Contacts of the helix formed by residues 74 - 84 (chain C) in PDB entry 2GRA
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 ILE 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C PRO* 6.0 4.3 - - + -
70C VAL* 3.3 26.9 - - + -
71C LYS* 2.6 25.0 + - - +
73C HIS* 1.3 116.3 - - + +
75C ILE* 1.3 65.5 + - - +
76C PRO* 2.8 5.0 - - - -
77C PHE* 3.1 34.6 + - + -
78C ILE* 3.3 21.2 + - + +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.7 38.1 - - + +
70C VAL* 3.0 43.1 - - + +
71C LYS 3.1 4.9 + - - +
72C PRO* 3.8 11.9 - - + +
74C ILE* 1.3 73.9 - - - +
76C PRO* 1.3 64.9 - - + +
78C ILE* 3.6 7.3 + - - +
79C LEU* 3.0 40.9 + - + +
94C SER* 4.3 1.3 - - - +
96C ALA* 4.0 7.0 - - + -
99C VAL* 4.0 28.7 - - + -
104C ILE* 4.5 3.6 - - + -
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Residues in contact with PRO 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PRO 3.1 16.4 - - - +
73C HIS* 4.0 3.6 - - - +
74C ILE* 2.8 8.0 - - - +
75C ILE* 1.3 89.6 - - + +
77C PHE* 1.3 74.2 + - + +
78C ILE 2.8 3.6 + - - -
79C LEU* 2.9 13.3 + - + -
80C ASP* 2.8 22.1 - - - +
107C LYS* 4.3 18.6 - - - +
272C ALA* 6.3 3.8 - - + -
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C HIS 4.2 20.4 - - - -
74C ILE* 3.1 24.2 + - + +
76C PRO* 1.3 84.3 - - + +
78C ILE* 1.3 65.7 + - + +
80C ASP* 3.3 22.4 - - - +
81C GLU* 3.3 8.2 + - - +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.5 28.5 - - + +
35C PRO* 5.8 4.0 - - + -
56C ASN* 3.5 28.7 - - - +
68C LEU* 3.5 21.5 - - + -
70C VAL* 4.6 6.7 - - + -
74C ILE* 3.5 28.0 - - + +
75C ILE 3.7 7.2 - - - +
76C PRO 2.8 1.6 + - - -
77C PHE* 1.3 74.4 - - + +
79C LEU* 1.3 58.2 + - + +
80C ASP 2.9 2.0 - - - -
81C GLU* 2.6 34.4 + - - +
82C ILE* 2.9 24.4 + - + +
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.6 21.8 - - + -
75C ILE* 3.0 37.2 + - + +
76C PRO* 2.9 10.4 + - + +
78C ILE* 1.3 73.1 - - + +
80C ASP* 1.3 57.8 + - - +
82C ILE* 4.6 3.4 - - + +
83C GLY* 2.7 33.0 + - - -
92C VAL* 5.7 1.6 - - + -
103C SER* 5.3 1.8 - - - +
104C ILE* 3.7 31.9 - - + -
107C LYS* 4.0 24.7 - - + -
108C LEU* 3.1 41.0 - - + +
111C PHE* 4.7 1.8 - - - -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 2.8 18.7 - - - +
77C PHE* 3.3 13.8 - - - +
78C ILE 2.9 0.4 - - - -
79C LEU* 1.3 75.7 - - - +
81C GLU* 1.3 64.8 + - - +
83C GLY 3.3 7.8 + - - -
84C ALA 4.5 0.7 + - - -
107C LYS* 3.0 27.4 + - - -
111C PHE* 3.9 24.5 - - + -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C HIS* 5.5 0.2 - - - +
56C ASN* 3.4 38.5 + - - +
57C LYS* 3.3 41.6 - - - +
77C PHE 3.3 7.0 + - - +
78C ILE* 2.6 24.5 + - - +
80C ASP* 1.3 75.9 - - - +
82C ILE* 1.3 58.7 + - + +
84C ALA 4.7 0.3 + - - -
85C ASP* 2.5 29.6 - - - +
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 5.1 4.5 - - + -
56C ASN 3.0 27.6 - - - +
57C LYS* 4.6 2.7 - - + -
60C VAL* 4.0 23.1 - - + -
66C LEU* 6.0 1.3 - - + -
78C ILE* 2.9 26.1 + - + +
79C LEU* 3.7 3.8 - - + +
81C GLU* 1.3 83.4 - - + +
83C GLY* 1.3 65.3 + - - +
84C ALA 3.3 2.5 - - - -
85C ASP* 2.9 43.3 + - + +
86C ILE* 2.8 17.9 - - + +
90C HIS* 5.8 1.8 - - + -
108C LEU* 4.4 2.9 - - + -
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU 2.7 21.0 + - - -
80C ASP 3.3 3.2 + - - -
82C ILE* 1.3 76.4 - - - +
84C ALA* 1.3 57.0 + - - +
86C ILE* 2.7 26.2 - - - +
108C LEU* 3.3 13.9 - - - -
111C PHE* 3.1 30.9 - - - +
112C ARG* 4.2 0.7 + - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASP 4.5 1.6 + - - +
81C GLU 5.6 0.4 - - - +
83C GLY* 1.3 71.4 - - - +
85C ASP* 1.3 64.8 + - - +
86C ILE* 3.0 14.2 + - - +
111C PHE* 3.0 24.3 - - + -
112C ARG* 5.6 3.3 - - - +
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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