Contacts of the helix formed by residues 70 - 77 (chain C) in PDB entry 3G4C
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 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 3.5 53.4 - - - +
152B LEU* 4.2 22.9 - - + -
68C ALA 3.7 0.2 + - - -
69C PRO* 1.3 69.3 - - - +
71C PHE* 1.3 66.4 + - - +
72C VAL 2.9 0.5 + - - -
73C ALA* 2.9 7.9 + - + -
74C ARG* 2.8 31.3 + - + +
151C PRO 5.2 0.4 - - - +
152C LEU* 3.4 12.7 + - + +
154C LEU* 2.8 44.4 + - + +
156C THR* 4.2 17.5 - - + -
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG* 3.8 35.7 - - - +
148B ILE* 3.6 26.9 - - + -
308B UMP 4.8 1.6 + - - -
69C PRO* 3.7 22.2 - - + -
70C ILE* 1.3 71.9 - - - +
72C VAL* 1.3 73.7 + - + +
74C ARG* 3.8 13.9 + - - +
75C GLN* 3.5 25.4 + - - +
99C TYR* 3.8 16.8 - + - -
152C LEU* 2.9 37.4 + - + +
153C ASN* 4.3 1.6 - - - -
180C GLN* 3.3 28.3 - - - -
182C GLU* 3.7 22.7 - - + -
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA* 4.0 10.1 - - + -
69C PRO* 2.8 32.3 + - + +
71C PHE* 1.3 80.7 - - + +
73C ALA* 1.3 65.2 + - - +
74C ARG 3.1 1.6 - - - -
75C GLN* 3.1 18.8 + - - +
76C TRP* 3.1 17.6 + - + +
180C GLN* 6.1 0.2 - - - -
182C GLU* 3.6 33.4 - - + -
183C ILE* 3.6 26.8 - - + +
186C TYR* 3.9 18.4 - - + -
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Residues in contact with ALA 73 (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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74B ARG* 5.7 1.6 - - - +
68C ALA* 4.7 1.9 - - + +
69C PRO 2.9 10.4 + - - +
70C ILE* 3.7 9.2 - - + +
72C VAL* 1.3 74.1 - - - +
74C ARG* 1.3 57.9 + - + +
76C TRP* 4.2 7.0 - - - -
77C PHE* 2.9 52.0 + - + -
86C GLU* 4.8 5.8 - - - +
156C THR* 3.6 31.0 - - + -
158C PHE* 4.4 7.9 - - + -
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Residues in contact with ARG 74 (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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70B ILE* 3.7 32.2 - - - +
73B ALA* 5.6 2.2 - - - +
74B ARG* 3.4 45.8 - - + +
86B GLU* 3.1 31.5 + - - -
147B ARG* 4.4 8.7 - - - +
156B THR* 4.8 1.0 + - - -
308B UMP 3.6 42.0 + - + +
70C ILE* 2.8 21.3 + - + +
71C PHE* 4.1 8.8 + - - +
73C ALA* 1.3 74.7 - - - +
75C GLN* 1.3 63.5 + - - +
77C PHE* 4.0 5.9 + - - +
78C ARG* 3.3 22.7 + - - +
152C LEU* 4.1 16.3 - - - +
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Residues in contact with GLN 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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90B ARG* 3.8 10.1 - - - +
147B ARG* 3.6 2.6 - - - +
308B UMP 3.0 60.8 + - + +
71C PHE* 3.5 14.8 + - - +
72C VAL* 3.1 9.8 + - - +
74C ARG* 1.3 77.0 - - - +
76C TRP* 1.3 61.5 + - - +
78C ARG* 3.0 14.7 + - - +
174C ARG* 2.7 27.8 + - - +
180C GLN* 3.1 29.2 + - - +
183C ILE* 3.7 30.2 - - + +
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Residues in contact with TRP 76 (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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11C VAL* 4.6 0.4 - - + -
66C VAL* 3.8 28.0 - - + -
68C ALA* 5.2 0.2 - - + -
72C VAL* 3.1 26.0 + - + +
73C ALA* 3.2 10.5 + - - +
75C GLN* 1.3 75.9 - - - +
77C PHE* 1.3 60.6 + - + +
78C ARG 3.0 6.1 + - - -
79C HIS* 3.0 25.4 + - - +
84C TYR* 3.3 24.2 + + - -
158C PHE* 3.9 15.9 - + - -
160C TRP* 3.3 52.0 - + - -
170C PHE* 3.6 23.5 - + - -
183C ILE* 4.2 12.7 - - + +
186C TYR* 3.4 43.7 - + + -
190C ILE* 4.0 14.6 - - + -
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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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77B PHE* 4.5 16.7 - - + +
78B ARG* 3.7 27.4 - - - -
80B ARG* 5.7 2.3 - - - +
73C ALA* 2.9 29.7 + - + +
74C ARG* 4.5 6.3 - - - +
75C GLN 3.4 0.2 - - - -
76C TRP* 1.3 74.7 - - + +
78C ARG* 1.3 59.9 + - - +
79C HIS 3.0 10.9 + - - +
80C ARG* 4.7 4.0 + - - +
84C TYR* 3.6 50.7 - + + -
86C GLU* 3.4 27.1 - - + -
158C PHE* 3.6 44.4 - + + -
313C UMP 3.7 6.5 - - - -
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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