Contacts of the helix formed by residues 163 - 177 (chain A) in PDB entry 2VZ9
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 SER 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 4.0 14.8 - - - -
157A ILE* 4.0 9.4 - - - -
158A ASP* 3.9 2.8 + - - -
159A THR* 2.9 27.1 + - - +
160A ALA 2.5 23.7 + - - -
162A SER* 1.3 79.6 + - - +
164A SER* 1.3 54.2 + - - -
166A LEU* 2.6 15.4 + - - +
167A ALA* 2.6 33.2 + - - -
334A PRO* 3.6 17.5 - - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY* 3.7 6.1 - - - -
162A SER 2.8 4.2 + - - -
163A SER* 1.3 77.1 - - - +
165A LEU* 1.3 51.7 + - - -
167A ALA* 3.2 9.4 - - - +
168A LEU 2.8 29.5 + - - -
185A VAL* 3.9 0.3 - - - +
186A GLY 3.9 1.1 - - - -
187A GLY* 3.7 23.6 - - - -
334A PRO 2.6 20.8 + - - -
335A ALA* 3.3 4.6 + - - -
337A GLY 3.5 1.6 + - - -
338A VAL* 2.9 47.5 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER 3.0 5.0 + - - +
163A SER 2.8 3.8 + - - -
164A SER* 1.3 76.4 + - - +
166A LEU* 1.3 57.6 + - - +
168A LEU* 3.3 14.6 + - + +
169A GLN* 2.9 24.9 + - - +
337A GLY* 3.4 35.2 - - - +
338A VAL* 4.2 2.2 - - - +
341A LEU* 5.0 4.3 - - + -
390A ILE* 3.7 24.0 - - + +
392A SER* 3.5 21.1 - - - -
400A VAL* 3.2 37.5 - - + +
402A VAL* 3.6 23.7 - - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.4 31.6 - - + -
159A THR* 4.3 21.3 - - + +
162A SER* 4.5 1.3 - - - +
163A SER* 2.6 18.3 + - - +
165A LEU* 1.3 72.8 - - - +
167A ALA* 1.3 58.2 + - - +
169A GLN* 3.6 9.4 - - + +
170A SER* 2.8 27.9 + - - +
251A THR* 3.3 37.2 - - + +
398A SER* 5.3 2.2 - - - +
400A VAL* 3.7 19.8 - - + +
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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
----------------------------------------------------------
108A TRP* 4.0 27.0 - - + +
110A GLY 4.3 3.4 - - - +
157A ILE* 3.2 28.8 - - + +
163A SER 2.6 13.3 + - - +
164A SER* 3.2 15.7 - - - +
166A LEU* 1.3 73.0 - - - +
168A LEU* 1.3 57.3 + - - +
169A GLN 3.0 0.2 - - - -
170A SER* 3.1 3.6 + - - -
171A ALA* 2.8 30.7 + - - +
185A VAL* 4.3 4.5 - - + -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.5 5.8 - - + -
164A SER 2.8 17.1 + - - +
165A LEU* 3.3 15.9 + - + +
167A ALA* 1.3 73.3 - - - +
169A GLN* 1.3 61.6 + - - +
171A ALA 4.0 0.4 - - - -
172A TYR* 3.4 20.3 + - - +
185A VAL* 3.5 24.3 - - + +
231A VAL* 3.8 17.3 - - + -
233A LEU* 3.9 18.1 - - + +
246A ILE* 4.6 6.3 - - + -
338A VAL* 4.4 5.2 - - + -
341A LEU* 3.5 31.6 - - + -
402A VAL* 4.2 31.2 - - + -
404A LEU* 6.0 0.7 - - + -
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Residues in contact with GLN 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 LEU 2.9 15.9 + - - +
166A LEU* 3.6 11.0 + - - +
167A ALA 3.0 0.2 - - - -
168A LEU* 1.3 77.0 - - + +
170A SER* 1.3 85.0 + - - +
171A ALA 2.8 5.3 + - - -
172A TYR* 3.0 16.3 + - + +
173A GLN* 3.0 45.4 + - - +
249A ALA* 3.3 31.4 - - + -
250A GLY* 3.1 26.5 - - - +
251A THR* 3.2 20.8 + - + +
400A VAL* 4.8 4.7 - - + -
401A HIS 5.1 0.9 - - - +
402A VAL* 6.0 0.4 - - + -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TRP* 3.3 35.3 - - - -
157A ILE* 4.6 4.6 - - - +
166A LEU* 2.8 25.7 + - - +
167A ALA* 3.5 5.6 - - - -
169A GLN* 1.3 83.2 + - - +
171A ALA* 1.3 59.3 + - - +
173A GLN* 3.8 7.0 + - - +
174A ALA* 3.4 20.6 + - - +
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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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108A TRP* 3.7 24.6 + - + +
167A ALA 2.8 16.7 + - - +
168A LEU 4.1 2.2 - - - +
169A GLN 2.8 0.8 + - - -
170A SER* 1.3 75.7 - - - +
172A TYR* 1.3 57.2 + - - +
174A ALA* 2.8 25.5 + - - +
175A ILE* 3.1 15.5 + - - +
183A ALA* 3.9 10.5 - - + +
185A VAL* 3.5 25.6 - - + -
233A LEU* 4.1 3.8 - - + -
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Residues in contact with TYR 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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2A GLU 5.9 0.9 - - - -
4A VAL* 3.6 28.0 - - + +
168A LEU 3.4 16.4 + - - +
169A GLN* 3.0 6.9 + - + +
171A ALA* 1.3 79.3 - - - +
173A GLN* 1.3 82.8 + - + +
175A ILE* 3.3 3.4 + - - +
176A ARG* 2.9 73.9 + - + +
233A LEU* 3.7 7.9 - - - +
246A ILE* 3.2 58.3 + - + -
247A LEU 3.8 14.9 + - - -
248A ASN* 4.1 3.3 - - - -
249A ALA* 4.6 21.1 - - + -
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Residues in contact with GLN 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 GLN* 3.0 45.2 + - - +
170A SER* 3.9 7.5 + - - +
172A TYR* 1.3 92.1 - - + +
174A ALA* 1.3 57.4 - - - +
176A ARG* 3.4 17.0 - - - +
177A GLY* 3.0 27.5 + - - -
249A ALA 4.2 10.7 + - - -
250A GLY* 5.2 1.0 - - - -
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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
----------------------------------------------------------
108A TRP* 4.1 20.4 - - + +
170A SER 3.4 10.8 + - - +
171A ALA* 2.8 15.6 + - - +
173A GLN* 1.3 74.9 - - - +
175A ILE* 1.3 57.8 + - + +
177A GLY* 3.9 2.2 + - - -
179A GLU* 3.1 39.3 + - + +
180A CYS* 3.2 20.4 + - - -
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Residues in contact with ILE 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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2A GLU* 4.6 6.9 - - + +
4A VAL* 3.4 26.7 - - + -
171A ALA 3.1 11.9 + - - +
172A TYR 3.7 1.3 - - - +
174A ALA* 1.3 74.1 - - + +
176A ARG* 1.3 67.6 + - - +
177A GLY 2.8 3.2 + - - -
178A GLY* 2.9 14.6 + - - -
180A CYS* 3.8 23.8 - - + +
181A SER 4.6 1.8 - - - -
182A ALA* 4.3 12.1 - - - +
183A ALA* 4.2 10.8 - - + +
233A LEU* 3.5 46.2 - - + +
234A THR* 3.8 3.6 - - - +
235A LYS* 4.1 25.1 - - + +
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Residues in contact with ARG 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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1A MET* 3.4 34.0 + - - +
2A GLU* 3.4 23.9 + - - +
4A VAL* 3.6 12.1 - - + +
172A TYR* 2.9 56.1 + - + +
173A GLN* 3.4 18.1 - - - +
175A ILE* 1.3 79.2 - - - +
177A GLY* 1.3 60.3 + - - +
178A GLY 3.6 0.7 + - - -
247A LEU 5.6 1.8 + - - -
248A ASN* 4.2 14.5 - - - +
249A ALA 5.6 0.2 + - - -
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Residues in contact with GLY 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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1A MET* 5.4 4.7 - - - -
173A GLN 3.0 14.9 + - - -
174A ALA* 3.9 1.8 + - - -
175A ILE 2.8 6.3 + - - -
176A ARG* 1.3 74.4 - - - +
178A GLY* 1.3 53.8 + - - -
179A GLU* 3.4 8.7 + - - +
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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