Contacts of the strand formed by residues 46 - 56 (chain B) in PDB entry 2OG9
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 GLU 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.4 27.3 - - + +
25B LEU 3.1 19.3 - - - +
26B PRO* 4.2 4.0 - - + +
27B LEU* 3.9 4.2 - - - +
44B MSE 3.6 14.8 - - - +
45B THR* 1.3 93.9 + - - +
47B ILE* 1.3 71.3 + - - +
48B ALA 4.4 0.2 - - - -
70B ARG* 4.9 4.3 + - - -
376B ARG* 3.0 30.3 + - - -
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Residues in contact with ILE 47 (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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24B TYR* 3.7 2.9 - - - -
25B LEU* 2.9 45.2 + - + +
27B LEU* 4.1 8.7 - - + -
44B MSE 3.8 19.3 - - + -
46B GLU* 1.3 80.5 - - - +
48B ALA* 1.3 65.5 + - - +
49B ILE* 3.5 24.4 + - + +
67B TYR* 4.1 13.9 - - + -
68B SER 3.7 14.1 - - - +
69B LYS* 4.4 13.5 - - + -
316B PHE* 4.4 11.0 - - + -
337B PHE* 4.9 0.7 - - + -
339B TRP* 3.8 30.1 - - + -
340B LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 48 (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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22B SER* 5.1 2.2 - - - +
23B CYS 3.7 4.5 - - - -
24B TYR* 3.7 28.6 - - + -
47B ILE* 1.3 71.6 - - - +
49B ILE* 1.3 59.2 + - - +
67B TYR* 3.2 6.4 - - - +
68B SER* 2.9 38.5 + - - +
70B ARG 5.4 2.0 - - - +
73B GLY* 3.6 32.5 - - - +
76B GLN* 5.1 0.9 - - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 3.5 1.7 - - - +
22B SER* 3.6 3.0 - - - -
23B CYS* 2.7 49.3 + - + +
25B LEU* 4.4 6.3 - - + -
47B ILE* 3.7 29.8 - - + +
48B ALA* 1.3 73.5 - - - +
50B LEU* 1.3 61.8 + - - +
51B PHE* 3.6 37.5 + - + -
65B PHE* 4.1 13.0 - - + -
66B SER 3.6 8.7 - - - +
67B TYR* 3.7 13.7 - - + -
316B PHE* 5.3 0.2 - - + -
340B LEU* 4.3 16.6 - - + -
343B LEU* 3.8 23.8 - - + -
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.2 9.9 - - + -
21B SER 3.4 15.0 - - - +
22B SER* 4.7 2.2 - - - +
48B ALA 4.1 0.8 + - - -
49B ILE* 1.3 71.2 - - - +
51B PHE* 1.3 67.7 + - - +
65B PHE* 3.0 8.2 - - - -
66B SER* 2.9 33.7 + - - +
67B TYR* 4.6 0.2 - - - +
73B GLY 6.0 0.4 - - - +
76B GLN* 3.9 29.8 + - + +
77B PHE* 4.1 28.9 - - + -
80B ALA* 3.9 20.9 - - + -
118B ALA* 3.9 21.5 - - - -
121B ALA* 3.9 16.0 - - + +
122B PHE* 6.2 0.2 - - + -
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Residues in contact with PHE 51 (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 ARG 3.7 0.8 - - - +
20B ILE* 3.2 8.0 - - - +
21B SER* 2.8 45.2 + - - +
23B CYS* 3.9 30.1 - - + -
49B ILE* 3.6 22.0 - - + -
50B LEU* 1.3 75.2 - - - +
52B ALA* 1.3 59.0 + - - +
53B GLU* 4.3 2.9 - - + -
63B LEU* 4.1 11.0 - - + -
64B GLY 3.5 5.2 - - - -
65B PHE* 3.7 22.4 - + + -
343B LEU* 3.9 21.3 - - + -
344B PHE* 3.7 18.8 - + - -
367B LEU* 3.4 36.6 - - + -
371B VAL* 4.1 13.2 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG 3.4 4.5 - - - -
20B ILE* 4.4 2.7 - - + -
50B LEU 4.0 0.2 + - - -
51B PHE* 1.3 74.5 - - - +
53B GLU* 1.3 60.9 - - - +
54B ILE* 5.3 0.2 - - + -
62B GLY 3.8 0.5 - - - +
63B LEU* 3.4 7.5 - - - +
64B GLY 2.9 30.2 + - - +
121B ALA* 3.6 35.4 - - + +
122B PHE* 3.8 26.9 - - + -
125B ALA* 3.8 3.9 - - + +
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Residues in contact with GLU 53 (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 TRP* 4.0 17.5 - - + -
18B VAL* 3.2 7.3 - - - +
19B ARG* 2.8 83.2 + - + +
21B SER* 4.2 9.9 + - - -
51B PHE* 5.4 2.2 - - + +
52B ALA* 1.3 78.6 - - - +
54B ILE* 1.3 62.8 + - - +
55B GLU* 5.3 1.5 - - + +
62B GLY 3.4 6.7 - - - +
63B LEU* 4.0 16.4 - - + -
367B LEU* 4.2 19.4 - - + +
384B ARG* 4.8 3.1 + - - -
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Residues in contact with ILE 54 (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* 3.8 35.2 - - + -
17B TRP* 3.6 3.4 - - - +
18B VAL* 4.4 11.7 - - + -
53B GLU* 1.3 80.5 - - - +
55B GLU* 1.3 68.3 + - - +
61B GLN* 3.1 4.7 - - - +
62B GLY* 2.8 39.3 + - - +
87B LEU* 4.2 18.8 - - + -
122B PHE* 3.7 29.4 - - + +
125B ALA* 3.8 13.9 - - + -
126B LEU* 3.9 18.2 - - + -
129B LEU* 4.1 13.9 - - + +
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Residues in contact with GLU 55 (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* 3.8 3.5 - - - +
16B THR* 3.0 21.1 + - - -
17B TRP* 3.1 33.5 + - + +
53B GLU* 5.3 0.9 - - + +
54B ILE* 1.3 80.3 - - - +
56B THR* 1.3 65.3 + - - +
60B HIS 3.2 4.9 - - - +
61B GLN* 2.9 41.6 + - + +
384B ARG* 2.9 44.5 + - - +
385B PRO* 3.3 29.5 - - + +
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Residues in contact with THR 56 (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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13B ASP* 2.5 28.9 + - - +
14B ARG 3.2 15.9 - - - +
15B ILE* 4.2 4.9 - - + -
16B THR* 3.5 6.3 - - - -
54B ILE* 5.0 0.2 - - + -
55B GLU* 1.3 78.4 - - - +
57B ALA* 1.3 59.4 + - - +
58B GLY 3.3 1.7 + - - -
59B GLY 2.9 15.9 + - - -
60B HIS* 3.0 23.9 + - + +
92B PRO* 3.8 18.2 - - + -
129B LEU* 3.8 24.9 - - + -
385B PRO* 3.5 16.3 - - - +
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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
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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