Contacts of the helix formed by residues 70 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO* 1.3 71.8 - - - +
71B PHE* 1.3 60.0 + - - +
72B VAL 3.0 0.3 + - - -
73B ALA* 3.0 5.3 + - - -
74B ARG* 2.8 30.8 + - - +
151B PRO 4.9 1.1 - - - +
152B LEU* 3.2 29.1 + - + +
154B LEU* 2.8 45.0 + - + +
156B THR* 4.1 19.7 - - + -
74C ARG* 3.7 43.3 - - - +
152C LEU* 4.1 21.3 - - + -
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.6 18.2 - - + -
70B ILE* 1.3 76.6 - - - +
72B VAL* 1.3 74.5 + - + +
74B ARG* 3.9 11.0 + - - +
75B GLN* 3.4 29.0 + - - +
99B TYR* 3.7 32.3 - + - -
152B LEU* 2.9 34.5 + - + +
153B ASN* 4.2 2.2 - - + -
180B GLN* 3.6 32.8 - - - -
182B GLU* 3.8 13.5 - - + -
147C ARG* 4.2 19.5 - - - +
148C ILE* 3.4 33.2 - - + -
313C UMP 4.8 1.6 + - - -
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 4.1 6.3 - - + -
69B PRO* 2.9 24.4 + - + +
71B PHE* 1.3 99.3 - - + +
73B ALA* 1.3 66.6 + - - +
75B GLN* 3.1 11.3 + - - +
76B TRP* 2.9 29.9 + - + +
180B GLN* 6.2 0.4 - - + -
182B GLU* 3.8 20.2 - - + +
183B ILE* 3.8 27.5 - - + +
186B TYR* 4.0 18.6 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 4.7 1.0 - - + +
69B PRO 2.9 12.0 + - - +
70B ILE* 3.6 8.7 - - + +
72B VAL* 1.3 75.8 - - - +
74B ARG* 1.3 65.0 + - - +
76B TRP* 2.9 9.8 + - - +
77B PHE* 2.8 39.1 + - + -
86B GLU* 4.5 6.1 - - - +
156B THR* 3.9 23.1 - - + -
158B PHE* 4.3 15.7 - - + -
74C ARG* 5.6 2.5 - - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 2.8 24.2 + - - +
71B PHE* 3.9 9.4 - - - +
73B ALA* 1.3 72.9 - - - +
75B GLN* 1.3 60.8 + - + +
77B PHE* 3.8 8.9 + - - +
78B ARG* 3.5 18.5 + - - +
152B LEU* 4.5 8.0 - - - +
70C ILE* 3.5 47.9 - - - +
73C ALA* 5.7 2.0 - - - +
74C ARG* 3.4 32.0 - - + +
77C PHE* 5.9 0.3 - - - -
86C GLU* 2.6 37.8 + - - -
87C LEU 5.2 0.4 + - - -
147C ARG* 4.1 11.9 - - - +
156C THR* 4.5 0.2 + - - -
313C UMP 3.6 42.4 + - + +
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Residues in contact with GLN 75 (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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71B PHE* 3.4 16.1 + - - +
72B VAL* 3.1 10.7 + - - +
74B ARG* 1.3 75.1 - - + +
76B TRP* 1.3 65.5 + - - +
78B ARG* 3.3 11.4 - - - +
174B ARG* 2.8 23.1 + - - +
180B GLN* 3.2 28.8 + - - +
183B ILE* 3.6 33.2 - - + +
90C ARG* 3.8 11.9 - - - +
147C ARG* 3.6 2.8 - - - +
313C UMP 3.1 61.9 + - + +
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Residues in contact with TRP 76 (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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11B VAL* 4.5 0.7 - - + -
66B VAL* 3.8 27.4 - - + -
68B ALA* 5.1 0.2 - - + -
72B VAL* 2.9 26.0 + - + +
73B ALA* 2.9 11.8 + - - +
75B GLN* 1.3 77.0 - - - +
77B PHE* 1.3 59.6 + - + +
78B ARG 3.1 5.3 + - - -
79B HIS* 3.1 23.0 + - - -
84B TYR* 3.3 19.5 + + - -
158B PHE* 3.8 16.4 - + + -
160B TRP* 3.3 47.0 - + - -
170B PHE* 3.4 28.2 - + - -
183B ILE* 4.0 11.8 - - + +
186B TYR* 3.4 41.3 - + + -
190B ILE* 4.1 12.3 - - + -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 2.8 24.7 + - + +
74B ARG* 4.2 7.0 - - - +
75B GLN 3.3 0.4 - - - -
76B TRP* 1.3 76.1 - - + +
78B ARG* 1.3 59.2 + - - +
79B HIS* 3.1 12.6 + - - +
80B ARG* 4.5 4.3 + - - +
84B TYR* 3.6 48.7 - + + -
86B GLU* 3.3 32.3 - - + -
158B PHE* 3.7 35.9 - + - -
308B UMP 3.7 2.0 - - - -
77C PHE* 4.5 16.6 - - + +
78C ARG* 3.3 41.1 - - - -
80C ARG* 5.7 2.4 - - - +
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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
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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