Contacts of the helix formed by residues 172 - 182 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169G ILE* 3.4 22.9 - - + -
170G PRO 3.0 2.6 + - - +
171G GLY* 1.3 72.8 - - - +
173G GLY* 1.3 65.1 + - - +
174G HIS 2.7 0.2 + - - -
175G SER* 2.6 46.2 + - - -
176G ILE* 3.3 30.5 + - + -
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Residues in contact with GLY 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G PHE 3.3 23.8 - - - +
167G GLY* 3.5 9.9 - - - -
169G ILE* 3.2 27.2 + - - -
171G GLY 3.4 0.6 - - - -
172G ILE* 1.3 82.4 - - - +
174G HIS* 1.3 60.2 + - - -
176G ILE* 3.5 4.1 + - - +
177G GLN 3.1 16.6 + - - -
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Residues in contact with HIS 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G GLY* 4.6 5.4 + - - -
169G ILE 4.7 0.2 + - - -
171G GLY 4.2 6.0 + - - +
172G ILE 2.7 6.4 + - - +
173G GLY* 1.3 68.6 - - - +
175G SER* 1.3 69.0 + - - +
177G GLN* 3.1 16.1 + - - +
178G THR* 2.9 39.0 + - - -
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Residues in contact with SER 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G GLY 5.1 1.2 + - - -
172G ILE* 2.6 22.8 + - - -
174G HIS* 1.3 75.9 - - - +
176G ILE* 1.3 66.1 + - - -
177G GLN 2.9 0.3 + - - -
178G THR* 3.0 6.2 + - - -
179G TRP* 3.0 22.3 + - - +
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Residues in contact with ILE 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G PHE* 3.7 33.4 - - + -
169G ILE* 4.6 11.7 - - + -
172G ILE* 3.3 39.4 + - + +
173G GLY* 3.7 8.5 - - - +
175G SER* 1.3 79.1 - - - +
177G GLN* 1.3 60.9 + - - +
179G TRP* 3.3 17.0 - - + +
180G LEU* 3.1 26.5 + - + +
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Residues in contact with GLN 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G THR 4.4 2.4 + - - -
163G THR* 2.9 41.6 + - - +
164G GLY* 3.6 18.9 - - - +
166G PHE* 4.8 0.7 - - - -
167G GLY* 3.9 13.8 - - - +
173G GLY 3.1 13.8 + - - +
174G HIS* 3.5 19.3 - - + +
175G SER 2.9 1.2 + - - -
176G ILE* 1.3 75.4 - - - +
178G THR* 1.3 67.7 + - - +
179G TRP 3.0 1.1 - - - -
180G LEU* 3.0 6.9 + - + +
181G LEU* 2.9 40.8 + - + +
132L LEU 5.3 1.0 + - - -
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Residues in contact with THR 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G HIS* 2.9 31.5 + - - -
175G SER* 3.6 8.5 - - - -
177G GLN* 1.3 75.6 - - - +
179G TRP* 1.3 51.7 + - - +
181G LEU* 3.2 2.5 + - - -
182G GLY* 2.7 32.4 + - - -
183G GLY 3.4 21.1 + - - +
184G PRO* 5.0 1.2 - - + +
39L ASN* 5.6 1.1 - - - +
40L PRO* 3.8 28.3 - - + +
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Residues in contact with TRP 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G SER 3.0 11.3 + - - +
176G ILE* 3.3 22.4 - - + +
178G THR* 1.3 76.4 - - - +
180G LEU* 1.3 98.5 + - + +
182G GLY 3.1 9.2 + - - -
193G ARG* 3.3 14.6 + - - -
35L ILE* 3.3 43.9 + - + +
38L MET* 3.5 35.0 - - + +
39L ASN* 3.2 35.8 - - - +
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Residues in contact with LEU 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G THR* 4.4 20.6 - - + +
166G PHE* 4.0 33.9 - - + -
176G ILE* 3.1 13.2 + - + +
177G GLN* 3.0 8.8 + - - +
179G TRP* 1.3 107.7 - - + +
181G LEU* 1.3 57.3 + - - +
190G THR* 3.9 6.2 - - - +
193G ARG* 3.0 29.2 - - - -
194G PHE* 4.6 4.3 - - + -
503G SMA 3.7 40.8 - - + -
38L MET* 4.6 7.9 - - + -
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Residues in contact with LEU 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G THR* 3.6 24.0 - - + +
177G GLN* 2.9 40.6 + - - +
178G THR* 3.7 1.6 - - - +
180G LEU* 1.3 75.1 - - - +
182G GLY* 1.3 62.2 + - - +
183G GLY* 2.9 24.3 + - - +
184G PRO 4.3 4.5 - - - +
185G ALA* 3.9 18.4 - - - +
186G VAL* 3.3 40.8 - - + +
187G ASP* 5.7 0.3 - - - +
189G ALA* 4.1 1.7 - - - +
190G THR* 3.0 31.1 + - + -
193G ARG* 4.4 1.8 - - - -
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Residues in contact with GLY 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G THR 2.7 12.8 + - - -
179G TRP 3.1 4.4 + - - -
180G LEU 3.2 0.6 + - - -
181G LEU* 1.3 74.3 - - - +
183G GLY* 1.3 56.0 + - - +
189G ALA* 4.2 8.5 - - - +
193G ARG* 3.3 25.5 + - - -
38L MET 3.5 12.8 - - - -
40L PRO* 3.6 21.6 - - - +
41L SER* 4.6 0.9 + - - -
44L VAL* 3.9 13.5 - - - +
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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