Contacts of the helix formed by residues 172 - 182 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169P ILE* 3.4 25.1 - - + -
170P PRO 2.9 3.9 + - - +
171P GLY* 1.3 72.7 - - - +
173P GLY* 1.3 62.0 + - - +
174P HIS 2.7 0.7 + - - -
175P SER* 2.6 46.9 + - - -
176P ILE* 3.3 28.5 + - + -
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Residues in contact with GLY 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P PHE 3.3 23.6 - - - +
167P GLY* 3.6 9.8 - - - -
169P ILE* 3.1 27.2 + - - -
171P GLY 3.4 0.4 - - - -
172P ILE* 1.3 82.4 - - - +
174P HIS* 1.3 59.5 + - - +
176P ILE* 3.5 4.5 + - - +
177P GLN 3.1 17.7 + - - -
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Residues in contact with HIS 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P GLY* 4.6 5.5 + - - -
171P GLY 4.2 6.2 + - - +
172P ILE 2.7 5.9 + - - -
173P GLY* 1.3 69.1 - - - +
175P SER* 1.3 69.7 + - - +
177P GLN* 3.1 18.0 + - + +
178P THR* 2.9 40.0 + - - -
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Residues in contact with SER 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ASN* 5.6 0.3 + - - -
171P GLY 5.1 1.6 + - - -
172P ILE* 2.6 22.9 + - - -
174P HIS* 1.3 77.6 + - - +
176P ILE* 1.3 66.2 + - - -
177P GLN 3.0 0.2 + - - -
178P THR* 3.1 5.7 + - - -
179P TRP* 3.0 22.3 + - - +
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Residues in contact with ILE 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P PHE* 3.7 33.7 - - + +
169P ILE* 4.6 11.0 - - + -
172P ILE* 3.3 40.7 + - + +
173P GLY* 3.7 9.0 - - - +
175P SER* 1.3 80.1 - - - +
177P GLN* 1.3 62.0 + - - +
179P TRP* 3.4 16.2 - - + +
180P LEU* 3.2 25.9 + - + +
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Residues in contact with GLN 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O LEU 5.2 1.0 + - - -
160P THR 4.4 1.8 + - - -
163P THR* 3.3 22.0 + - - +
164P GLY* 3.1 35.4 - - - +
166P PHE* 4.8 0.7 - - - -
167P GLY* 3.8 14.9 - - - +
173P GLY 3.1 13.5 + - - +
174P HIS* 3.5 19.9 - - + +
175P SER 3.1 1.0 - - - -
176P ILE* 1.3 74.4 - - - +
178P THR* 1.3 69.6 + - - +
179P TRP 3.0 1.3 - - - -
180P LEU* 3.0 7.3 + - - +
181P LEU* 2.9 39.8 + - + +
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Residues in contact with THR 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ASN* 5.7 0.7 - - - +
40O PRO* 3.8 26.1 - - + +
174P HIS* 2.9 34.0 + - - -
175P SER* 3.6 8.5 - - - -
177P GLN* 1.3 75.4 - - - +
179P TRP* 1.3 52.7 + - - +
181P LEU* 3.3 2.9 + - - -
182P GLY* 2.7 31.9 + - - -
183P GLY 3.4 24.3 + - - +
184P PRO* 5.5 1.0 - - + +
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Residues in contact with TRP 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ILE* 3.2 44.8 + - + +
38O MET* 3.4 39.7 - - + +
39O ASN* 3.3 34.0 - - - +
175P SER 3.0 12.0 + - - +
176P ILE* 3.4 19.7 - - + +
178P THR* 1.3 76.9 - - - +
180P LEU* 1.3 99.1 + - + +
182P GLY 3.0 9.7 + - - -
193P ARG* 3.3 15.2 + - - -
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Residues in contact with LEU 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O MET* 4.4 10.5 - - + -
163P THR* 4.4 15.3 - - + -
166P PHE* 4.1 31.2 - - + -
176P ILE* 3.2 13.2 + - + +
177P GLN* 3.0 9.4 + - - +
179P TRP* 1.3 107.8 - - + +
181P LEU* 1.3 58.8 + - - +
190P THR* 3.8 6.8 - - - +
193P ARG* 3.1 28.2 - - - -
194P PHE* 4.6 3.5 - - + -
503P SMA 3.6 40.6 - - + -
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Residues in contact with LEU 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P THR* 3.5 26.2 - - + +
177P GLN* 2.9 36.6 + - + +
178P THR* 3.7 1.3 - - - +
180P LEU* 1.3 76.8 - - - +
182P GLY* 1.3 63.3 + - - +
183P GLY* 3.0 25.0 + - - +
184P PRO 4.3 4.0 - - - +
185P ALA* 4.0 19.2 - - - +
186P VAL* 3.3 38.8 - - + +
187P ASP* 5.7 0.2 - - - +
189P ALA* 4.2 1.7 - - - +
190P THR* 2.9 31.7 + - + -
193P ARG* 4.4 1.6 - - - -
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Residues in contact with GLY 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O MET 3.5 13.0 - - - -
39O ASN 4.8 0.2 - - - +
40O PRO* 3.6 21.9 - - - +
41O SER* 4.5 2.1 + - - -
44O VAL* 4.0 9.4 - - - +
178P THR 2.7 12.4 + - - -
179P TRP 3.0 4.6 + - - -
180P LEU 3.2 0.4 - - - -
181P LEU* 1.3 74.0 - - - +
183P GLY* 1.3 56.2 + - - +
189P ALA* 4.3 11.4 - - - +
193P ARG* 3.3 25.7 + - - -
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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