Contacts of the helix formed by residues 75 - 88 (chain A) in PDB entry 2C9Y
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 SER 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU 3.5 3.3 + - - -
74A VAL* 1.3 76.5 - - - +
76A ASP* 1.3 64.9 + - - +
77A GLU* 3.6 17.7 + - - +
78A MET* 3.2 41.9 + - - +
79A VAL* 3.0 19.9 + - - +
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Residues in contact with ASP 76 (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 VAL 5.1 1.6 - - - +
75A SER* 1.3 72.3 - - - +
77A GLU* 1.3 57.1 + - - +
79A VAL* 3.1 10.1 + - - +
80A VAL* 2.9 32.9 + - + +
101A PHE* 5.1 0.6 - - - -
104A THR* 4.5 1.2 + - - -
106A ARG* 3.0 42.4 + - - +
107A GLN* 2.7 45.2 + - + +
110A MET* 3.6 15.0 - - - -
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Residues in contact with GLU 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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75A SER* 3.7 18.1 + - - +
76A ASP* 1.3 77.4 + - - +
78A MET* 1.3 56.6 - - + +
80A VAL* 3.3 5.1 + - - +
81A GLU* 3.0 31.1 + - - +
106A ARG* 3.2 30.4 + - - -
110A MET* 3.8 20.1 - - + +
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Residues in contact with MET 78 (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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60A LEU* 4.7 11.5 - - + +
63A LYS* 5.0 15.9 - - + -
64A LEU* 4.1 28.5 - - + +
67A THR* 3.9 28.9 - - + +
73A LEU 4.2 2.5 - - - +
74A VAL* 3.9 10.8 - - + -
75A SER* 3.2 43.7 + - - +
77A GLU* 1.3 75.8 - - + +
79A VAL* 1.3 61.1 + - - +
81A GLU* 3.7 12.5 - - - +
82A LEU* 2.8 28.9 + - - +
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Residues in contact with VAL 79 (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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46A THR* 4.8 9.2 - - + -
49A MET* 6.4 0.2 - - + -
50A LEU* 5.7 2.7 - - + -
64A LEU* 6.2 0.4 - - + -
74A VAL* 3.6 28.7 - - + +
75A SER 3.0 15.1 + - - +
76A ASP* 3.5 9.2 - - - +
78A MET* 1.3 76.6 - - - +
80A VAL* 1.3 61.5 + - - +
82A LEU* 3.2 17.5 - - + +
83A ILE* 3.0 26.0 + - + +
101A PHE* 3.0 45.1 - - + -
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Residues in contact with VAL 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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76A ASP 2.9 20.9 + - - +
77A GLU* 3.3 6.9 + - - +
79A VAL* 1.3 75.1 - - - +
81A GLU* 1.3 57.5 + - - +
83A ILE* 3.4 9.5 + - + +
84A GLU* 2.8 28.0 + - + +
101A PHE* 4.0 20.9 - - + -
110A MET* 4.0 37.2 - - + +
111A LEU* 4.9 1.3 - - - +
114A LEU* 3.8 30.5 - - + +
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Residues in contact with GLU 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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60A LEU* 3.8 29.7 - - + +
63A LYS* 5.9 2.6 - - - +
77A GLU* 3.0 19.3 + - - +
78A MET* 3.7 11.6 - - - +
80A VAL* 1.3 74.4 - - - +
82A LEU* 1.3 67.1 + - - +
84A GLU* 3.3 16.7 + - - +
85A LYS* 3.1 40.1 + - - +
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Residues in contact with LEU 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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46A THR* 4.6 4.0 - - + +
49A MET* 3.7 28.3 - - + +
50A LEU* 3.7 39.7 - - + +
53A MET* 3.7 42.4 - - + -
60A LEU* 3.8 8.6 - - + +
64A LEU* 4.0 10.3 - - + -
78A MET 2.8 15.1 + - - +
79A VAL* 3.2 20.4 - - + +
81A GLU* 1.3 78.6 - - - +
83A ILE* 1.3 62.1 + - - +
85A LYS* 3.3 8.0 + - - +
86A ASN* 3.0 22.0 + - - +
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Residues in contact with ILE 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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44A LEU* 4.9 3.1 - - + -
49A MET* 4.0 25.8 - - + -
79A VAL* 3.0 16.5 + - + +
80A VAL* 3.6 10.5 - - + +
82A LEU* 1.3 70.6 - - + +
84A GLU* 1.3 67.4 + - - +
86A ASN* 3.1 4.3 + - - +
87A LEU* 2.8 41.0 + - + +
96A PHE* 6.0 1.3 - - + -
98A LEU* 3.9 24.2 - - + -
101A PHE* 3.3 42.8 - - + -
111A LEU* 4.4 10.3 - - + -
114A LEU* 4.1 11.9 - - + -
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Residues in contact with GLU 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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80A VAL* 2.8 21.3 + - - +
81A GLU* 3.3 18.7 + - + +
83A ILE* 1.3 71.9 - - - +
85A LYS* 1.3 66.4 + - + +
87A LEU* 3.2 5.8 + - - +
88A GLU* 3.1 42.6 + - + +
114A LEU* 3.8 27.7 - - + +
117A LYS* 3.0 37.4 + - - -
118A ARG* 5.3 7.1 + - - +
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A MET* 3.7 19.7 - - + -
60A LEU* 4.0 20.0 - - + -
81A GLU* 3.1 34.2 + - - +
82A LEU 3.6 7.4 - - - +
83A ILE 3.3 0.2 - - - -
84A GLU* 1.3 77.7 - - - +
86A ASN* 1.3 60.6 + - - +
88A GLU* 3.5 29.8 + - - +
89A THR* 3.4 17.3 - - - +
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Residues in contact with ASN 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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44A LEU* 4.1 19.7 - - + +
49A MET* 3.6 38.9 + - - +
53A MET* 4.4 12.9 - - - +
82A LEU* 3.0 22.2 + - - +
83A ILE 3.1 7.4 + - - +
85A LYS* 1.3 75.9 - - - +
87A LEU* 1.3 62.9 + - - +
88A GLU 3.1 1.6 - - - -
89A THR* 2.7 32.3 + - - +
92A CYS* 3.3 11.1 - - - -
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Residues in contact with LEU 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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44A LEU* 3.8 20.9 - - + -
83A ILE* 2.8 33.7 + - + +
84A GLU* 3.6 8.1 - - - +
86A ASN* 1.3 72.7 - - - +
88A GLU* 1.3 57.6 + - - +
89A THR 3.3 2.6 + - - +
92A CYS* 3.9 13.1 - - + +
96A PHE* 3.5 31.4 - - + -
114A LEU* 4.1 5.2 - - + -
115A MET* 3.2 34.8 - - + -
118A ARG* 3.4 32.0 + - - +
120A GLU* 4.7 0.4 - - - +
1234A EDO 3.2 20.8 + - - -
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Residues in contact with GLU 88 (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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84A GLU* 3.1 38.5 + - + +
85A LYS* 3.6 29.5 + - - +
86A ASN 3.1 0.4 - - - -
87A LEU* 1.3 74.0 - - - +
89A THR* 1.3 63.7 + - + +
90A PRO* 3.9 1.7 - - - +
118A ARG* 4.0 15.5 - - - +
1234A EDO 4.6 5.5 + - - -
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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