Contacts of the helix formed by residues 178 - 183 (chain A) in PDB entry 2IB8
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 LEU 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.7 4.6 - - + +
97A GLY* 4.7 12.1 - - - +
159A VAL* 3.6 11.7 - - + -
160A PRO* 3.3 36.0 + - + +
162A VAL* 3.5 42.8 - - + -
176A GLU 3.6 1.0 + - - -
177A ASP* 1.3 70.5 + - - +
179A ILE* 1.3 65.8 + - - +
181A LYS* 4.2 7.4 - - + +
182A ASP* 2.9 40.7 + - + +
183A GLY 3.3 4.0 + - - -
97B GLY* 4.3 11.0 - - - -
98B GLY* 3.4 27.1 - - - +
162B VAL* 4.8 1.6 - - + -
178B LEU* 5.3 0.2 - - + -
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Residues in contact with ILE 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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55A PHE* 3.7 20.2 - - + -
95A LEU* 4.3 11.2 - - + -
156A MET* 3.5 37.7 - - + +
159A VAL* 3.7 17.6 - - + +
177A ASP* 3.0 9.3 + - - +
178A LEU* 1.3 76.0 - - - +
180A VAL* 1.3 58.2 + - - +
183A GLY* 3.0 27.4 + - - -
184A LEU* 3.1 18.5 + - + +
286A LEU* 4.0 12.8 - - + -
165B ARG* 3.5 23.6 - - - +
170C TYR* 3.6 22.7 - - + +
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Residues in contact with VAL 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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177A ASP* 3.0 20.4 + - + +
179A ILE* 1.3 77.4 - - - +
181A LYS* 1.3 60.4 + - - +
184A LEU* 3.5 7.9 + - + -
185A THR* 2.7 46.1 + - - +
192A HIS* 5.4 11.0 - - + -
170C TYR* 3.5 35.9 - - + +
171C GLY* 4.2 10.5 - - - +
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Residues in contact with LYS 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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162A VAL* 4.6 5.2 - - + +
164A ASN* 4.2 16.8 + - - +
176A GLU* 3.2 47.4 + - + +
177A ASP 2.8 20.7 + - - +
178A LEU* 4.4 7.9 - - + -
180A VAL* 1.3 75.4 - - - +
182A ASP* 1.3 68.5 + - - +
185A THR* 4.2 14.5 - - - +
98B GLY* 3.2 37.0 + - - +
100B GLY* 3.7 15.4 - - - +
101B GLN 3.7 3.3 + - - -
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Residues in contact with ASP 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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94A VAL* 4.7 8.6 - - + +
95A LEU* 3.7 15.5 - - + +
125A VAL* 4.9 0.3 - - - +
178A LEU* 2.9 24.8 + - - +
181A LYS* 1.3 79.8 - - - +
183A GLY* 1.3 62.4 + - - +
96B GLN 3.6 4.5 - - - +
97B GLY* 3.5 8.5 - - - -
98B GLY* 2.8 31.7 + - - -
100B GLY* 2.9 36.5 + - - +
101B GLN* 3.3 24.9 - - - +
102B ALA 4.6 0.5 + - - -
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Residues in contact with GLY 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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94A VAL* 5.0 0.9 - - - -
95A LEU* 3.8 14.1 - - - +
125A VAL* 4.1 7.6 - - - +
126A CYS* 5.6 0.9 - - - -
178A LEU 3.3 1.8 + - - -
179A ILE* 3.0 14.5 + - - -
182A ASP* 1.3 81.0 - - - +
184A LEU* 1.3 69.4 + - - +
193A MET* 3.9 3.5 - - - +
387A ILE* 4.4 15.0 - - - +
101B GLN* 2.9 19.7 + - - -
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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