Contacts of the helix formed by residues 78 - 86 (chain A) in PDB entry 3GNI
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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LEU 3.4 4.6 + - - -
75A TYR 3.7 2.5 + - - -
76A ASN 3.5 3.0 - - - -
77A SER* 1.3 78.5 + - - +
79A LEU* 1.3 59.0 + - - +
80A LEU 3.3 2.7 - - - -
81A SER* 3.2 11.8 + - - -
82A THR* 3.1 28.1 + - - -
119A TYR* 3.5 19.7 - - - -
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Residues in contact with LEU 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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16A VAL* 3.7 33.9 - - + +
19A LEU* 4.2 7.6 - - + -
20A LYS* 4.1 29.8 - - + +
23A MET* 4.5 7.6 - - + -
50A MET* 4.2 12.6 - - + -
74A LEU* 3.6 25.6 + - + -
77A SER* 3.2 13.2 + - - +
78A GLY* 1.3 73.4 - - - +
80A LEU* 1.3 60.4 + - - +
81A SER 3.1 1.8 - - - -
82A THR* 3.6 20.9 - - + +
83A LEU* 2.8 51.9 + - + +
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Residues in contact with LEU 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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74A LEU* 4.1 37.0 + - + +
75A TYR* 3.9 33.7 - - + -
78A GLY 3.3 0.2 - - - -
79A LEU* 1.3 79.7 - - - +
81A SER* 1.3 58.4 + - - +
83A LEU* 4.7 8.1 - - + +
84A VAL* 3.4 26.5 + - - +
101A ILE* 5.2 4.3 - - + -
102A PHE* 4.0 33.1 - - + -
105A ILE* 4.2 18.2 - - + -
116A THR* 4.7 5.8 - - + -
119A TYR* 4.1 23.3 - - + +
120A ILE* 6.3 1.6 - - + -
126A ILE* 4.3 4.1 - - + +
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Residues in contact with SER 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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78A GLY* 3.2 12.0 + - - -
79A LEU 3.1 0.4 - - - -
80A LEU* 1.3 78.7 - - - +
82A THR* 1.3 59.2 + - - +
84A VAL* 3.3 4.0 + - - +
85A ALA* 2.9 29.9 + - - +
119A TYR* 4.6 3.6 + - - -
123A GLN* 4.3 18.3 + - - +
126A ILE* 3.9 26.5 - - - +
129A MET* 3.8 9.2 - - - +
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Residues in contact with THR 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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23A MET* 4.3 18.4 - - + -
27A GLU* 3.7 9.2 - - - +
77A SER 5.1 1.4 + - - -
78A GLY 3.1 17.9 + - - -
79A LEU* 3.3 18.1 + - + +
81A SER* 1.3 77.4 - - - +
83A LEU* 1.3 57.3 + - - +
85A ALA* 3.8 5.3 - - - -
86A ASP* 2.9 53.7 + - - +
-15B ALA 6.0 0.9 - - - +
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Residues in contact with LEU 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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19A LEU* 4.4 11.4 - - + -
23A MET* 3.9 31.6 - - + -
47A LEU* 4.2 27.4 - - + -
50A MET* 5.5 2.5 - - - -
74A LEU* 5.0 7.9 - - + -
79A LEU* 2.8 41.5 + - + +
80A LEU* 4.7 9.0 - - + +
82A THR* 1.3 70.1 - - - +
84A VAL* 1.3 61.5 + - + +
86A ASP* 3.8 0.6 - - - -
87A LEU* 3.0 33.3 + - - +
90A ILE* 4.2 14.1 - - + +
98A VAL* 4.0 21.8 - - + -
101A ILE* 5.5 6.7 - - + -
102A PHE* 6.5 0.2 - - + -
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Residues in contact with VAL 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 LEU 3.4 16.3 + - - +
81A SER 3.3 7.7 + - - +
83A LEU* 1.3 78.9 - - - +
85A ALA* 1.3 63.2 + - - +
86A ASP 3.3 0.9 + - - -
87A LEU* 3.3 20.8 + - + +
98A VAL* 5.2 2.2 - - + -
102A PHE* 3.8 25.6 - - + -
126A ILE* 4.0 10.5 - - + +
129A MET* 3.8 31.9 - - + +
130A LEU* 3.8 31.9 - - + +
139A ILE* 5.9 1.2 - - - +
143A CYS* 5.7 2.3 - - - -
146A MET* 4.4 7.4 - - + -
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Residues in contact with ALA 85 (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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81A SER* 2.9 18.8 + - - +
82A THR* 3.8 7.2 - - - +
84A VAL* 1.3 77.1 - - - +
86A ASP* 1.3 64.8 + - - +
87A LEU 3.5 0.2 - - - -
88A GLN* 5.2 2.1 + - - +
129A MET* 3.5 27.1 - - + +
-15B ALA 4.4 13.9 - - - +
-14B HIS* 3.5 19.9 + - + -
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Residues in contact with ASP 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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23A MET* 3.1 25.2 - - + +
27A GLU* 2.3 37.2 - - - +
82A THR* 2.9 26.8 + - - +
83A LEU 3.8 1.6 - - - +
85A ALA* 1.3 78.3 - - - +
87A LEU* 1.3 54.8 + - - +
88A GLN 3.1 3.4 - - - -
89A LEU* 2.7 41.9 + - + +
90A ILE* 3.9 4.9 + - - +
-15B ALA 4.0 6.7 + - - -
-14B HIS* 3.4 26.0 - - - +
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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