Contacts of the helix formed by residues 164 - 179 (chain D) in PDB entry 2GL7
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 ASP 164 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ASP* 3.2 18.1 + - - +
163D GLU* 1.3 76.1 - - - +
165D GLN* 1.3 64.6 + - - +
166D VAL 3.3 7.8 + - - -
167D VAL* 3.4 14.4 + - + +
168D VAL* 3.3 21.5 + - - +
355F GLN* 5.0 7.3 - - - +
358F HIS* 5.2 9.0 - - + +
359F ARG* 3.2 55.5 + - - +
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Residues in contact with GLN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASP 3.7 11.8 - - - +
163D GLU* 3.2 20.2 + - - +
164D ASP* 1.3 71.9 + - - +
166D VAL* 1.3 65.2 + - - +
167D VAL 3.2 0.2 - - - -
168D VAL* 3.4 18.5 + - - +
169D ASN* 3.2 22.0 + - - +
204D ASN* 5.5 4.4 + - - +
205D THR* 4.9 17.8 + - - +
206D ASN 5.3 2.4 - - - +
207D ASP* 6.1 0.9 - - - +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ASP* 3.3 1.8 + - - +
165D GLN* 1.3 75.6 - - + +
167D VAL* 1.3 63.8 + - - +
169D ASN* 3.5 10.4 + - - +
170D LYS* 3.2 21.5 + - + +
359F ARG* 3.5 37.0 - - - +
363F LEU* 4.5 13.0 - - + -
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 3.7 36.8 - - + +
162D ASP* 3.3 27.8 - - - +
164D ASP* 3.4 19.3 + - + +
165D GLN 3.2 0.6 - - - -
166D VAL* 1.3 76.2 - - - +
168D VAL* 1.3 63.8 + - - +
170D LYS* 3.3 7.7 + - - +
171D ALA* 3.2 21.3 + - - +
359F ARG* 4.4 19.3 - - - +
362F SER* 4.0 16.8 - - - -
363F LEU* 4.6 7.9 - - + +
366F LEU* 3.8 7.8 - - + +
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Residues in contact with VAL 168 (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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159D LEU 3.6 13.2 - - - +
160D LEU* 3.4 21.1 - - + +
162D ASP 3.2 27.1 - - - +
164D ASP 3.3 8.6 + - - +
165D GLN* 3.6 24.9 - - - +
166D VAL 3.3 0.4 - - - -
167D VAL* 1.3 77.9 - - - +
169D ASN* 1.3 56.6 + - - +
171D ALA* 3.4 3.9 + - - +
172D ALA* 2.9 26.3 + - - +
201D THR* 3.6 30.5 - - + -
205D THR* 5.5 0.4 - - - +
210D THR* 4.3 7.4 - - + -
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Residues in contact with ASN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLN 3.2 14.0 + - - +
166D VAL* 3.8 11.2 + - - +
167D VAL 3.3 0.2 - - - -
168D VAL* 1.3 76.5 - - - +
170D LYS* 1.3 69.0 + - - +
172D ALA* 3.4 1.3 + - - +
173D VAL* 3.2 24.8 + - - +
207D ASP* 3.0 21.9 - - + +
209D GLU* 2.7 33.9 + - - +
210D THR* 3.1 21.8 + - - +
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Residues in contact with LYS 170 (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 VAL* 3.2 12.3 + - + +
167D VAL* 3.6 9.6 - - - +
168D VAL 3.3 0.4 - - - -
169D ASN* 1.3 83.8 - - - +
171D ALA* 1.3 62.7 + - - +
173D VAL* 3.7 5.6 + - - +
174D MET* 3.4 27.0 + - + +
363F LEU* 4.8 13.7 - - + -
366F LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 171 (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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156D LEU* 4.5 7.0 - - + +
159D LEU* 4.1 17.0 - - + -
160D LEU* 4.4 16.8 - - + +
167D VAL 3.2 12.9 + - - +
168D VAL 3.7 4.7 - - - +
170D LYS* 1.3 77.5 - - - +
172D ALA* 1.3 59.3 + - - +
174D MET* 3.3 3.4 + - - +
175D VAL* 2.9 36.3 + - + +
366F LEU* 4.0 22.1 - - + +
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Residues in contact with ALA 172 (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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160D LEU* 4.2 13.2 - - + -
168D VAL 2.9 18.0 + - - +
169D ASN* 3.6 6.7 - - - +
170D LYS 3.3 0.4 - - - -
171D ALA* 1.3 78.6 - - - +
173D VAL* 1.3 60.3 + - - +
175D VAL* 3.5 5.2 + - - +
176D HIS* 3.2 16.6 + - - +
210D THR* 3.8 31.4 - - + +
213D CYS* 3.5 17.6 - - + +
214D THR* 4.5 7.7 + - + +
217D THR* 4.9 0.3 + - - -
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Residues in contact with VAL 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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169D ASN* 3.2 16.9 + - - +
170D LYS* 3.9 6.5 - - - +
172D ALA* 1.3 75.6 - - + +
174D MET* 1.3 63.7 + - - +
176D HIS* 3.3 4.3 + - - +
177D GLN* 3.1 36.5 + - + +
209D GLU* 3.8 31.6 - - + +
210D THR* 6.4 0.2 - - - -
213D CYS* 3.9 19.1 - - - -
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Residues in contact with MET 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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156D LEU* 4.4 16.8 - - + -
170D LYS* 3.4 12.0 + - + +
171D ALA* 3.3 9.3 + - - +
173D VAL* 1.3 81.0 - - - +
175D VAL* 1.3 59.2 + - + +
177D GLN* 3.4 7.8 + - + +
178D LEU* 3.1 45.0 + - + +
366F LEU* 3.4 57.4 - - + +
369F ILE* 4.8 5.4 - - - +
370F GLN* 4.7 17.7 - - + -
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LEU* 3.9 27.6 - - + +
160D LEU* 4.7 5.8 - - + -
171D ALA 2.9 21.8 + - - +
172D ALA* 4.0 5.8 - - - +
173D VAL 3.3 0.2 - - - -
174D MET* 1.3 75.6 - - - +
176D HIS* 1.3 57.7 + - - +
178D LEU* 3.5 9.0 + - + +
179D SER* 3.2 24.8 + - - -
188D ILE* 3.8 10.2 - - + +
194D MET* 3.7 33.4 - - + -
198D ILE* 3.9 19.7 - - + -
217D THR* 4.1 9.9 - - + +
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Residues in contact with HIS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ALA 3.2 12.1 + - - +
173D VAL 3.6 8.1 - - - +
174D MET 3.3 0.2 - - - -
175D VAL* 1.3 75.8 - - - +
177D GLN* 1.3 67.0 + - - +
179D SER* 2.7 22.6 + - - -
180D LYS* 3.2 39.8 + - - +
212D ARG* 4.0 23.7 + - - -
213D CYS* 3.4 23.3 - - + +
216D GLY* 3.4 17.4 + - - -
217D THR* 3.3 34.9 + - - +
220D ASN* 4.0 7.4 + - - -
254D TYR* 4.4 10.7 + - - -
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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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173D VAL* 3.1 31.4 + - + +
174D MET* 3.4 11.9 + - + +
176D HIS* 1.3 79.0 + - - +
178D LEU* 1.3 66.4 + - + +
180D LYS* 3.3 46.2 + - - +
181D LYS* 4.0 12.6 + - - +
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Residues in contact with LEU 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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149D ALA* 4.6 13.5 - - + +
152D ALA* 5.8 3.4 - - + -
153D ILE* 5.0 8.3 - - + -
156D LEU* 4.0 24.2 - - + -
174D MET* 3.1 34.5 + - + +
175D VAL* 3.7 9.9 - - - +
176D HIS 3.3 0.4 - - - -
177D GLN* 1.3 80.5 - - + +
179D SER* 1.3 61.4 + - - +
180D LYS 3.1 1.8 + - - -
181D LYS* 3.3 10.5 + - - +
184D SER* 2.6 45.6 + - - +
185D ARG 3.5 1.2 + - - -
188D ILE* 3.9 13.5 - - + -
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Residues in contact with SER 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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175D VAL 3.2 12.4 + - - -
176D HIS* 2.7 25.5 + - - -
178D LEU* 1.3 76.2 - - - +
180D LYS* 1.3 57.4 + - - +
181D LYS 4.2 1.1 - - - -
185D ARG* 3.1 35.6 + - - +
188D ILE* 4.0 10.5 - - - +
217D THR* 3.7 22.8 - - - -
220D ASN* 3.2 28.5 + - - +
221D LEU* 5.4 1.6 - - - -
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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