Contacts of the helix formed by residues 172 - 182 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D ILE* 3.5 22.7 - - + -
170D PRO 3.0 3.0 + - - +
171D GLY* 1.3 71.1 - - - +
173D GLY* 1.3 64.6 + - - +
174D HIS 2.7 0.2 + - - -
175D SER* 2.6 46.5 + - - -
176D ILE* 3.3 30.4 + - + -
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Residues in contact with GLY 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE 3.3 23.1 - - - +
167D GLY* 3.6 6.0 - - - -
169D ILE* 3.2 25.6 + - - -
171D GLY 3.3 2.6 - - - -
172D ILE* 1.3 81.9 - - - +
174D HIS* 1.3 60.1 + - - -
176D ILE* 3.5 4.3 + - - +
177D GLN* 3.1 20.4 + - - +
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Residues in contact with HIS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLY* 4.6 3.7 + - - -
171D GLY 4.1 5.7 + - - +
172D ILE 2.7 5.7 + - - -
173D GLY* 1.3 69.2 - - - +
175D SER* 1.3 67.0 + - - +
177D GLN* 3.2 20.0 + - + +
178D THR* 3.0 42.6 + - - -
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Residues in contact with SER 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASN* 5.5 0.3 + - - -
171D GLY 5.1 1.2 + - - -
172D ILE* 2.6 21.9 + - - -
174D HIS* 1.3 76.5 + - - +
176D ILE* 1.3 65.8 + - - -
177D GLN 3.0 0.7 + - - -
178D THR* 3.0 5.8 + - - -
179D TRP* 2.9 24.2 + - - +
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Residues in contact with ILE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.6 34.3 - - + -
169D ILE* 4.6 10.8 - - + -
172D ILE* 3.3 39.6 + - + +
173D GLY* 3.7 9.4 - - - +
175D SER* 1.3 80.5 - - - +
177D GLN* 1.3 57.3 + - - +
179D TRP* 3.4 16.5 - - + +
180D LEU* 3.1 30.4 + - + +
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Residues in contact with GLN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU 5.1 1.6 + - - -
160D THR 5.0 0.8 + - - -
163D THR* 3.4 20.8 + - - +
164D GLY* 3.1 35.0 + - - +
166D PHE* 4.8 0.7 - - - -
167D GLY* 3.8 15.4 - - - +
173D GLY 3.1 11.9 + - - +
174D HIS* 3.4 22.9 - - - +
175D SER 3.0 0.8 + - - -
176D ILE* 1.3 75.8 - - - +
178D THR* 1.3 67.0 + - - +
179D TRP 3.1 1.1 - - - -
180D LEU* 3.1 7.1 + - - +
181D LEU* 3.0 39.7 + - + +
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Residues in contact with THR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASN* 5.5 1.3 - - - +
40C PRO* 3.8 25.9 - - + +
174D HIS* 3.0 35.9 + - - -
175D SER* 3.6 9.3 - - - -
177D GLN* 1.3 74.6 - - - +
179D TRP* 1.3 53.5 + - - +
181D LEU* 3.3 2.2 + - - -
182D GLY* 2.8 32.1 + - - -
183D GLY 3.4 23.6 + - - +
184D PRO* 5.5 1.5 - - + +
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Residues in contact with TRP 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.2 47.5 + - + +
38C MET* 3.4 36.9 - - + +
39C ASN* 3.3 34.4 - - - +
175D SER 2.9 12.4 + - - +
176D ILE* 3.4 21.8 - - + +
178D THR* 1.3 76.8 - - - +
180D LEU* 1.3 96.0 + - + +
182D GLY 3.1 9.2 + - - -
193D ARG* 3.2 15.6 + - - -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C MET* 4.6 9.2 - - + -
2D SMA 3.8 37.2 - - + -
163D THR* 4.3 18.6 - - + +
166D PHE* 4.0 34.8 - - + -
176D ILE* 3.1 15.2 + - + +
177D GLN* 3.1 9.2 + - - +
179D TRP* 1.3 106.9 - - + +
181D LEU* 1.3 58.7 + - - +
190D THR* 3.9 6.4 - - - +
193D ARG* 3.1 27.7 - - - -
194D PHE* 4.5 2.8 - - + -
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D THR* 3.5 26.2 - - + +
177D GLN* 3.0 34.1 + - + +
178D THR* 4.7 0.9 - - - -
180D LEU* 1.3 77.5 - - - +
182D GLY* 1.3 62.0 + - - +
183D GLY* 3.0 25.5 + - - +
184D PRO 4.4 4.3 - - - +
185D ALA* 4.0 18.4 - - - +
186D VAL* 3.2 40.8 - - + +
187D ASP* 5.7 0.5 - - - +
189D ALA* 4.1 1.9 - - - +
190D THR* 3.0 30.3 + - + -
193D ARG* 4.4 1.8 - - - -
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C MET 3.4 12.8 - - - -
40C PRO* 3.5 22.2 - - - +
41C SER* 4.5 0.9 + - - -
44C VAL* 3.9 13.3 - - - +
178D THR 2.8 8.4 + - - -
179D TRP 3.1 4.8 + - - -
180D LEU 3.2 0.4 + - - -
181D LEU* 1.3 77.2 - - - +
183D GLY* 1.3 55.9 + - - +
189D ALA* 4.2 7.7 - - - +
193D ARG* 3.2 26.2 + - - -
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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