Contacts of the helix formed by residues 167 - 178 (chain A) in PDB entry 2X9D
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 PRO 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASN 3.7 4.2 - - - +
166A LEU* 1.3 87.3 - - + +
168A PRO* 1.3 69.3 - - + +
169A LEU 3.5 1.3 - - - +
170A LEU* 3.1 34.9 + - + +
171A ARG* 2.8 29.8 + - - +
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Residues in contact with PRO 168 (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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166A LEU 3.9 1.3 - - - +
167A PRO* 1.3 87.0 - - + +
169A LEU* 1.3 71.0 + - + +
171A ARG* 3.4 24.4 + - + +
172A GLU* 3.1 24.5 + - - +
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Residues in contact with LEU 169 (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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167A PRO* 3.5 1.0 - - - +
168A PRO* 1.3 84.6 - - + +
170A LEU* 1.4 53.4 + - - +
172A GLU* 3.5 14.2 + - + +
173A ALA* 2.8 35.0 + - - +
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Residues in contact with LEU 170 (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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166A LEU* 4.3 5.2 - - + -
167A PRO* 3.1 38.3 + - + +
169A LEU* 1.4 76.2 - - - +
171A ARG* 1.3 66.3 + - - +
172A GLU 3.1 0.2 - - - -
173A ALA* 3.2 7.5 + - + +
174A LEU* 2.9 56.0 + - + +
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Residues in contact with ARG 171 (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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166A LEU* 3.7 44.1 + - + +
167A PRO 2.8 18.6 + - - +
168A PRO* 3.6 21.1 + - - +
170A LEU* 1.3 73.3 - - - +
172A GLU* 1.3 57.2 + - - +
174A LEU* 3.6 2.1 + - - +
175A GLN* 3.1 47.5 + - + +
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Residues in contact with GLU 172 (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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168A PRO 3.1 17.3 + - - +
169A LEU* 3.8 14.4 - - - +
171A ARG* 1.3 76.7 - - - +
173A ALA* 1.3 61.8 + - - +
175A GLN* 3.5 16.6 + - + +
176A ILE* 3.2 41.2 + - + +
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Residues in contact with ALA 173 (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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169A LEU 2.8 19.2 + - - +
170A LEU* 3.2 13.7 + - + +
172A GLU* 1.3 77.3 - - - +
174A LEU* 1.3 59.9 + - + +
176A ILE* 3.1 12.9 + - - +
177A MET* 2.9 34.3 + - + +
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Residues in contact with LEU 174 (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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151A HIS* 5.9 0.2 + - - -
166A LEU* 3.7 25.4 - - + -
170A LEU* 2.9 37.5 + - + +
171A ARG 4.1 2.7 - - - +
173A ALA* 1.3 76.3 - - + +
175A GLN* 1.3 64.4 + - - +
177A MET* 4.1 16.4 - - + +
178A ASP* 3.3 25.1 + - - +
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Residues in contact with GLN 175 (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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171A ARG* 3.1 41.0 + - + +
172A GLU* 3.7 18.4 - - + +
173A ALA 3.2 0.2 - - - -
174A LEU* 1.3 78.8 - - - +
176A ILE* 1.3 53.2 + - + +
178A ASP* 3.7 3.0 + - - +
179A SER* 2.5 39.0 + - - +
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Residues in contact with ILE 176 (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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172A GLU* 3.2 31.2 + - + +
173A ALA* 3.1 11.5 + - - +
175A GLN* 1.3 76.9 - - + +
177A MET* 1.3 71.6 + - + +
179A SER* 3.8 15.0 + - - -
180A ASP* 4.5 5.7 - - - +
184A GLN* 5.0 10.4 + - - +
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Residues in contact with MET 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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151A HIS* 5.8 6.8 - - + -
173A ALA* 2.9 24.2 + - + +
174A LEU* 4.1 19.3 - - + +
175A GLN 3.4 0.6 - - - -
176A ILE* 1.3 88.6 - - + +
178A ASP* 1.3 58.9 + - - +
179A SER 3.3 1.4 + - - -
180A ASP* 3.6 17.7 - - - +
182A GLY* 4.7 4.5 + - - -
185A ALA* 3.7 30.5 - - + -
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Residues in contact with ASP 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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151A HIS* 4.5 24.8 + - - +
174A LEU 3.3 16.0 + - - +
175A GLN* 4.0 2.9 - - - +
176A ILE 3.5 0.2 - - - -
177A MET* 1.3 76.2 - - - +
179A SER* 1.3 55.7 + - - +
180A ASP* 3.1 15.9 + - - +
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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