Contacts of the helix formed by residues 172 - 182 (chain A) in PDB entry 2QJK
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 ILE 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.5 22.9 - - + -
170A PRO 3.0 3.0 + - - +
171A GLY* 1.3 70.9 - - - +
173A GLY* 1.3 65.5 + - - +
175A SER* 2.6 46.3 + - - -
176A ILE* 3.3 30.0 + - + -
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Residues in contact with GLY 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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166A PHE 3.3 23.1 - - - +
167A GLY* 3.5 8.9 - - - -
169A ILE* 3.2 25.6 + - - -
171A GLY 3.3 2.0 - - - -
172A ILE* 1.3 83.2 - - - +
174A HIS* 1.3 61.4 + - - -
176A ILE* 3.5 4.3 + - - +
177A GLN 3.1 17.0 + - - -
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Residues in contact with HIS 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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167A GLY* 4.6 5.3 + - - -
171A GLY 4.1 5.6 + - - +
172A ILE 2.7 5.3 + - - -
173A GLY* 1.3 70.1 - - - +
175A SER* 1.3 66.6 + - - +
177A GLN* 3.2 21.8 + - - -
178A THR* 3.0 39.1 + - - -
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Residues in contact with SER 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 GLY 5.1 1.4 + - - -
172A ILE* 2.6 22.6 + - - -
174A HIS* 1.3 77.4 - - - +
176A ILE* 1.3 67.4 + - - -
178A THR* 3.0 5.8 + - - -
179A TRP* 2.9 22.3 + - - +
39F ASN* 5.4 0.5 + - - -
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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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166A PHE* 3.6 33.7 - - + -
169A ILE* 4.6 11.7 - - + -
172A ILE* 3.3 40.9 + - + +
173A GLY* 3.7 8.1 - - - +
175A SER* 1.3 80.6 - - - +
177A GLN* 1.3 57.6 + - - +
179A TRP* 3.3 17.2 - - + +
180A LEU* 3.1 31.0 + - + +
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Residues in contact with GLN 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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160A THR 4.5 1.9 - - - +
163A THR* 3.0 36.3 + - - +
164A GLY* 3.5 23.0 + - - -
166A PHE* 4.8 0.9 - - - -
167A GLY* 4.0 15.0 - - - +
173A GLY 3.1 16.0 + - - +
174A HIS* 3.6 21.3 - - - +
175A SER 3.1 1.0 - - - -
176A ILE* 1.3 75.9 - - - +
178A THR* 1.3 66.3 + - - +
179A TRP 3.1 1.6 - - - -
180A LEU* 3.1 6.3 + - - +
181A LEU* 2.9 39.3 + - + +
132F LEU 5.3 0.7 - - - +
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Residues in contact with THR 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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174A HIS* 3.0 32.8 + - - -
175A SER* 3.6 8.6 - - - -
177A GLN* 1.3 76.1 - - - +
179A TRP* 1.3 52.6 + - - +
181A LEU* 3.2 3.1 + - - -
182A GLY* 2.7 32.7 + - - -
183A GLY 3.4 21.5 + - - +
184A PRO* 5.5 1.5 - - + +
39F ASN* 5.4 1.3 - - - +
40F PRO* 3.8 28.2 - - + +
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Residues in contact with TRP 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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175A SER 2.9 12.2 + - - +
176A ILE* 3.3 22.2 - - + +
178A THR* 1.3 76.5 - - - +
180A LEU* 1.3 95.5 + - + +
182A GLY 3.1 9.0 + - - -
193A ARG* 3.3 15.2 + - - -
35F ILE* 3.1 49.1 + - + +
38F MET* 3.5 37.3 - - + +
39F ASN* 3.2 33.8 - - - +
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Residues in contact with LEU 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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1A SMA 3.9 41.3 - - + -
163A THR* 4.3 17.9 - - + +
166A PHE* 4.0 34.8 - - + -
176A ILE* 3.1 13.8 + - + +
177A GLN* 3.1 9.6 + - - +
179A TRP* 1.3 109.0 - - + +
181A LEU* 1.3 58.1 + - - +
190A THR* 3.9 7.4 - - - +
193A ARG* 3.2 27.4 - - - -
194A PHE* 4.5 4.9 - - + -
38F MET* 4.6 9.6 - - + -
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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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163A THR* 3.6 23.6 - - + +
177A GLN* 2.9 39.5 + - - +
178A THR* 4.6 1.3 - - - -
180A LEU* 1.3 76.7 - - - +
182A GLY* 1.3 62.3 + - - +
183A GLY* 3.0 24.3 + - - +
184A PRO 4.4 4.3 - - - +
185A ALA* 4.0 17.6 - - - +
186A VAL* 3.2 40.8 - - + -
187A ASP* 5.7 0.5 - - - +
189A ALA* 4.1 2.1 - - - +
190A THR* 3.0 29.7 + - + -
193A ARG* 4.5 1.6 - - - -
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Residues in contact with GLY 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 THR 2.7 12.0 + - - -
179A TRP 3.1 4.9 + - - -
180A LEU 3.2 0.6 + - - -
181A LEU* 1.3 73.8 - - - +
183A GLY* 1.3 55.7 + - - +
189A ALA* 4.2 9.4 - - - +
193A ARG* 3.3 25.7 + - - -
38F MET 3.3 12.3 - - - -
39F ASN 4.5 0.2 - - - -
40F PRO* 3.5 22.5 - - - +
41F SER* 4.5 0.9 + - - -
44F VAL* 4.0 12.3 - - - +
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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