Contacts of the helix formed by residues 172 - 182 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169J ILE* 3.4 24.0 - - + -
170J PRO 2.9 3.2 + - - +
171J GLY* 1.3 72.1 - - - +
173J GLY* 1.3 60.8 + - - +
174J HIS 2.7 0.5 + - - -
175J SER* 2.6 47.4 + - - -
176J ILE* 3.3 29.2 + - + -
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Residues in contact with GLY 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J PHE 3.3 23.4 - - - +
167J GLY* 3.5 9.7 - - - -
169J ILE* 3.1 26.7 + - - -
171J GLY 3.3 2.2 - - - -
172J ILE* 1.3 82.1 - - - +
174J HIS* 1.3 61.7 + - - -
176J ILE* 3.5 5.2 + - - +
177J GLN* 3.1 17.0 + - - +
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Residues in contact with HIS 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J GLY* 4.6 5.1 + - - -
171J GLY 4.1 6.2 + - - +
172J ILE 2.7 6.5 + - - -
173J GLY* 1.3 68.4 - - - +
175J SER* 1.3 68.9 + - - +
177J GLN* 3.1 16.8 + - - +
178J THR* 3.0 33.4 + - - -
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Residues in contact with SER 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ASN* 5.4 0.5 + - - -
171J GLY 5.1 1.2 + - - -
172J ILE* 2.6 22.6 + - - -
174J HIS* 1.3 76.6 - - - +
176J ILE* 1.3 66.8 + - - -
177J GLN 2.9 0.5 + - - -
178J THR* 3.1 5.7 + - - -
179J TRP* 3.0 21.7 + - - +
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Residues in contact with ILE 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J PHE* 3.6 33.4 - - + +
169J ILE* 4.6 11.0 - - + -
172J ILE* 3.3 40.5 + - + +
173J GLY* 3.7 8.5 - - - +
175J SER* 1.3 80.3 - - - +
177J GLN* 1.3 60.6 + - - +
179J TRP* 3.4 15.8 - - + +
180J LEU* 3.2 26.0 + - + +
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Residues in contact with GLN 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I LEU 5.4 1.0 + - - -
160J THR 4.4 1.8 + - - -
163J THR* 3.1 20.8 + - - +
164J GLY* 3.0 38.1 - - - +
166J PHE* 4.8 0.9 - - - -
167J GLY* 4.2 13.6 - - - +
173J GLY 3.1 13.7 + - - +
174J HIS* 3.5 18.8 - - + +
175J SER 3.1 0.8 - - - -
176J ILE* 1.3 75.2 - - - +
178J THR* 1.3 68.3 + - - +
179J TRP 3.0 1.3 - - - -
180J LEU* 3.1 6.9 + - - +
181J LEU* 2.9 42.1 + - + +
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Residues in contact with THR 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ASN* 5.6 0.9 - - - +
40I PRO* 3.8 29.0 - - + +
174J HIS* 3.0 30.3 + - - -
175J SER* 3.6 8.5 - - - -
177J GLN* 1.3 76.1 - - - +
179J TRP* 1.3 53.4 + - - +
181J LEU* 3.3 1.5 + - - -
182J GLY* 2.7 31.7 + - - -
183J GLY 3.3 22.5 + - - +
184J PRO* 5.5 1.6 - - + +
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Residues in contact with TRP 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ILE* 3.0 49.5 + - + +
38I MET* 3.4 39.0 - - + +
39I ASN* 3.3 34.2 - - - +
175J SER 3.0 12.6 + - - +
176J ILE* 3.4 21.8 - - + +
178J THR* 1.3 75.8 - - - +
180J LEU* 1.3 95.5 + - + +
182J GLY 3.1 9.9 + - - -
193J ARG* 3.2 15.6 + - - -
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Residues in contact with LEU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I MET* 4.3 8.7 - - + -
163J THR* 4.4 17.7 - - + +
166J PHE* 4.1 31.2 - - + -
176J ILE* 3.2 12.8 + - + +
177J GLN* 3.1 9.4 + - - +
179J TRP* 1.3 109.4 - - + +
181J LEU* 1.3 57.9 + - - +
190J THR* 3.9 6.4 - - - +
193J ARG* 3.1 27.7 - - - -
194J PHE* 4.5 2.7 - - + -
503J SMA 3.3 42.0 - - + -
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Residues in contact with LEU 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J THR* 3.5 24.2 - - + +
177J GLN* 2.9 40.6 + - + +
178J THR* 3.7 0.7 - - - +
180J LEU* 1.3 78.8 - - - +
182J GLY* 1.3 62.2 + - - +
183J GLY* 2.9 25.2 + - - +
184J PRO 4.3 4.5 - - - +
185J ALA* 4.0 17.4 - - - +
186J VAL* 3.3 38.8 - - + -
187J ASP* 5.7 0.5 - - - +
189J ALA* 4.1 2.3 - - - +
190J THR* 3.0 31.1 + - + -
193J ARG* 4.4 1.6 - - - -
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Residues in contact with GLY 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I MET 3.4 14.4 - - - -
40I PRO* 3.6 20.9 - - - +
41I SER* 4.5 2.6 + - - -
44I VAL* 4.4 8.3 - - - +
178J THR 2.7 12.0 + - - -
179J TRP 3.1 4.8 + - - -
180J LEU 3.2 0.4 + - - -
181J LEU* 1.3 74.0 - - - +
183J GLY* 1.3 55.2 + - - +
189J ALA* 4.2 11.0 - - - +
193J ARG* 3.3 24.9 + - - -
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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