILE* 3.5 46.2 - - + -
103D LEU* 4.6 9.9 - - + -
365D TRP* 3.6 4.2 - - - -
366D ILE* 2.6 37.9 + - - +
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Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 1.3 77.3 - - - +
8D LEU* 1.3 61.3 + - - +
9D ARG* 2.0 41.5 + - - +
33D LEU 4.1 0.2 - - - +
34D LEU* 3.9 2.6 - - - -
35D ARG* 2.8 72.5 + - + +
363D LYS* 3.0 29.7 - - + +
364D VAL 3.1 10.8 - - - +
365D TRP* 3.5 22.5 - - + -
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL 3.4 1.7 + - - +
7D GLU* 1.3 71.3 - - - +
9D ARG* 1.3 61.4 + - - +
10D ARG* 5.8 1.1 - - + -
32D LEU* 4.5 8.3 - - + -
33D LEU 3.8 3.6 - - - -
34D LEU* 3.7 20.9 - - + -
64D GLU* 4.2 42.0 - - + +
67D LEU* 4.7 8.3 - - + -
68D ARG* 4.7 1.8 - - + -
72D ILE* 3.7 10.8 - - + -
363D LYS* 3.1 7.6 - - - +
364D VAL* 2.5 52.2 + - + +
366D ILE* 3.0 45.3 - - + -
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Residues in contact with ARG 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLU* 2.0 55.3 + - + +
8D LEU* 1.3 78.5 - - - +
10D ARG* 1.3 68.8 + - - +
11D VAL* 3.8 10.0 + - + -
32D LEU* 3.4 8.1 - - - +
33D LEU* 3.0 39.8 + - + +
35D ARG* 3.9 9.1 - - - +
44D TRP* 4.8 12.5 - - - -
353D PRO* 6.4 0.2 - - - +
356D LEU* 4.4 20.2 - - - +
357D ASP* 3.5 21.6 + - - -
360D THR* 3.5 24.2 + - + +
362D ALA 3.5 11.2 - - - +
363D LYS* 4.2 18.4 - - + +
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 5.8 0.9 - - + -
9D ARG* 1.3 76.2 - - - +
11D VAL* 1.3 66.2 + - - +
30D GLU* 5.4 8.3 - - + -
31D LEU 3.7 7.6 - - - +
32D LEU* 5.3 6.7 - - + -
61D ASP* 5.2 8.6 + - - -
64D GLU* 2.9 38.2 + - - +
360D THR* 3.1 5.4 - - - -
361D THR* 2.6 44.1 + - + +
362D ALA* 3.1 38.7 + - + +
364D VAL* 4.2 16.2 - - - +
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ARG* 4.4 8.3 - - + -
10D ARG* 1.3 82.4 - - - +
12D GLN* 1.3 64.8 + - - +
13D MET* 3.5 30.5 - - + -
30D GLU* 3.3 11.8 - - - +
31D LEU* 3.1 44.7 + - + +
33D LEU* 4.4 24.9 - - + -
328D ILE* 5.3 1.8 - - + -
356D LEU* 4.7 5.2 - - + -
359D VAL* 3.7 19.3 - - + -
360D THR* 4.1 17.7 - - - +
361D THR* 4.9 1.1 - - - -
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 1.3 79.8 - - - +
13D MET* 1.3 63.1 + - - +
14D PRO* 3.6 7.1 - - - +
28D VAL* 4.3 21.6 - - + +
29D ARG 3.4 4.3 - - - -
30D GLU* 4.4 22.7 - - + +
359D VAL* 3.2 22.3 + - - +
361D THR* 3.9 19.9 + - - +
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Residues in contact with MET 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.5 18.4 - - + -
12D GLN* 1.3 76.1 - - - +
14D PRO* 1.3 73.4 - - + +
28D VAL* 3.4 3.1 - - - -
29D ARG* 2.7 38.9 + - - +
31D LEU* 3.8 22.0 - - + -
295D THR* 4.1 9.6 - - - -
324D TYR* 3.5 35.8 - - + -
326D THR 3.3 26.5 - - - +
327D ASP* 4.2 7.0 - - - +
328D ILE* 3.9 22.0 - - + -
359D VAL* 3.9 11.0 - - + -
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Residues in contact with PRO 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN 3.6 7.4 - - - +
13D MET* 1.3 91.2 - - + +
15D LEU* 1.3 65.7 + - - +
16D VAL 3.8 0.7 + - - -
27D SER 4.8 0.2 - - - +
28D VAL* 3.6 20.8 - - + -
323D PHE 3.8 0.7 - - - +
324D TYR* 3.4 17.5 - - - +
325D LYS* 5.0 2.6 + - - +
359D VAL* 5.2 5.2 - - + -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D MET 3.9 0.4 - - - +
14D PRO* 1.3 76.0 - - - +
16D VAL* 1.3 68.5 + - - +
17D ALA* 3.2 18.7 + - - +
18D PRO* 4.8 2.3 - - - +
19D PHE* 4.4 8.7 - - + +
26D GLN* 3.8 44.4 - - + +
27D SER 2.9 27.3 + - - +
28D VAL* 4.0 2.7 - - - +
29D ARG* 3.8 9.9 - - + -
293D ILE* 4.2 14.8 - - + -
323D PHE* 3.5 10.3 - - + +
324D TYR* 2.7 46.2 - - + +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO 3.8 0.8 + - - -
15D LEU* 1.3 74.4 - - - +
17D ALA* 1.3 68.8 + - + +
18D PRO* 4.5 2.1 - - - +
321D ASP 4.6 8.3 - - - +
322D ARG* 4.2 13.5 - - - +
323D PHE* 2.8 37.6 + - - +
324D TYR 4.0 1.8 - - - -
325D LYS* 3.8 23.6 - - + +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.7 14.8 - - - +
16D VAL* 1.3 86.6 - - + +
18D PRO* 1.3 80.3 - - + +
19D PHE* 3.3 7.1 + - - +
322D ARG* 5.1 9.6 + - - +
323D PHE* 5.5 1.4 - - - -
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Residues in contact with PRO 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU 4.8 2.9 - - - +
16D VAL 4.5 2.7 - - - +
17D ALA* 1.3 90.3 - - + +
19D PHE* 1.3 59.1 + - - +
20D ARG 4.0 1.8 + - - -
25D THR* 4.0 17.1 - - + +
26D GLN 2.8 19.1 - - - +
27D SER* 4.2 17.3 - - - +
139D MET* 6.2 0.2 - - - +
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.4 8.9 - - + +
17D ALA 3.3 7.1 + - - +
18D PRO* 1.3 72.9 - - - +
20D ARG* 1.3 60.1 + - - +
21D THR* 3.4 25.4 - - - -
23D PHE* 5.6 1.6 - + - -
24D GLY 3.7 2.8 - - - +
25D THR* 3.5 1.7 - - - -
26D GLN* 2.7 38.4 + - + +
135D SER* 3.7 30.3 - - - -
137D GLY* 4.2 18.4 - - - -
163D LYS* 4.1 8.1 - - + -
293D ILE* 3.9 16.2 - - + -
322D ARG* 4.3 11.2 - - - +
323D PHE* 4.5 15.3 - + + -
1300D OSB 3.3 44.4 - + + -
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PRO 4.0 2.6 + - - -
19D PHE* 1.3 76.3 - - - +
21D THR* 1.3 74.5 + - - +
24D GLY* 3.9 2.9 - - - -
25D THR* 3.5 31.9 - - + +
137D GLY* 3.3 11.9 - - - -
138D ILE* 3.0 72.7 + - + +
139D MET 4.1 4.2 + - - -
140D ASP* 3.0 30.9 + - - +
163D LYS* 3.9 3.1 - - - +
165D GLU* 3.8 20.2 + - - -
168D TRP* 5.8 0.8 - - - +
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Residues in contact with THR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.4 29.8 - - - -
20D ARG* 1.3 82.2 + - - +
22D SER* 1.3 77.6 + - - +
23D PHE* 3.0 53.9 + - + +
24D GLY* 3.2 21.3 + - - -
138D ILE* 3.6 10.1 - - - +
163D LYS* 3.8 12.4 - - - -
165D GLU* 4.1 2.4 - - - +
191D ASN* 3.8 11.0 - - - +
1300D OSB 5.1 0.3 - - - -
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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
------------------------------------------------------------
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