Contacts of the helix formed by residues 165 - 177 (chain A) in PDB entry 3QI6
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU 4.7 3.0 + - - -
135A ALA* 5.4 1.6 - - - +
137A LEU* 4.5 17.0 - - + +
164A ALA* 1.3 68.1 - - - +
166A ILE* 1.3 65.9 + - - +
167A ALA* 3.4 8.5 + - - +
168A GLY* 3.0 24.2 + - - +
169A ILE* 2.9 28.7 + - - +
298A VAL* 3.6 21.4 - - + +
301A ARG* 2.8 32.1 + - - -
302A GLN* 3.9 2.8 - - - +
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Residues in contact with ILE 166 (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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153A VAL* 4.4 5.6 - - + -
155A THR* 3.8 22.4 - - + -
164A ALA 4.1 1.1 - - - +
165A ASP* 1.3 70.1 - - - +
167A ALA* 1.3 59.4 + - - +
169A ILE* 3.1 7.5 + - - +
170A ALA* 2.8 31.3 + - + +
180A VAL* 5.3 3.0 - - + +
182A VAL* 4.1 30.7 - - + -
192A GLN* 3.7 35.7 - - + +
194A PRO* 4.0 13.5 - - + +
197A LEU* 3.6 34.8 - - + +
199A ALA 4.5 5.2 - - - +
302A GLN* 3.1 18.4 + - - +
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Residues in contact with ALA 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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165A ASP* 3.3 6.7 + - - +
166A ILE* 1.3 78.1 - - - +
168A GLY* 1.3 63.9 + - - +
170A ALA* 3.5 2.3 + - - +
171A GLN* 3.1 22.7 + - - +
197A LEU* 3.3 36.7 - - + +
301A ARG* 6.0 0.7 - - - +
302A GLN* 4.6 1.2 + - - +
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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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137A LEU* 3.8 20.0 - - - +
165A ASP* 3.0 25.3 + - - -
167A ALA* 1.3 79.2 - - - +
169A ILE* 1.3 59.4 + - - +
171A GLN* 3.4 8.1 + - - +
172A LEU* 3.3 22.3 + - - +
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Residues in contact with ILE 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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134A LEU* 3.9 24.2 - - + +
137A LEU* 3.6 16.2 - - + -
140A VAL* 4.4 11.4 - - + -
151A ILE* 3.6 35.9 - - + -
153A VAL* 3.9 23.1 - - + -
164A ALA* 3.8 28.0 - - + -
165A ASP 2.9 13.6 + - - +
166A ILE 3.9 3.1 - - - +
168A GLY* 1.3 72.4 - - - +
170A ALA* 1.3 59.7 + - - +
171A GLN 3.1 1.8 - - - -
172A LEU* 3.0 8.0 + - + +
173A GLY* 2.8 25.8 + - - -
180A VAL* 3.9 5.0 - - + +
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Residues in contact with ALA 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 ILE* 2.8 20.1 + - + +
167A ALA 3.6 5.4 - - - +
169A ILE* 1.3 73.6 - - - +
171A GLN* 1.3 57.4 + - - +
173A GLY* 3.4 0.7 + - - -
174A ALA* 3.1 27.5 + - - +
180A VAL* 3.8 17.0 - - + +
197A LEU 3.7 7.4 - - - +
198A GLY* 3.6 36.3 - - - +
199A ALA* 4.2 1.8 - - - +
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Residues in contact with GLN 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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167A ALA 3.1 13.5 + - - +
168A GLY* 3.7 10.1 - - - +
169A ILE 3.1 0.8 - - - -
170A ALA* 1.3 73.0 - - - +
172A LEU* 1.3 67.8 + - + +
174A ALA* 3.3 13.4 + - - +
175A ASP* 3.0 50.7 + - - +
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Residues in contact with LEU 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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137A LEU* 3.4 37.0 - - + +
140A VAL* 4.0 14.1 - - + -
141A ARG* 3.7 45.8 - - + +
144A ILE* 4.3 12.7 - - + +
151A ILE* 4.7 4.5 - - + -
168A GLY 3.3 12.7 + - - +
169A ILE* 3.0 10.2 + - - +
171A GLN* 1.3 79.7 - - + +
173A GLY* 1.3 62.5 + - - +
175A ASP* 3.4 17.3 + - + +
176A SER* 3.2 22.7 + - - -
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Residues in contact with GLY 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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151A ILE* 4.0 15.8 - - - +
169A ILE 2.8 16.4 + - - -
170A ALA 3.4 2.9 + - - -
171A GLN 3.3 0.4 - - - -
172A LEU* 1.3 72.5 - - - +
174A ALA* 1.3 56.9 + - - +
176A SER* 3.0 2.8 + - - -
177A SER* 2.8 27.0 + - - -
178A ALA* 2.9 31.5 + - - -
180A VAL* 4.0 4.7 - - - -
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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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170A ALA 3.1 17.7 + - - +
171A GLN* 3.6 16.4 - - - +
172A LEU 3.2 0.2 - - - -
173A GLY* 1.3 78.0 - - - +
175A ASP* 1.4 64.8 + - - +
176A SER 3.2 0.9 + - - -
177A SER* 3.4 10.8 + - - +
180A VAL* 5.3 0.2 - - - +
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Residues in contact with ASP 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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141A ARG* 4.9 12.0 + - - +
171A GLN* 3.0 43.4 + - - +
172A LEU* 3.6 24.1 - - + +
174A ALA* 1.4 75.4 - - - +
176A SER* 1.3 62.7 + - - +
177A SER* 4.0 1.0 + - - -
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Residues in contact with SER 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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141A ARG* 6.0 1.6 - - - +
144A ILE* 3.7 33.5 - - - +
148A THR 4.4 2.1 - - - +
149A ARG* 3.6 10.4 + - - -
172A LEU 3.2 10.6 + - - -
173A GLY 3.0 4.0 + - - -
175A ASP* 1.3 81.5 + - - +
177A SER* 1.3 70.9 + - - +
178A ALA* 3.3 4.5 + - - -
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Residues in contact with SER 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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149A ARG* 3.0 28.1 + - - +
173A GLY 2.8 10.4 + - - -
174A ALA* 3.4 9.9 + - - +
175A ASP 3.6 1.2 + - - -
176A SER* 1.3 75.2 - - - +
178A ALA* 1.3 57.4 + - - +
179A LYS* 4.2 1.8 + - - +
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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