Contacts of the helix formed by residues 56 - 67 (chain B) in PDB entry 2O1S
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 THR 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY 3.1 14.1 + - - +
54B LEU 3.3 0.2 - - - -
55B GLY* 1.3 80.7 - - - +
57B VAL* 1.3 56.4 + - - +
58B GLU 3.5 2.0 - - - -
59B LEU* 3.5 12.5 + - + +
60B THR* 2.6 42.0 + - - -
76B TRP* 4.3 14.1 - - + -
81B GLN* 3.0 51.3 + - + +
84B PRO* 3.3 7.7 - - - +
179B ASN* 3.8 14.8 - - + +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B CYS* 3.6 39.0 - - + +
35B LEU* 3.9 18.1 - - + +
36B ARG* 4.1 20.6 - - + +
39B LEU* 4.4 12.6 - - + -
53B GLY 4.5 1.3 - - - +
54B LEU* 3.2 32.8 - - - +
55B GLY 3.5 1.8 - - - -
56B THR* 1.3 78.1 - - - +
58B GLU* 1.3 67.0 + - - +
60B THR* 3.3 1.2 + - - -
61B VAL* 3.2 28.1 + - - +
84B PRO* 4.5 11.0 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B CYS* 3.8 24.2 - - - +
33B ASP* 5.6 1.0 - - - +
36B ARG* 2.8 36.2 + - - -
55B GLY 4.8 0.5 - - - +
56B THR 3.5 0.2 - - - -
57B VAL* 1.3 80.9 + - - +
59B LEU* 1.3 62.8 + - - +
61B VAL* 3.6 2.3 + - - +
62B ALA* 3.1 24.0 + - - +
256B GLY 3.5 14.5 - - - +
257B HIS* 2.9 48.3 + - - +
259B VAL* 3.5 29.0 - - + +
262B LEU* 4.3 2.5 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 5.8 0.4 - - - +
56B THR* 3.5 15.3 + - + +
57B VAL 3.2 0.6 - - - -
58B GLU* 1.3 76.6 - - - +
60B THR* 1.3 66.3 + - - +
62B ALA* 3.3 6.8 + - + +
63B LEU* 2.9 48.2 + - + +
76B TRP* 4.5 7.4 - - + -
149B VAL* 3.9 28.3 - - + -
177B ILE* 4.1 17.5 - - + -
179B ASN* 5.0 2.2 - - + -
256B GLY 4.2 6.3 + - - +
262B LEU* 4.8 13.9 - - + -
266B LEU* 5.2 3.8 - - + -
278B LEU* 6.1 1.1 - - + -
280B ILE* 3.6 33.9 - - + -
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR 2.6 27.8 + - - -
57B VAL 3.3 4.2 + - - -
59B LEU* 1.3 77.4 - - - +
61B VAL* 1.3 63.0 + - - +
63B LEU* 3.5 2.4 + - - +
64B HIS* 3.1 31.8 + - + -
76B TRP* 3.4 24.7 - - + -
84B PRO* 3.6 18.1 - - + +
85B HIS* 3.5 35.7 - - + +
88B LEU* 3.8 13.9 - - + -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.0 12.7 - - + +
28B LEU* 3.8 31.4 - - + -
31B LEU* 4.3 10.5 - - + -
32B CYS* 3.8 19.1 - - - -
35B LEU* 4.3 20.2 - - + -
57B VAL 3.2 17.4 + - - +
58B GLU 3.8 3.6 - - - +
60B THR* 1.3 74.3 - - - +
62B ALA* 1.3 67.6 + - - +
63B LEU 3.1 0.3 + - - -
64B HIS* 3.1 1.7 + - - +
65B TYR* 2.8 26.4 + - + +
88B LEU* 4.2 11.4 - - + -
259B VAL* 4.3 10.3 - - + -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.1 15.6 + - - +
59B LEU* 3.3 6.0 + - + +
61B VAL* 1.3 78.5 - - - +
63B LEU* 1.3 57.7 + - - +
65B TYR* 3.3 1.8 + - - +
66B VAL* 2.9 35.3 + - - +
259B VAL* 4.2 3.3 - - - +
262B LEU* 3.7 27.4 - - + -
263B ILE* 3.8 24.0 - - + -
266B LEU* 3.9 10.3 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 2.9 42.2 + - + +
60B THR* 3.7 4.0 - - - +
62B ALA* 1.3 77.6 - - - +
64B HIS* 1.3 61.4 + - + +
67B TYR* 2.8 63.9 + - + +
69B THR* 5.6 0.7 - - - -
74B LEU* 3.5 32.5 - - + -
76B TRP* 4.4 10.1 - - + -
147B VAL* 4.0 2.0 - - + -
149B VAL* 3.9 16.4 - - + -
177B ILE* 3.9 20.0 - - + -
266B LEU* 3.9 8.7 - - + -
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Residues in contact with HIS 64 (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 THR* 3.6 20.7 - - + +
20B LEU* 3.6 22.2 - - + -
21B ARG* 2.7 31.7 + - - +
60B THR* 3.1 31.5 + - + +
63B LEU* 1.3 82.2 - - + +
65B TYR* 1.3 59.7 + - - +
67B TYR 3.3 2.1 - - - +
69B THR* 2.9 40.0 + - + +
74B LEU* 4.9 8.0 - - + +
76B TRP* 5.5 0.6 - + - -
85B HIS* 2.7 45.8 + + - -
88B LEU* 4.2 9.6 - - + -
89B THR* 4.7 0.2 - - - -
115B TYR* 4.5 4.0 - + - -
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Residues in contact with TYR 65 (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 LEU* 3.4 32.9 - - + +
21B ARG* 3.4 34.8 + - + +
23B LEU 3.1 23.5 + - - -
24B PRO* 4.3 0.5 - - - +
25B LYS* 3.5 34.3 + - + +
28B LEU* 3.7 29.4 - - + -
61B VAL* 2.8 20.1 + - + +
62B ALA* 3.6 5.2 - - - +
64B HIS* 1.3 79.3 - - - +
66B VAL* 1.3 62.5 + - + +
263B ILE* 3.5 25.8 - - + -
267B LYS* 5.7 0.9 - - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 5.4 0.5 - - - -
62B ALA 2.9 16.8 + - - +
63B LEU 4.3 0.9 - - - +
65B TYR* 1.3 82.4 - - + +
67B TYR* 1.3 72.8 + - + +
68B ASN 4.0 0.5 + - - -
263B ILE* 3.9 39.7 - - + +
266B LEU* 4.2 20.4 - - + +
267B LYS* 4.2 23.6 - - + +
270B ARG* 6.5 0.2 - - + -
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 3.0 26.0 + - - -
63B LEU* 2.8 58.2 + - + +
64B HIS 3.3 4.3 - - - +
66B VAL* 1.3 85.6 - - + +
68B ASN* 1.3 57.0 + - - +
69B THR* 3.0 20.4 + - + -
72B ASP* 3.7 17.9 - - + +
74B LEU* 6.0 0.4 - - + -
145B ARG* 3.9 28.7 - - + -
146B THR 5.4 1.5 + - - -
147B VAL* 4.4 21.1 - - + -
175B LEU* 3.5 26.9 - - - +
266B LEU* 4.4 19.3 + - + +
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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