Contacts of the helix formed by residues 53 - 68 (chain B) in PDB entry 2OQH
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 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.5 25.4 - - - -
32B THR* 3.8 5.5 - - - +
34B THR* 3.4 5.7 + - - -
52B TRP* 1.3 77.9 - - - +
54B ALA* 1.3 66.6 + - - +
55B PRO* 3.4 3.0 - - - +
56B VAL* 2.9 15.8 + - - -
57B ALA 3.0 10.6 + - - -
374B ASP* 3.5 12.1 + - - +
376B THR 5.6 1.0 - - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.2 5.9 - - - +
53B GLY* 1.3 69.2 - - - -
55B PRO* 1.3 65.2 - - + +
57B ALA* 3.8 5.9 - - - +
58B ALA* 2.9 29.7 + - - +
374B ASP* 2.8 20.7 + - - +
62D ARG* 4.3 7.2 - - - +
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Residues in contact with PRO 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 3.8 28.3 - - + -
53B GLY 3.5 4.9 - - - +
54B ALA* 1.3 95.4 - - + +
56B VAL* 1.3 62.7 + - + +
58B ALA* 3.4 7.6 + - + +
59B ILE* 3.3 27.6 + - - +
92B LEU* 3.8 14.4 - - + -
374B ASP* 4.2 1.1 - - - +
58D ALA* 6.5 1.6 - - + -
62D ARG* 4.1 21.3 - - - +
89D TYR* 4.2 11.9 - - + +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.9 4.5 - - - +
50B THR* 3.5 30.3 - - + -
51B MSE 3.4 22.9 - - + +
52B TRP* 3.7 8.5 - - + -
53B GLY 2.9 6.5 + - - +
55B PRO* 1.3 73.0 - - - +
57B ALA* 1.3 68.8 + - - +
59B ILE* 3.0 18.8 + - - +
60B VAL* 3.0 14.9 + - + +
92B LEU* 3.7 35.7 - - + +
95B ALA 4.5 0.4 - - - -
96B ALA* 3.9 20.6 - - + +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.8 17.2 - - + +
12B VAL* 3.6 31.4 - - + -
34B THR* 3.9 11.6 + - + -
53B GLY 3.0 8.8 + - - +
54B ALA* 3.8 4.5 - - - +
56B VAL* 1.3 76.7 - - - +
58B ALA* 1.3 58.1 + - - +
60B VAL* 3.2 3.3 + - - +
61B ARG* 2.9 47.3 + - - +
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Residues in contact with ALA 58 (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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54B ALA 2.9 18.8 + - - +
55B PRO* 3.5 10.1 - - + +
56B VAL 3.1 0.4 - - - -
57B ALA* 1.3 77.7 - - - +
59B ILE* 1.3 61.7 + - + +
61B ARG* 3.5 10.1 + - - +
62B ARG* 3.1 33.2 + - + +
55D PRO* 6.5 0.9 - - + -
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Residues in contact with ILE 59 (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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55B PRO 3.3 15.7 - - - +
56B VAL* 3.0 6.8 + - - +
58B ALA* 1.3 74.8 - - + +
60B VAL* 1.3 66.5 + - - +
62B ARG* 3.1 18.3 + - + +
63B MSE 3.1 19.9 + - + +
85B VAL* 3.8 24.7 - - + -
89B TYR* 3.5 49.4 - - + -
92B LEU* 3.6 33.4 - - + +
96B ALA* 3.5 17.3 - - + -
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Residues in contact with VAL 60 (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 VAL* 4.6 4.7 - - + -
10B VAL* 3.5 24.5 - - + -
34B THR* 4.9 1.8 - - + -
36B VAL* 3.8 26.5 - - + -
56B VAL* 3.0 19.3 + - + +
57B ALA* 3.6 8.5 - - - +
59B ILE* 1.3 76.4 - - - +
61B ARG* 1.3 56.9 + - - +
63B MSE 3.1 10.8 + - - +
64B ALA* 2.9 26.5 + - - +
67B LEU* 5.7 0.2 - - - +
96B ALA* 3.7 31.4 - - + +
99B ALA* 4.9 1.1 - - + -
100B VAL* 4.1 15.0 - - + +
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL 6.0 0.9 - - - +
10B VAL* 2.9 51.1 + - + +
11B TRP* 4.4 3.4 - - - +
12B VAL* 5.2 4.9 - - - +
57B ALA* 2.9 35.1 + - - +
58B ALA* 3.9 7.9 - - - +
60B VAL* 1.3 75.9 - - - +
62B ARG* 1.3 61.7 + - + +
64B ALA* 3.3 10.4 - - + +
65B PRO* 3.3 19.8 - - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.1 23.2 + - + +
59B ILE* 3.1 10.6 + - + +
61B ARG* 1.3 78.1 - - + +
63B MSE 1.3 60.2 + - + +
65B PRO* 3.8 7.9 - - - +
66B ASP* 4.1 7.4 - - - +
89B TYR* 3.7 31.3 + - + -
52D TRP* 5.6 6.7 - - - -
55D PRO* 6.2 3.3 - - - +
374D ASP* 6.1 2.6 - - - +
376D THR 5.4 10.7 - - - -
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Residues in contact with MSE 63 (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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59B ILE* 3.1 13.3 + - + +
60B VAL* 3.1 16.8 + - - +
62B ARG* 1.3 79.6 - - + +
64B ALA* 1.3 66.9 + - - +
65B PRO 3.3 1.1 - - - -
66B ASP* 2.8 28.9 + - - +
67B LEU* 3.6 11.4 + - + +
78B PHE* 4.4 5.4 - - + -
82B GLN* 3.6 35.6 + - - +
85B VAL* 4.2 11.2 - - + -
96B ALA* 3.7 33.9 - - + +
97B ILE* 3.7 24.9 - - - +
100B VAL* 3.8 19.5 - - + -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.9 33.0 - - + +
10B VAL* 6.1 0.7 - - + -
60B VAL 2.9 12.7 + - - +
61B ARG* 3.3 15.0 - - + +
63B MSE 1.3 74.9 - - - +
65B PRO* 1.3 71.8 - - + +
67B LEU* 2.9 24.7 + - - +
68B ILE* 3.5 11.0 + - + +
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG 3.3 11.9 - - - +
62B ARG* 3.8 7.6 - - - +
63B MSE 3.5 3.1 - - - -
64B ALA* 1.3 94.7 - - + +
66B ASP* 1.3 62.3 + - - +
67B LEU 3.3 0.7 + - - -
68B ILE* 3.5 23.5 + - + +
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Residues in contact with ASP 66 (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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62B ARG 4.1 10.2 - - - +
63B MSE 2.8 18.8 + - - +
65B PRO* 1.3 75.7 - - - +
67B LEU* 1.3 60.4 + - + +
68B ILE 4.6 1.7 - - - +
70B THR* 3.6 15.8 - - - +
78B PHE* 6.3 1.3 - - + -
81B LYS* 3.7 30.8 - - + +
82B GLN* 3.4 27.7 + - - +
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Residues in contact with LEU 67 (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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5B ILE* 3.4 27.9 - - + +
8B VAL* 3.9 33.0 - - + -
38B VAL* 5.5 0.9 - - + -
60B VAL 5.7 0.2 - - - +
63B MSE 4.2 7.2 - - + +
64B ALA* 2.9 15.9 + - - +
66B ASP* 1.3 80.2 - - - +
68B ILE* 1.3 64.0 + - - +
69B GLY 3.2 0.5 + - - -
70B THR* 2.6 28.7 + - - +
78B PHE* 3.6 37.7 - - + -
100B VAL* 3.6 31.9 - - + -
104B CYS* 5.1 3.1 - - - -
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Residues in contact with ILE 68 (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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5B ILE* 3.5 9.2 - - + +
6B THR* 3.4 34.1 - - - +
7B ASP* 3.9 9.9 - - - +
8B VAL* 4.0 18.2 - - + +
64B ALA* 3.6 11.4 - - + +
65B PRO* 3.5 18.3 + - + +
66B ASP 4.6 1.0 - - - +
67B LEU* 1.3 74.8 - - - +
69B GLY* 1.3 63.6 + - - +
70B THR* 3.3 4.4 + - - +
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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
------------------------------------------------------------
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