Contacts of the helix formed by residues 158 - 175 (chain B) in PDB entry 3QVL
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 GLY 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ASP* 4.1 1.8 + - - -
156B GLY 3.5 2.6 - - - +
157B SER* 1.3 78.9 + - - +
159B LEU* 1.3 63.2 + - - +
160B ALA 3.4 2.2 - - - -
161B GLN* 3.3 25.4 + - - +
162B GLU* 3.1 22.9 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.3 24.2 - - + -
152B ALA* 6.4 0.2 - - + -
155B ASP* 5.8 1.1 - - - +
157B SER* 3.3 18.8 + - - +
158B GLY* 1.3 75.7 - - - +
160B ALA* 1.3 61.8 + - - +
162B GLU* 3.3 8.6 + - + +
163B LYS* 3.0 47.7 + - + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 5.6 0.2 - - + -
146B ILE* 3.7 7.3 - - + +
148B LEU* 3.7 24.8 - - + +
152B ALA* 3.7 28.2 + - + +
153B LEU* 3.8 22.7 - - + +
158B GLY 3.4 0.4 - - - -
159B LEU* 1.3 78.8 - - - +
161B GLN* 1.3 59.6 + - - +
163B LYS* 3.3 3.4 + - - +
164B VAL* 3.0 35.8 + - - +
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA 4.5 1.0 - - - +
153B LEU* 2.9 44.0 + - + +
155B ASP* 5.5 0.2 - - - +
158B GLY* 3.3 29.2 + - - +
159B LEU 3.3 0.2 - - - -
160B ALA* 1.3 80.8 + - - +
162B GLU* 1.3 59.2 + - - +
164B VAL* 3.6 3.9 + - - +
165B ARG* 3.3 20.4 + - - +
186B GLY 4.6 3.6 + - - -
190B LEU* 3.7 44.2 - - + +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY 3.1 17.6 + - - +
159B LEU* 3.3 9.4 + - + +
161B GLN* 1.3 73.9 - - - +
163B LYS* 1.3 60.4 + - + +
165B ARG* 3.2 38.9 + - - +
166B GLU* 3.0 54.7 + - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 3.8 31.6 + - + +
147B ASP 5.7 0.4 - - - -
148B LEU* 3.8 28.9 - - + -
159B LEU* 3.0 38.6 + - + +
160B ALA 3.6 4.7 - - - +
162B GLU* 1.3 73.8 - - + +
164B VAL* 1.3 60.3 + - - +
166B GLU* 3.5 12.6 + - - +
167B ARG* 3.0 31.0 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 4.4 5.6 - - + +
146B ILE* 3.9 18.4 - - + -
153B LEU* 4.7 1.3 - - + -
160B ALA 3.0 23.4 + - - +
161B GLN* 3.7 6.3 - - - +
163B LYS* 1.3 72.8 - - - +
165B ARG* 1.3 59.3 + - - +
167B ARG* 3.2 2.8 + - - +
168B CYS* 2.9 41.9 + - - -
182B LEU* 3.8 28.7 - - + -
187B MET* 3.7 35.9 - - + -
190B LEU* 4.2 8.7 - - + -
194B LEU* 4.2 8.3 - - + -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLN 3.3 11.5 + - - +
162B GLU* 3.2 39.1 + - - +
163B LYS 3.4 0.2 - - - -
164B VAL* 1.3 78.2 - - - +
166B GLU* 1.3 67.0 + - - +
168B CYS* 3.3 4.8 + - - +
169B ILE* 3.1 49.5 + - + +
194B LEU* 3.7 29.3 - - + +
197B GLU* 2.7 37.4 + - - +
198B LEU* 4.9 0.8 - - + +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLU* 3.0 48.4 + - - +
163B LYS* 3.9 11.4 + - - +
165B ARG* 1.3 82.7 - - - +
167B ARG* 1.3 58.1 + - - +
169B ILE* 3.4 13.5 + - + +
170B ARG* 3.2 25.3 + - - +
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 4.3 10.5 - - + -
144B HIS* 3.3 59.4 + - - +
145B ALA 4.9 8.9 + - - +
146B ILE* 4.2 17.0 - - + -
163B LYS 3.0 18.8 + - - +
164B VAL 3.8 2.9 - - - +
166B GLU* 1.3 74.3 - - - +
168B CYS* 1.3 61.7 + - - +
170B ARG* 3.1 53.1 + - - +
171B ALA* 3.0 41.4 + - - +
174B GLU* 4.6 3.6 + - - -
175B ASP* 5.1 0.2 + - - -
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.1 7.6 - - - -
164B VAL* 2.9 35.2 + - - -
165B ARG* 3.4 10.5 - - - +
167B ARG* 1.3 76.0 - - - +
169B ILE* 1.3 64.2 + - - +
171B ALA* 3.3 6.7 + - - +
172B LEU* 3.1 28.8 + - - +
180B ILE* 3.7 33.5 - - + +
182B LEU* 4.4 2.0 - - - -
194B LEU* 4.3 12.8 - - - -
198B LEU* 3.8 19.7 - - + -
202B VAL* 4.8 2.0 - - - -
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ARG* 3.1 54.6 + - + +
166B GLU* 3.6 11.0 - - + +
168B CYS* 1.3 77.2 - - - +
170B ARG* 1.3 61.8 + - - +
172B LEU* 3.5 9.1 + - - +
173B LYS* 3.2 21.0 + - + +
197B GLU* 4.7 0.2 - - - +
198B LEU* 3.6 24.7 - - + -
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLU 3.2 14.1 + - - +
167B ARG* 3.1 45.1 - - - +
168B CYS 3.3 0.2 - - - -
169B ILE* 1.3 77.0 - - - +
171B ALA* 1.3 59.5 + - - +
173B LYS* 3.2 6.0 + - - +
174B GLU* 2.9 70.8 + - + +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER* 4.2 1.6 - - - -
117B VAL* 4.9 1.6 - - + -
144B HIS* 4.1 8.5 - - + -
167B ARG* 3.0 27.4 + - - +
168B CYS* 3.5 7.0 - - - +
170B ARG* 1.3 75.9 - - - +
172B LEU* 1.3 57.7 + - - +
175B ASP* 2.9 57.8 + - - +
176B GLY 4.4 0.3 + - - -
177B SER* 4.2 3.1 + - - -
180B ILE* 3.9 18.4 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B CYS 3.1 21.9 + - - +
169B ILE* 3.8 6.1 - - - +
171B ALA* 1.3 76.7 - - - +
173B LYS* 1.3 60.5 + - - +
175B ASP 4.9 0.9 + - - -
176B GLY* 5.0 4.2 + - - -
177B SER* 4.2 25.3 - - - +
178B GLY 4.6 6.7 - - - -
179B ALA 4.7 0.2 - - - +
180B ILE* 4.2 17.3 - - + -
198B LEU* 3.8 28.0 - - + +
200B VAL* 3.6 46.9 - - + -
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 3.2 13.4 + - + +
170B ARG* 3.2 11.8 + - + +
172B LEU* 1.3 80.6 - - - +
174B GLU* 1.3 65.2 + - + +
176B GLY 5.3 0.4 + - - -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B HIS* 6.0 0.2 - - - -
167B ARG* 4.6 4.5 + - - -
170B ARG* 2.9 58.9 + - + +
173B LYS* 1.3 86.8 - - + +
175B ASP* 1.3 71.6 + - - +
176B GLY 3.4 3.2 + - - -
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ARG* 3.6 12.0 + - - -
115B SER* 2.7 27.9 + - - +
141B ALA* 3.7 10.2 - - + +
142B ALA* 3.5 14.6 - - + +
144B HIS* 2.6 37.6 + - - -
167B ARG* 5.1 0.2 + - - -
171B ALA* 2.9 29.7 + - - +
174B GLU* 1.3 83.3 - - - +
176B GLY* 1.3 60.8 + - - +
177B SER* 3.8 3.6 - - - +
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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