Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 2OHW
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 GLN 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU 3.9 3.8 + - - +
72A LEU* 1.3 74.9 - - - +
74A TYR* 1.3 65.7 + - - +
75A GLN* 2.6 41.6 + - - +
76A SER* 2.9 26.0 + - - +
77A TYR* 3.4 6.7 - - - -
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 1.3 72.7 - - - +
75A GLN* 1.3 65.3 + - + +
76A SER 3.0 0.9 + - - -
77A TYR* 3.1 31.1 + + - +
78A SER* 2.9 52.6 + - - -
81A ILE* 4.0 27.2 - - + +
82A GLN* 4.9 9.7 + - - -
93A ILE* 5.7 2.2 - - + -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 2.6 43.5 + - - +
74A TYR* 1.3 80.8 + - + +
76A SER* 1.3 66.1 + - - +
78A SER* 3.6 15.1 + - - -
79A SER* 5.3 2.3 + - - -
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.3 27.4 - - - +
46A LEU* 3.3 32.9 - - - +
72A LEU* 4.5 13.7 - - - -
73A GLN* 2.9 20.8 + - - +
75A GLN* 1.3 86.4 + - - +
77A TYR* 1.3 58.4 + - - +
79A SER* 5.2 2.0 + - - -
80A TYR* 4.4 4.5 - - - -
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.2 12.1 - - + -
68A ILE* 3.5 37.0 - - + -
69A ASN 4.7 1.1 - - - -
72A LEU* 3.5 34.9 + - + -
73A GLN 3.4 19.3 - - - -
74A TYR* 3.1 33.7 + + - +
76A SER* 1.3 77.8 - - - +
78A SER* 1.3 69.8 + - - +
79A SER 3.2 3.6 - - - -
80A TYR* 3.0 21.4 + - - +
81A ILE* 3.3 27.7 + - + +
93A ILE* 3.5 28.3 - - + +
105A ILE* 4.5 7.6 - - + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 2.9 48.2 + - - -
75A GLN* 3.6 14.2 + - - -
76A SER 3.7 0.4 - - - -
77A TYR* 1.3 82.7 - - - +
79A SER* 1.3 64.9 + - - +
81A ILE* 3.1 17.8 + - - +
82A GLN* 3.1 21.2 + - - +
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 5.5 0.9 + - - -
50A PRO* 4.1 32.1 - - - +
75A GLN 5.3 0.8 + - - -
76A SER 5.2 2.2 + - - -
77A TYR 3.2 1.0 + - - -
78A SER* 1.3 80.4 + - - +
80A TYR* 1.3 63.2 + - - +
82A GLN* 3.3 11.8 + - - +
83A MET* 3.1 30.3 + - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.8 12.0 - - + +
44A GLN 4.3 4.7 + - - -
45A VAL* 4.2 20.7 + - + -
47A ARG 5.4 0.5 + - - -
50A PRO* 3.4 17.3 - - + +
51A TYR* 3.0 42.8 + - - -
54A ALA* 3.9 22.9 - - + -
58A LEU* 4.2 0.4 - - + +
66A LEU* 3.5 20.4 - - + +
68A ILE* 5.9 0.2 - - + -
76A SER 4.4 2.9 - - - -
77A TYR* 3.0 18.8 + - - +
79A SER* 1.3 78.8 - - - +
81A ILE* 1.3 60.6 + - - +
83A MET* 3.2 32.3 + - + +
84A ALA* 2.9 23.2 + - - +
105A ILE* 3.4 33.9 - - + -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 4.3 4.5 - - + -
68A ILE* 3.8 18.2 - - + -
74A TYR* 4.0 23.3 - - + +
77A TYR* 3.3 34.3 + - + +
78A SER* 3.1 9.3 + - - +
80A TYR* 1.3 76.4 - - - +
82A GLN* 1.3 66.1 + - - +
84A ALA* 3.3 3.1 + - - +
85A SER* 2.9 33.5 + - - +
91A PHE* 3.7 49.8 - - + -
93A ILE* 5.1 0.4 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TYR* 4.9 9.7 + - - -
78A SER* 3.1 17.5 + - - +
79A SER* 3.4 12.3 - - - +
80A TYR 3.3 0.2 - - - -
81A ILE* 1.3 82.1 - - - +
83A MET* 1.3 61.8 + - - +
85A SER* 3.5 5.3 + - - -
86A ARG* 3.0 39.9 + - - +
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Residues in contact with MET 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 4.6 11.4 - - + -
51A TYR 4.3 4.7 - - - +
54A ALA* 3.9 2.0 - - + -
55A GLU* 3.7 41.1 - - + +
58A LEU* 3.1 28.0 - - + -
79A SER* 3.1 12.5 + - - +
80A TYR* 3.2 42.4 - - + +
81A ILE 3.3 0.2 - - - -
82A GLN* 1.3 79.3 - - - +
84A ALA* 1.3 63.3 + - - +
86A ARG* 3.3 29.3 - - - +
87A TYR* 3.0 26.4 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.9 9.1 - - + +
66A LEU* 3.8 20.6 - - + -
80A TYR 2.9 16.9 + - - +
81A ILE* 3.6 5.2 - - - +
83A MET* 1.3 77.1 - - - +
85A SER* 1.3 62.3 + - - +
87A TYR* 3.0 8.8 + - - -
89A VAL* 2.9 56.0 + - + +
90A PRO 4.9 0.4 - - - +
91A PHE* 5.1 4.0 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 2.9 26.0 + - - +
82A GLN* 4.0 4.7 - - - -
84A ALA* 1.3 76.3 - - - +
86A ARG* 1.3 62.4 + - - +
88A GLY* 3.1 13.5 + - - +
89A VAL 4.4 7.0 + - - +
91A PHE* 4.9 7.8 - - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 2.8 35.6 + - - -
82A GLN* 3.0 33.7 + - - +
83A MET* 3.3 22.6 - - - +
84A ALA 3.2 0.2 - - - -
85A SER* 1.3 75.6 - - - +
87A TYR* 1.3 87.9 + - + +
88A GLY 3.9 0.2 + - - -
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 4.9 1.2 + - - -
55A GLU* 2.7 43.9 + - + +
58A LEU* 3.6 20.8 - - + +
59A LYS* 3.7 53.6 - - + +
61A SER* 5.2 0.9 + - - -
83A MET 3.0 24.5 - - - -
84A ALA 3.0 5.5 + - - +
86A ARG* 1.3 100.0 - - + +
88A GLY* 1.3 63.3 + - - +
89A VAL* 3.3 8.0 + - + +
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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