Contacts of the helix formed by residues 164 - 177 (chain A) in PDB entry 1QGI
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 ALA 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.0 21.3 - - + +
25A GLN* 3.9 18.1 - - + +
29A ILE* 3.7 8.2 - - + +
162A THR 3.8 1.0 + - - -
163A SER* 1.3 73.6 - - - +
165A VAL* 1.3 58.7 + - - +
167A ILE* 3.9 0.2 - - - -
168A GLY* 2.8 28.2 + - - -
241A MET 3.3 10.5 + - - +
242A ASN* 3.7 20.6 + - - +
243A LEU* 3.8 17.5 - - + -
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Residues in contact with VAL 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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163A SER* 3.2 0.4 - - - +
164A ALA* 1.3 77.5 - - - +
166A THR* 1.3 58.7 + - - +
169A SER* 2.9 32.2 + - - -
203A MET* 5.2 1.6 - - + -
207A HIS* 5.2 0.9 - - + -
232A TRP* 3.7 23.6 - - + +
235A LEU* 4.1 12.6 - - + -
236A VAL* 3.8 29.2 - - + -
240A LYS 3.4 25.8 - - - +
241A MET* 3.1 26.8 + - + +
243A LEU* 3.9 15.9 - - + -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA* 4.1 6.1 - - + -
161A PHE* 4.0 20.4 - - + -
163A SER* 3.0 16.9 + - - -
165A VAL* 1.3 78.1 - - - +
167A ILE* 1.3 63.5 + - - +
169A SER* 3.7 0.5 - - - -
170A PHE* 3.0 46.0 + - + -
199A GLU* 2.7 29.2 + - - +
203A MET* 3.5 33.1 - - - +
241A MET* 4.2 1.6 - - - +
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Residues in contact with ILE 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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19A THR* 3.8 22.4 - - - +
21A LEU* 4.1 21.5 - - + -
26A TRP* 4.4 9.6 - - + -
152A SER* 5.3 0.9 - - - -
153A VAL* 4.0 35.0 - - + +
156A ALA* 4.2 18.8 - - + -
157A ARG* 6.3 1.1 - - + +
162A THR* 3.9 18.6 - - - +
163A SER 3.0 17.8 + - - +
164A ALA 4.0 2.0 - - - +
166A THR* 1.3 74.8 - - - +
168A GLY* 1.3 58.8 + - - +
170A PHE* 3.3 7.9 + - - +
171A VAL* 2.9 44.4 + - + +
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Residues in contact with GLY 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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29A ILE* 4.0 19.0 - - - +
33A ILE* 4.5 1.9 - - - +
164A ALA 2.8 17.8 + - - -
167A ILE* 1.3 77.8 - - - +
169A SER* 1.3 55.2 + - - +
171A VAL* 3.4 4.2 + - - +
172A ASP* 2.9 29.8 + - - +
232A TRP* 3.5 23.0 - - - -
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Residues in contact with SER 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 VAL 2.9 18.6 + - - -
168A GLY* 1.3 72.5 - - - +
170A PHE* 1.3 65.8 + - - +
172A ASP* 3.3 3.0 + - - +
173A THR* 2.9 29.1 + - - -
203A MET* 3.6 18.9 - - - +
206A PHE* 3.8 5.0 - - - -
207A HIS* 2.9 30.3 + - - -
210A ARG* 4.4 2.9 + - - -
232A TRP* 3.7 23.3 - - - +
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Residues in contact with PHE 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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152A SER* 3.5 34.0 + - - -
155A GLN* 4.1 13.9 - - + -
156A ALA* 3.7 29.6 - - + -
159A ARG* 5.3 1.1 - - - -
161A PHE* 5.2 2.7 - + - -
166A THR* 3.0 30.9 + - + +
167A ILE* 3.6 4.7 - - - +
169A SER* 1.3 76.4 - - - +
171A VAL* 1.3 57.2 + - - +
173A THR* 3.2 6.2 + - - -
174A ALA* 2.9 28.6 + - - +
186A LEU* 3.8 13.1 - - + +
190A LEU* 3.6 26.2 - - + -
202A PHE* 4.0 12.1 - + - -
203A MET* 3.7 21.3 - - + -
206A PHE* 4.0 21.8 - + - -
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Residues in contact with VAL 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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26A TRP* 4.3 9.6 - - + -
33A ILE* 4.0 12.1 - - + -
144A PHE* 3.9 34.1 - - + -
148A TYR* 4.8 4.0 - - + +
149A ILE* 4.2 22.2 - - + -
152A SER* 3.6 22.7 - - - +
167A ILE* 2.9 32.0 + - + +
168A GLY* 3.7 6.1 - - - +
170A PHE* 1.3 73.2 - - - +
172A ASP* 1.3 66.1 + - - +
174A ALA* 3.3 2.6 + - - +
175A LEU* 2.9 23.8 + - + +
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Residues in contact with ASP 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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33A ILE* 3.6 31.6 - - + +
36A PRO* 4.5 1.7 - - - +
168A GLY 2.9 17.9 + - - +
169A SER 3.3 4.7 + - - +
171A VAL* 1.3 75.9 - - - +
173A THR* 1.3 58.0 + - - +
175A LEU* 3.5 4.5 + - - +
176A ASN* 2.9 32.7 + - - +
210A ARG* 2.9 25.8 + - - +
228A ARG* 2.9 40.2 + - - +
232A TRP* 3.9 20.1 + - - +
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Residues in contact with THR 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 SER 2.9 14.2 + - - -
170A PHE 3.4 8.7 - - - -
172A ASP* 1.3 74.2 - - - +
174A ALA* 1.3 57.4 + - - +
177A GLN* 2.8 38.9 + - - +
178A GLY 3.7 0.3 + - - +
186A LEU* 3.9 21.3 - - - +
189A LEU* 3.8 28.5 - - + -
206A PHE* 3.5 16.3 - - + -
210A ARG* 3.4 31.9 + - - +
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Residues in contact with ALA 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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148A TYR* 3.4 27.6 - - + +
152A SER* 4.0 13.5 - - - +
170A PHE 2.9 16.5 + - - +
171A VAL 3.8 2.9 - - - +
173A THR* 1.3 76.0 - - - +
175A LEU* 1.3 59.7 + - - +
178A GLY* 2.8 38.3 + - - -
179A ALA* 4.0 17.0 - - + +
186A LEU* 4.4 6.9 - - + +
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Residues in contact with LEU 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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33A ILE* 3.9 24.0 - - + -
37A GLU* 3.4 37.7 - - + +
63A LEU 4.5 4.5 - - - +
64A PHE* 4.1 23.1 - - + +
144A PHE* 3.9 23.8 - - + -
148A TYR* 3.9 26.5 + - + -
171A VAL* 2.9 18.0 + - + +
172A ASP 3.8 2.5 - - - +
174A ALA* 1.3 78.8 - - - +
176A ASN* 1.3 62.8 + - - +
178A GLY 4.5 0.7 + - - -
228A ARG* 4.3 5.2 - - - +
3B GCS 4.0 19.7 + - - +
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Residues in contact with ASN 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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37A GLU* 4.1 3.0 - - - +
172A ASP 2.9 18.9 + - - +
175A LEU* 1.3 83.8 - - - +
177A GLN* 1.3 70.6 + - - +
210A ARG* 3.1 23.4 - - - +
214A VAL* 4.0 0.4 - - - +
219A TYR* 3.1 36.2 - - - +
220A ASN* 2.9 23.2 + - - -
228A ARG* 3.3 26.0 + - - +
2B GCS 5.8 3.1 + - - -
3B GCS 5.8 0.3 + - - -
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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 THR* 2.8 17.5 + - + +
176A ASN* 1.3 81.1 - - - +
178A GLY* 1.3 58.8 + - - +
184A ASP* 2.8 33.5 + - - +
185A THR* 3.6 17.5 - - - +
189A LEU* 3.5 20.0 - - - +
210A ARG* 2.8 34.8 + - - +
213A VAL* 3.8 12.3 - - - +
214A VAL* 3.5 15.8 - - - +
219A TYR* 3.7 42.2 + - + -
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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