Contacts of the strand formed by residues 31 - 40 (chain B) in PDB entry 2OA8
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 VAL 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.8 26.9 - - + -
20B GLU 3.5 6.5 - - - +
21B ALA* 4.1 0.7 - - - -
29B PRO 4.4 0.4 + - - -
30B GLU* 1.3 72.3 - - - +
32B THR* 1.3 62.7 + - - +
33B GLU 3.6 16.4 - - - +
71B ILE* 3.6 44.8 - - + +
73B PRO* 4.1 7.6 - - - +
100B PHE* 4.3 9.6 - - + -
133B LEU* 3.7 21.5 - - + -
134B LEU* 5.4 0.4 - - - -
137B GLU* 3.0 36.5 + - + +
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Residues in contact with THR 32 (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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20B GLU* 3.0 24.5 + - - +
21B ALA* 3.3 8.2 + - - -
22B THR* 3.8 9.9 - - + -
30B GLU 3.6 11.2 - - - +
31B VAL* 1.3 77.2 - - - +
33B GLU* 1.3 63.6 + - - +
70B CYS* 3.5 3.8 - - - +
71B ILE* 2.8 34.7 + - - +
73B PRO* 3.7 26.5 - - + -
77B CYS* 4.1 10.5 - - - -
85B THR* 5.3 1.0 + - - -
87B LEU* 3.6 19.6 - - - +
92B LEU* 4.2 7.1 - - + +
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Residues in contact with GLU 33 (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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62A ARG* 2.9 38.9 + - - +
64A VAL* 5.1 2.8 - - - +
19B LEU* 3.4 4.0 - - - -
20B GLU* 3.0 33.8 + - + +
31B VAL* 3.6 6.7 - - - +
32B THR* 1.3 83.5 + - - +
34B LEU* 1.3 66.9 + - - +
68B SER* 4.1 11.3 + - - +
69B LEU 3.2 17.0 - - - +
70B CYS* 4.0 14.0 - - - -
71B ILE* 4.4 1.3 - - - -
87B LEU* 3.9 9.9 - - + -
196B THR* 4.2 3.3 - - - -
197B ALA* 2.8 37.9 + - + +
198B GLU 5.0 0.2 + - - -
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Residues in contact with LEU 34 (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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17B LEU* 5.2 0.7 - - + -
18B ASP 3.5 6.5 - - - -
19B LEU* 3.6 21.1 - - + -
33B GLU* 1.3 75.9 - - - +
35B CYS* 1.3 61.9 + - - +
36B LEU* 3.8 26.9 - - + +
67B LEU* 4.4 14.6 - - + +
68B SER* 3.4 2.1 + - - -
69B LEU* 2.9 39.6 + - + +
71B ILE* 4.1 19.5 - - + -
100B PHE* 4.7 6.3 - - + -
104B LEU* 4.9 3.8 - - + -
108B LEU* 4.0 35.0 - - + -
134B LEU* 4.6 11.0 - - + -
197B ALA* 4.0 2.9 - - - -
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Residues in contact with CYS 35 (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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16B PHE 4.2 0.7 - - - -
17B LEU* 3.4 9.9 - - - +
18B ASP 2.8 32.9 + - - -
34B LEU* 1.3 74.5 - - - +
36B LEU* 1.3 72.9 + - - +
37B LEU* 5.2 0.2 - - - -
66B LYS* 4.4 7.6 - - - -
67B LEU 3.3 11.4 - - - +
68B SER* 4.2 8.3 - - - +
197B ALA* 3.7 25.7 - - + +
198B GLU* 3.7 29.6 - - - +
201B VAL* 3.8 16.1 - - + +
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Residues in contact with LEU 36 (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 ILE* 3.6 19.1 - - + -
16B PHE 3.3 4.3 - - - -
17B LEU* 3.2 35.4 - - + -
34B LEU* 3.8 16.8 - - + -
35B CYS* 1.3 74.3 - - - +
37B LEU* 1.3 61.3 + - - +
38B ALA 4.0 0.4 - - - -
65B ASP 4.4 0.2 - - - -
66B LYS* 3.4 6.4 - - - +
67B LEU* 2.8 40.5 + - + +
108B LEU* 4.4 18.2 - - + -
111B PHE* 3.6 35.9 - - + -
112B LEU* 5.0 13.0 - - + -
121B LEU* 5.2 4.5 - - + -
134B LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 37 (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 LEU 3.5 1.4 - - - +
15B ILE* 3.3 2.7 - - - +
16B PHE* 2.8 49.1 + - + +
36B LEU* 1.3 74.3 - - - +
38B ALA* 1.3 61.5 + - - +
39B VAL* 4.4 7.0 - - + -
60B PRO* 6.0 0.7 - - + -
61B PRO* 6.0 0.7 - - + -
64B VAL* 3.2 34.5 - - + -
65B ASP 3.4 4.5 - - - +
66B LYS* 4.6 15.0 - - + +
201B VAL* 3.4 25.1 - - + -
202B LEU* 3.7 29.8 - - + -
205B LEU* 4.1 20.9 - - + -
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Residues in contact with ALA 38 (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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97A ARG* 5.2 2.3 + - - -
13B THR* 3.8 9.2 - - + -
14B LEU 3.5 4.5 - - - -
15B ILE* 3.9 10.7 - - + +
36B LEU 4.0 0.8 - - - -
37B LEU* 1.3 72.7 - - - +
39B VAL* 1.3 60.6 + - - +
63B VAL 4.7 0.2 - - - +
64B VAL* 3.4 7.4 - - - +
65B ASP* 2.9 35.2 + - + +
111B PHE* 4.2 8.4 - - + -
115B GLN* 3.4 37.4 - - + +
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Residues in contact with VAL 39 (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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97A ARG* 5.2 1.6 - - - +
13B THR* 3.3 7.8 - - - +
14B LEU* 2.8 51.5 + - + +
16B PHE* 3.6 23.3 - - + -
37B LEU* 4.4 10.3 - - + -
38B ALA* 1.3 76.6 - - - +
40B HIS* 1.3 64.8 + - - +
43B ALA* 3.6 27.6 - - + -
44B LEU* 4.6 10.3 - - + -
61B PRO* 3.8 18.6 - - + -
63B VAL 4.1 11.0 - - - +
64B VAL* 5.1 1.3 - - + -
205B LEU* 5.6 0.4 - - + -
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Residues in contact with HIS 40 (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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94A VAL 3.9 8.5 + - - -
95A GLN* 3.2 56.4 + - + +
96A GLY* 4.3 2.9 - - - -
97A ARG* 4.3 8.3 - - - +
12B GLN* 3.7 27.9 + - + -
13B THR* 4.6 1.6 - - - +
39B VAL* 1.3 80.8 - - - +
41B ARG* 1.3 70.3 + - + +
42B ARG* 2.9 48.8 + - + +
43B ALA* 3.1 15.8 + - - +
44B LEU* 3.9 1.6 + - - +
63B VAL 5.1 1.4 + - - -
116B PRO* 3.6 26.7 - - + +
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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