Contacts of the helix formed by residues 164 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.4 13.6 + - - +
163A GLU* 1.3 77.3 - - - +
165A GLN* 1.3 62.3 + - - +
166A VAL* 3.1 35.3 + - - +
167A VAL* 3.1 31.1 + - + +
168A VAL* 3.1 13.7 + - - +
355C GLN* 4.5 10.6 - - - +
358C HIS* 4.9 9.5 + - + -
359C ARG* 3.2 35.1 + - + +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP 4.1 5.7 + - - -
163A GLU* 2.6 29.0 + - - +
164A ASP* 1.3 70.4 + - - +
166A VAL* 1.3 60.6 + - + +
168A VAL* 3.7 17.8 - - - +
169A ASN* 3.0 28.2 + - - +
205A THR* 4.9 12.8 + - - -
207A ASP* 6.1 4.1 - - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.1 8.6 + - - +
165A GLN* 1.3 76.0 - - + +
167A VAL* 1.3 64.8 + - - +
169A ASN* 3.7 7.2 + - - +
170A LYS* 3.4 22.0 + - - +
359C ARG* 3.5 38.8 - - - +
363C LEU* 4.0 24.9 - - + +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 3.6 44.9 - - + +
162A ASP* 3.6 19.5 - - + +
164A ASP* 3.1 24.4 + - + +
166A VAL* 1.3 76.9 - - - +
168A VAL* 1.3 62.1 + - - +
170A LYS* 3.5 5.8 + - - +
171A ALA* 3.1 21.7 + - - +
358C HIS* 5.0 1.1 - - - +
359C ARG* 4.5 13.9 - - + +
362C SER* 3.6 23.1 - - - -
363C LEU* 5.1 4.3 - - + +
366C LEU* 4.3 6.7 - - + +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU 3.9 11.7 - - - +
160A LEU* 3.5 26.9 - - + +
162A ASP 3.2 27.8 - - - +
164A ASP 3.1 12.4 + - - +
165A GLN* 3.9 21.5 - - - +
166A VAL 3.3 0.2 - - - -
167A VAL* 1.3 72.8 - - - +
169A ASN* 1.3 66.4 + - - +
171A ALA* 3.4 3.5 + - - +
172A ALA* 3.0 23.0 + - - +
201A THR* 3.8 24.9 - - + +
205A THR* 5.8 0.9 - - - +
210A THR* 4.5 5.4 - - + -
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN 3.0 18.3 + - - +
166A VAL* 4.0 8.1 + - - +
167A VAL 3.3 0.4 - - - -
168A VAL* 1.3 76.5 - - - +
170A LYS* 1.3 67.4 + - - +
172A ALA* 3.3 2.9 + - - +
173A VAL* 3.1 30.1 + - - +
207A ASP* 3.2 22.0 - - - +
209A GLU* 2.7 33.8 + - - +
210A THR* 3.2 18.7 + - - +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL 3.4 14.0 + - - +
167A VAL* 3.9 3.8 - - - +
168A VAL 3.3 0.2 - - - -
169A ASN* 1.3 85.2 - - - +
171A ALA* 1.3 64.2 + - - +
173A VAL* 3.4 7.1 + - - +
174A MET* 3.2 26.4 + - + +
363C LEU* 4.6 17.3 - - + -
366C LEU* 4.4 17.5 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.5 6.3 - - + +
159A LEU* 4.1 12.6 - - + -
160A LEU* 4.0 31.0 - - + +
167A VAL 3.1 17.3 + - - +
168A VAL 3.7 4.3 - - - +
170A LYS* 1.3 76.5 - - - +
172A ALA* 1.3 56.9 + - - +
174A MET* 3.5 3.0 + - - +
175A VAL* 3.0 33.1 + - - +
366C LEU* 4.1 16.7 - - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.7 16.8 - - + -
168A VAL 3.0 17.4 + - - +
169A ASN 3.7 4.0 - - - +
171A ALA* 1.3 75.5 - - - +
173A VAL* 1.3 65.4 + - - +
174A MET 3.2 0.2 - - - -
175A VAL* 3.5 5.3 + - - +
176A HIS* 3.2 16.6 + - - +
210A THR* 4.0 21.8 - - + +
213A CYS* 3.5 18.9 - - + +
214A THR* 4.2 13.1 - - + +
217A THR* 4.7 0.3 + - - -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.1 21.4 + - - +
170A LYS* 3.7 8.7 - - - +
172A ALA* 1.3 78.4 - - + +
174A MET* 1.3 61.7 + - - +
176A HIS* 3.4 4.7 + - - +
177A GLN* 3.2 31.0 + - - +
209A GLU* 3.9 28.3 - - + +
213A CYS* 3.8 23.3 - - - -
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.1 8.1 - - + -
170A LYS* 3.2 15.1 + - + +
171A ALA* 3.8 6.1 - - - +
172A ALA 3.2 0.2 - - - -
173A VAL* 1.3 76.6 - - - +
175A VAL* 1.3 63.8 + - - +
176A HIS 3.1 0.2 - - - -
177A GLN* 3.2 6.9 + - + +
178A LEU* 3.0 30.2 + - + +
366C LEU* 3.5 50.7 - - + +
369C ILE* 4.0 26.2 - - - -
370C GLN* 4.0 24.0 - - + +
373C LEU* 5.0 1.6 - - + -
374C PHE* 4.5 16.6 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.5 15.9 - - + +
160A LEU* 4.5 8.1 - - + -
171A ALA 3.0 23.0 + - - +
172A ALA* 3.9 7.9 - - - +
173A VAL 3.4 0.2 - - - -
174A MET* 1.3 76.0 - - - +
176A HIS* 1.3 60.0 + - - +
178A LEU* 3.5 10.4 - - + +
179A SER* 3.1 21.5 + - - -
188A ILE* 3.9 9.4 - - + +
194A MET* 3.7 28.9 - - + -
198A ILE* 3.8 32.8 - - + -
217A THR* 3.8 11.2 - - + +
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.2 13.3 + - - +
173A VAL 3.5 8.5 + - - +
174A MET 3.1 0.8 - - - -
175A VAL* 1.3 74.8 - - - +
177A GLN* 1.3 71.4 + - - +
179A SER* 2.8 28.6 + - - -
180A LYS* 3.5 30.5 + - - +
212A ARG* 4.3 19.7 + - - -
213A CYS* 3.7 26.5 - - + +
216A GLY* 3.9 11.9 - - - -
217A THR* 3.3 26.8 + - - +
220A ASN* 4.0 8.1 + - - -
254A TYR* 4.3 13.2 + - - -
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Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL* 3.2 24.5 + - - +
174A MET* 3.6 10.5 - - + +
176A HIS* 1.3 85.5 + - - +
178A LEU* 1.3 61.7 + - - +
180A LYS* 3.2 49.3 + - + +
181A LYS* 3.8 15.2 - - - +
212A ARG* 6.2 0.4 - - - +
374C PHE* 4.0 25.4 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA* 4.8 6.7 - - + -
152A ALA* 5.8 0.2 - - + -
153A ILE* 5.6 3.6 - - + -
156A LEU* 3.4 33.2 - - + -
174A MET* 3.0 20.8 + - + +
175A VAL* 3.5 14.4 - - + +
177A GLN* 1.3 77.2 - - - +
179A SER* 1.3 60.9 + - - +
180A LYS 3.2 1.4 + - - -
181A LYS* 3.3 10.8 + - - +
184A SER* 2.6 44.4 + - - +
185A ARG 4.0 1.0 + - - -
188A ILE* 3.7 19.1 - - + -
373C LEU* 3.8 33.4 - - + -
374C PHE* 4.3 10.7 - - + -
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL 3.1 9.5 + - - -
176A HIS* 2.8 21.1 + - - -
178A LEU* 1.3 77.0 - - - +
180A LYS* 1.3 57.0 + - - +
181A LYS 3.5 0.4 - - - -
185A ARG* 3.0 42.0 + - - -
188A ILE* 4.0 8.0 - - - +
217A THR* 3.7 20.6 - - - -
220A ASN* 2.8 34.8 + - - -
221A LEU* 4.9 2.9 - - - -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A HIS* 3.8 34.7 - - - +
177A GLN* 3.2 41.6 + - + +
178A LEU 3.2 1.2 - - - -
179A SER* 1.3 78.4 + - - +
181A LYS* 1.3 67.6 - - + +
182A GLU 3.8 1.0 + - - -
185A ARG* 3.5 13.6 + - - +
212A ARG* 6.0 0.6 - - - +
220A ASN* 4.2 11.4 - - - +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ASP* 5.9 4.9 - - - +
177A GLN* 3.8 17.3 - - - +
178A LEU* 3.3 5.0 + - - +
180A LYS* 1.3 84.4 - - - +
182A GLU* 1.3 65.4 + - - +
183A ALA* 3.4 3.5 + - + +
184A SER* 3.6 14.6 - - - +
185A ARG* 3.2 24.3 + - - +
374C PHE* 3.7 33.1 - - + -
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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
------------------------------------------------------------
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