Contacts of the helix formed by residues 176 - 183 (chain A) in PDB entry 2IMT
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 4.4 10.7 - - - +
27A VAL* 4.2 13.0 - - - -
125A TRP* 4.1 1.7 - - - -
171A ILE* 2.9 32.2 + - - +
172A ALA* 3.6 4.5 + - - -
175A GLY* 1.3 68.7 - - - -
177A TRP* 1.3 61.6 + - - -
178A VAL* 3.1 4.0 - - - -
179A ALA* 2.9 25.8 + - - +
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Residues in contact with TRP 177 (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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22A ALA* 5.6 0.2 - - - +
27A VAL* 3.3 33.3 + - + +
30A ASP* 3.5 25.7 + - + -
31A THR* 3.3 21.0 + - + +
34A VAL* 3.8 26.0 - - + -
71A MET* 3.6 20.1 - - + +
74A VAL* 3.5 19.1 - - + +
78A LEU* 3.8 22.4 - - + -
125A TRP* 3.8 24.0 - + - -
128A VAL* 3.7 21.3 - - + -
132A LEU* 4.6 6.5 - - + -
162A MET* 3.5 27.1 - - + -
171A ILE* 3.4 14.7 - - + +
176A GLY* 1.3 70.7 - - - -
178A VAL* 1.3 62.1 + - - +
180A ALA* 3.0 23.4 + - - +
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Residues in contact with VAL 178 (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 THR* 3.5 28.9 - - + -
71A MET* 4.4 6.8 - - + +
74A VAL* 4.1 7.4 - - - +
175A GLY 3.5 17.5 - - - +
176A GLY* 3.1 1.9 - - - -
177A TRP* 1.3 79.6 - - - +
179A ALA* 1.3 64.2 + - - +
181A LEU* 3.1 27.9 + - + +
182A ASN* 4.6 1.0 + - - +
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Residues in contact with ALA 179 (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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125A TRP* 4.1 14.7 + - + +
174A ARG* 3.2 28.3 - - + +
175A GLY* 4.3 3.4 - - - -
176A GLY 2.9 17.7 + - - +
178A VAL* 1.3 82.0 - - - +
180A ALA* 1.3 58.4 + - - +
181A LEU 3.5 0.5 + - - -
182A ASN* 3.6 18.9 - - - +
183A LEU* 4.6 5.2 + - - +
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Residues in contact with ALA 180 (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 VAL* 3.9 16.8 - - + -
77A GLN* 4.8 6.3 - - - +
78A LEU* 4.0 20.1 - - + +
125A TRP* 3.9 26.4 - - + -
177A TRP 3.0 16.7 + - - +
179A ALA* 1.3 72.9 - - - +
181A LEU* 1.3 62.7 + - - +
182A ASN 3.1 2.7 - - - -
183A LEU* 3.1 29.3 + - + +
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Residues in contact with LEU 181 (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 THR* 5.0 4.5 - - + -
73A GLN* 3.6 43.1 - - + +
74A VAL* 3.9 15.7 - - + -
77A GLN* 3.3 41.1 - - + +
178A VAL* 3.1 25.7 + - + +
180A ALA* 1.3 77.4 - - - +
182A ASN* 1.3 61.9 + - - +
183A LEU 3.5 2.2 + - - +
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Residues in contact with ASN 182 (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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178A VAL 4.6 1.0 + - - +
179A ALA* 3.6 15.4 + - - +
180A ALA 3.1 0.2 - - - -
181A LEU* 1.3 77.1 - - - +
183A LEU* 1.3 70.6 + - + +
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Residues in contact with LEU 183 (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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77A GLN* 4.6 5.7 - - - +
78A LEU* 4.3 15.0 - - + -
81A ILE* 4.0 40.4 - - + +
125A TRP* 3.7 49.1 - - + -
129A VAL* 5.6 0.7 - - + -
179A ALA 4.8 6.1 - - - +
180A ALA* 3.1 24.2 + - - +
181A LEU 4.3 4.5 - - - +
182A ASN* 1.3 85.1 - - + +
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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