Contacts of the helix formed by residues 164 - 176 (chain A) in PDB entry 1PV2
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.4 27.0 - - - +
160A GLY 3.2 9.6 + - - -
161A LEU 3.0 7.4 + - - -
162A PRO 3.6 0.4 - - - -
163A GLU* 1.3 75.9 - - - +
165A GLN* 1.3 59.1 + - - +
166A ASP* 3.5 8.1 + - - +
167A VAL* 3.3 33.2 + - - -
168A ALA* 3.0 24.4 + - - +
193A ALA* 3.4 9.8 - - - +
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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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163A GLU 3.6 6.0 + - - +
164A SER* 1.3 72.3 + - - +
166A ASP* 1.3 61.3 + - - +
168A ALA* 3.7 6.7 - - - +
169A ALA* 3.1 27.5 + - - +
193A ALA 5.8 0.2 - - - -
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Residues in contact with ASP 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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97A ILE* 4.4 16.0 - - + +
132A LYS* 5.0 1.2 + - - -
133A LEU* 4.0 20.4 - - + -
134A ALA* 3.3 40.0 + - - +
137A VAL* 3.9 10.1 - - + +
164A SER* 3.1 7.6 + - - +
165A GLN* 1.3 78.6 - - - +
167A VAL* 1.3 58.8 + - - +
169A ALA* 3.2 6.5 + - - +
170A ALA* 2.9 30.8 + - - +
132B LYS* 5.9 0.7 + - - -
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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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54A ILE* 4.2 12.3 - - + +
97A ILE* 4.3 1.3 - - + -
133A LEU* 3.7 20.6 - - + -
151A VAL* 6.0 0.2 - - + -
161A LEU* 3.9 28.5 - - + +
164A SER* 3.3 28.9 + - - +
166A ASP* 1.3 78.1 - - - +
168A ALA* 1.3 51.8 + - - +
170A ALA* 3.2 3.5 + - - +
171A LEU* 2.7 47.1 + - + +
190A ALA* 3.7 32.5 - - + +
193A ALA* 4.0 0.4 - - + -
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Residues in contact with ALA 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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164A SER 3.0 14.3 + - - +
165A GLN* 3.7 8.7 - - - +
167A VAL* 1.3 75.5 - - - +
169A ALA* 1.3 51.4 + - - +
171A LEU* 2.7 7.4 + - - +
172A GLN* 2.6 46.1 + - - +
193A ALA* 3.6 32.9 - - + +
194A LEU* 4.1 13.5 - - + +
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Residues in contact with ALA 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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137A VAL* 3.8 21.5 - - + +
165A GLN 3.1 15.4 + - - +
166A ASP* 3.7 5.2 - - - +
168A ALA* 1.3 79.3 - - - +
170A ALA* 1.3 60.5 + - - +
172A GLN* 3.6 12.3 + - - +
173A TRP* 3.2 21.0 + - - +
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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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52A LEU* 5.2 2.0 - - + -
54A ILE* 4.4 12.1 - - + -
133A LEU* 4.5 10.5 - - + -
136A VAL* 6.3 0.9 - - + -
137A VAL* 3.9 11.8 - - + +
149A ILE* 3.8 27.2 - - + +
166A ASP 2.9 17.0 + - - +
167A VAL* 3.5 5.6 - - - +
169A ALA* 1.3 75.8 - - - +
171A LEU* 1.3 64.5 + - - +
173A TRP* 3.2 17.1 + - - +
174A ALA 3.2 9.7 + - - -
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Residues in contact with LEU 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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54A ILE* 5.7 1.6 - - + -
149A ILE* 4.7 18.2 - - + -
151A VAL* 5.3 4.5 - - + -
167A VAL* 2.7 26.7 + - + +
168A ALA* 2.7 11.2 + - - +
170A ALA* 1.3 70.5 - - + +
172A GLN* 1.3 63.3 + - - +
174A ALA* 3.5 8.2 + - + +
175A ILE* 3.2 29.1 - - + +
181A VAL* 4.2 28.9 - - + -
190A ALA* 3.9 11.4 - - + +
191A PHE* 3.5 42.8 - - + +
194A LEU* 3.7 19.5 - - + -
201A LEU* 5.3 1.3 - - + -
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Residues in contact with GLN 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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168A ALA* 2.6 37.0 + - - +
169A ALA* 3.8 10.1 - - - +
171A LEU* 1.3 72.3 - - - +
173A TRP* 1.3 59.8 + - - +
175A ILE* 3.2 8.7 + - - +
176A LYS* 2.9 34.5 + - + +
194A LEU* 4.0 12.2 - - + +
197A GLY* 5.6 6.2 - - - -
198A ASP* 3.1 27.0 + - - +
199A ASN 5.0 0.2 + - - -
200A PRO* 4.0 14.1 - - + +
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Residues in contact with TRP 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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52A LEU* 6.1 0.4 - - + -
137A VAL 6.1 0.7 - - - -
139A SER 5.5 6.1 + - - -
145A GLU 4.0 12.1 - - - -
146A TYR* 3.4 32.5 - + + -
148A ALA 3.9 20.9 - - - -
149A ILE* 4.6 8.1 - - + -
169A ALA 3.2 14.7 + - - +
170A ALA* 3.3 15.3 - - - +
172A GLN* 1.3 77.3 - - - +
174A ALA* 1.3 78.2 + - + +
176A LYS* 3.9 18.3 + - - +
177A ASN* 3.2 37.8 + - + +
179A ARG* 3.4 38.8 - - + -
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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 ALA 4.3 0.4 - - - +
149A ILE* 3.7 29.2 - - + -
170A ALA 3.2 4.3 + - - +
171A LEU* 3.9 9.4 - - + +
172A GLN 3.3 0.8 - - - -
173A TRP* 1.3 87.9 - - + +
175A ILE* 1.3 58.5 + - - +
178A ASP 3.4 0.9 + - - -
179A ARG* 2.7 45.6 + - + +
181A VAL* 3.9 20.9 - - + -
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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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171A LEU* 3.2 22.2 - - + +
172A GLN 3.2 3.7 + - - +
173A TRP 3.2 0.2 - - - -
174A ALA* 1.3 76.5 - - - +
176A LYS* 1.3 58.4 + - - +
177A ASN 2.9 10.4 + - - -
178A ASP* 3.1 12.3 + - - +
179A ARG 5.3 0.7 - - - -
181A VAL* 4.7 13.0 - - + -
194A LEU* 5.1 2.9 - - + -
200A PRO* 3.5 46.9 - - + +
201A LEU* 3.5 30.7 - - + -
204A TYR* 5.1 11.2 - - + +
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Residues in contact with LYS 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 GLN* 2.9 18.9 + - + +
173A TRP* 3.9 22.8 + - - +
175A ILE* 1.3 74.8 - - - +
177A ASN* 1.3 86.7 + - - +
178A ASP 3.7 0.2 - - - -
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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