Contacts of the helix formed by residues 79 - 87 (chain A) in PDB entry 3IH9
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU 2.9 22.5 + - - -
76A VAL 4.5 1.3 - - - -
77A ASP 3.7 1.2 - - - -
78A ARG* 1.3 82.7 - - - +
80A PHE* 1.3 65.4 + - - -
81A ALA 3.5 2.2 - - - -
82A ALA 3.7 0.3 + - - -
83A VAL* 3.4 21.6 + - - +
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Residues in contact with PHE 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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75A LEU* 3.7 24.9 - - + -
79A GLY* 1.3 70.9 - - - -
81A ALA* 1.3 61.4 + - - +
83A VAL* 3.3 1.0 + - - -
84A ASP* 2.8 41.5 + - - +
228A ILE* 3.4 44.9 - - + -
229A VAL* 4.1 14.8 - - + -
232A ARG* 3.4 51.1 - - + -
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Residues in contact with ALA 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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79A GLY 3.5 0.6 - - - -
80A PHE* 1.3 78.0 - - - +
82A ALA* 1.3 61.3 + - - +
84A ASP* 4.0 4.8 - - - +
85A ARG* 3.2 40.8 + - + +
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Residues in contact with ALA 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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78A ARG* 3.6 43.4 + - + +
79A GLY 3.7 1.8 + - - -
80A PHE 3.3 0.2 - - - -
81A ALA* 1.3 79.5 - - - +
83A VAL* 1.3 63.1 + - - +
85A ARG* 3.7 34.6 + - - +
86A GLN* 3.7 16.3 - - - +
123A LEU* 3.9 7.5 - - + +
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Residues in contact with VAL 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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71A TYR* 3.8 32.1 - - + -
74A ALA* 3.6 35.7 - - + +
75A LEU* 3.9 12.1 - - + -
78A ARG* 4.3 6.7 - - + -
79A GLY 3.4 16.8 + - - +
80A PHE 3.3 4.1 + - - +
82A ALA* 1.3 73.9 - - - +
84A ASP* 1.3 65.5 + - - +
86A GLN* 3.0 3.6 + - - -
87A VAL* 2.7 34.0 + - + +
120A VAL* 5.2 0.7 - - + -
123A LEU* 4.1 20.0 - - + -
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Residues in contact with ASP 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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71A TYR* 4.7 1.4 + - - -
75A LEU* 4.9 0.2 - - - +
80A PHE* 2.8 34.6 + - - +
81A ALA* 4.0 4.6 - - - +
83A VAL* 1.3 76.9 - - - +
85A ARG* 1.3 56.3 + - - +
87A VAL 3.2 18.5 - - - +
89A LEU* 4.8 6.9 - - - +
107A ARG* 2.5 34.1 + - - +
232A ARG* 3.0 41.6 + - - -
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Residues in contact with ARG 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 ALA* 3.2 26.9 + - - +
82A ALA* 3.7 37.9 + - - +
83A VAL 3.2 0.8 - - - -
84A ASP* 1.3 78.5 - - - +
86A GLN* 1.3 74.6 + - - +
105A SER 4.3 7.3 - - - +
106A HIS 4.4 1.2 - - - +
107A ARG* 3.5 21.7 - - - +
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Residues in contact with GLN 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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82A ALA 3.7 13.0 - - - +
83A VAL 3.0 5.8 + - - +
85A ARG* 1.3 96.9 + - - +
87A VAL* 1.3 61.6 + - + +
106A HIS 5.0 0.6 + - - -
107A ARG* 3.2 4.5 - - - +
108A PRO* 3.1 29.8 - - - +
119A ALA* 4.6 2.2 - - + -
123A LEU* 3.9 28.7 - - + -
178A GLY 4.3 4.7 + - - +
179A VAL* 3.3 52.3 + - + +
181A GLN* 5.6 3.1 - - - +
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Residues in contact with VAL 87 (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 TYR* 4.7 5.2 + - + -
83A VAL* 2.7 30.2 + - + +
84A ASP* 3.2 27.2 + - - +
86A GLN* 1.3 82.7 - - + +
88A GLY* 1.3 68.2 + - - +
89A LEU* 5.0 1.7 - - - +
107A ARG* 4.0 1.4 + - - -
108A PRO* 4.0 3.4 - - - +
110A ASN 3.6 6.3 - - - +
111A ALA* 3.5 39.3 - - + +
116A GLY* 4.4 5.2 - - - +
119A ALA* 4.1 14.4 - - + -
120A VAL* 3.9 21.3 - - + -
123A LEU* 4.3 2.9 - - + -
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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