Contacts of the helix formed by residues 70 - 77 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 1.3 72.1 - - - +
71A PHE* 1.3 58.3 + - - +
73A ALA* 3.1 6.4 + - - +
74A ARG* 2.8 31.0 + - - +
86A GLU* 5.6 0.2 - - - +
151A PRO 4.8 1.1 - - - +
152A LEU* 3.2 30.8 + - + +
154A LEU* 2.9 45.3 + - + +
156A THR* 4.1 19.5 - - + -
74D ARG* 3.7 35.9 - - - +
152D LEU* 4.0 22.4 - - + -
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Residues in contact with PHE 71 (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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69A PRO* 3.5 21.1 - - + -
70A ILE* 1.3 78.0 - - - +
72A VAL* 1.3 75.3 + - + +
74A ARG* 4.0 13.8 + - - +
75A GLN* 3.4 26.6 + - - +
99A TYR* 3.8 23.3 - + - -
152A LEU* 3.0 41.3 + - + +
153A ASN* 4.2 2.0 - - - -
180A GLN* 3.3 34.5 - - - -
182A GLU* 4.0 13.7 - - + -
147D ARG* 4.2 24.0 - - - +
148D ILE* 3.6 30.7 - - + -
318D UMP 4.8 1.2 + - - -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 4.0 5.4 - - + -
69A PRO* 3.1 34.4 + - + +
71A PHE* 1.3 82.4 - - + +
73A ALA* 1.3 65.8 + - - +
75A GLN* 3.1 11.9 + - - +
76A TRP* 2.9 31.5 + - + +
182A GLU* 3.9 27.1 - - + -
183A ILE* 3.8 28.4 - - + +
186A TYR* 3.9 20.0 - - + -
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Residues in contact with ALA 73 (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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68A ALA* 4.8 1.3 - - + +
69A PRO 3.0 12.7 + - - +
70A ILE* 3.7 6.1 - - - +
72A VAL* 1.3 76.4 - - - +
74A ARG* 1.3 56.9 + - - +
76A TRP* 3.2 8.7 + - - -
77A PHE* 2.8 44.3 + - + +
86A GLU* 4.8 0.7 - - - +
156A THR* 3.9 23.1 - - + -
158A PHE* 4.2 18.4 - - + -
74D ARG* 4.2 8.7 - - - +
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Residues in contact with ARG 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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70A ILE 2.8 20.4 + - - +
71A PHE* 4.0 11.5 - - - +
73A ALA* 1.3 73.5 - - - +
75A GLN* 1.3 60.7 + - + +
77A PHE* 3.9 3.6 + - - +
78A ARG* 3.5 22.0 + - - +
152A LEU* 4.3 13.6 - - - +
70D ILE* 3.7 47.4 - - - +
73D ALA* 6.0 1.4 - - - +
74D ARG* 3.7 29.1 - - + +
77D PHE* 6.5 0.7 - - + -
86D GLU* 3.3 28.7 + - - +
87D LEU 4.9 0.6 + - - -
147D ARG* 4.1 11.3 - - - +
156D THR* 4.5 2.2 + - - -
318D UMP 3.6 50.7 + - + +
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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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71A PHE* 3.4 16.3 + - - +
72A VAL* 3.1 8.4 + - - +
74A ARG* 1.3 74.8 - - + +
76A TRP* 1.3 67.3 + - - +
78A ARG* 3.2 13.3 + - - +
79A HIS* 3.8 0.2 - - - -
174A ARG* 2.8 25.8 + - - +
180A GLN* 3.3 29.0 + - - +
183A ILE* 3.6 31.5 + - + +
90D ARG* 3.8 11.1 - - - +
147D ARG* 3.5 3.0 - - - +
318D UMP 3.1 62.2 + - + +
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Residues in contact with TRP 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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11A VAL* 4.3 0.7 - - + -
66A VAL* 3.9 25.4 - - + -
72A VAL* 2.9 27.0 + - + +
73A ALA* 3.4 11.9 - - - +
75A GLN* 1.3 77.3 - - - +
77A PHE* 1.3 58.4 + - + +
78A ARG 3.0 1.7 + - - -
79A HIS* 3.0 31.0 + - - +
84A TYR* 3.4 18.7 + + - -
158A PHE* 3.8 17.0 - + - -
160A TRP* 3.4 49.4 - + - -
170A PHE* 3.6 23.0 - + - -
183A ILE* 3.9 13.2 - - + +
186A TYR* 3.4 43.7 - + + -
190A ILE* 4.1 15.9 - - + -
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 2.8 36.6 + - + +
74A ARG* 4.3 4.9 - - - +
75A GLN 3.4 0.2 - - - -
76A TRP* 1.3 71.8 - - + +
78A ARG* 1.3 60.4 + - - +
79A HIS 3.0 11.9 + - - +
80A ARG* 4.6 3.8 + - - +
84A TYR* 3.6 55.6 - + + -
86A GLU* 3.4 26.2 - - + -
158A PHE* 3.6 42.6 - + + -
303A UMP 3.9 6.7 - - - -
74D ARG* 5.4 4.0 - - - +
77D PHE* 4.6 16.6 - - + +
78D ARG* 3.7 26.7 - - - -
80D ARG* 5.8 1.7 - - - +
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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