Contacts of the helix formed by residues 164 - 177 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.5 33.7 - - - +
160B GLY 3.1 1.6 + - - -
161B LEU 3.0 12.6 + - - -
162B PRO 3.6 0.4 - - - -
163B GLU* 1.3 77.6 - - - +
165B GLN* 1.3 58.8 + - - +
166B ASP* 3.4 11.4 + - - +
167B VAL* 3.3 26.7 + - - -
168B ALA* 2.9 23.2 + - - +
193B ALA* 3.3 10.7 - - - +
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Residues in contact with GLN 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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163B GLU 3.4 8.3 + - - +
164B SER* 1.3 72.8 + - - +
166B ASP* 1.3 61.9 + - - +
168B ALA* 3.2 10.3 - - + +
169B ALA* 2.9 28.9 + - - +
193B ALA 5.7 0.2 - - - -
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Residues in contact with ASP 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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97B ILE* 4.6 12.7 - - + +
132B LYS* 5.7 1.6 - - - -
133B LEU* 4.1 23.0 - - + +
134B ALA* 3.5 32.3 + - - +
137B VAL* 3.9 12.5 - - + +
164B SER* 3.1 10.8 + - - +
165B GLN* 1.3 81.3 + - - +
167B VAL* 1.3 59.4 + - - +
169B ALA* 3.9 5.0 - - - +
170B ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 167 (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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54B ILE* 4.0 21.1 - - + -
97B ILE* 4.6 3.8 - - + -
133B LEU* 3.7 21.1 - - + -
151B VAL* 6.1 0.4 - - + -
161B LEU* 3.8 18.8 - - + +
164B SER* 3.3 25.2 + - - +
166B ASP* 1.3 74.0 - - - +
168B ALA* 1.3 74.8 + - - +
170B ALA* 3.2 5.4 + - - +
171B LEU* 3.0 30.8 + - + +
190B ALA* 3.5 33.0 - - + +
193B ALA* 3.9 1.1 - - + -
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Residues in contact with ALA 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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164B SER 2.9 14.9 + - - +
165B GLN* 3.2 17.7 - - + +
167B VAL* 1.3 81.1 - - - +
169B ALA* 1.3 62.8 + - - +
171B LEU* 3.0 5.4 + - - +
172B GLN* 3.0 29.7 + - - +
193B ALA* 3.5 25.4 - - - +
194B LEU* 3.3 13.2 - - + +
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Residues in contact with ALA 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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137B VAL* 3.9 20.9 - - + -
165B GLN 2.9 14.9 + - - +
166B ASP* 3.9 4.7 - - - +
168B ALA* 1.3 73.9 - - - +
170B ALA* 1.3 67.7 + - - +
172B GLN* 2.9 17.1 + - - +
173B TRP* 2.8 24.3 + - - +
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Residues in contact with ALA 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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52B LEU* 5.1 3.1 - - + -
54B ILE* 4.1 23.1 - - + -
133B LEU* 4.5 8.5 - - + -
137B VAL* 3.6 14.4 - - + +
140B LEU* 4.7 4.3 - - + -
149B ILE* 4.5 11.7 - - + +
166B ASP 2.9 18.9 + - - +
167B VAL* 3.5 4.7 - - - +
169B ALA* 1.3 76.1 - - - +
171B LEU* 1.3 58.3 + - - +
173B TRP* 3.3 10.9 + - - +
174B ALA* 3.0 26.6 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 5.6 0.9 - - + -
149B ILE* 4.3 18.4 - - + -
151B VAL* 5.1 4.0 - - + -
167B VAL* 3.0 29.9 + - + +
168B ALA 3.3 7.0 - - - +
170B ALA* 1.3 74.5 - - + +
172B GLN* 1.3 65.8 + - - +
174B ALA* 3.1 11.1 + - - +
175B ILE* 3.2 17.9 + - + +
181B VAL* 4.2 21.3 - - + -
190B ALA* 4.1 1.8 - - + +
191B PHE* 3.5 47.1 - - + -
194B LEU* 3.7 28.7 - - + -
200B PRO* 4.9 2.4 - - - +
201B LEU* 4.4 4.3 - - + -
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Residues in contact with GLN 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 ALA* 3.0 20.3 + - - +
169B ALA* 2.9 17.1 + - - +
171B LEU* 1.3 76.4 - - - +
173B TRP* 1.3 63.8 + - - +
175B ILE* 4.0 1.4 - - - +
176B LYS* 2.9 29.1 + - + +
194B LEU* 3.8 10.9 - - + +
197B GLY* 5.4 2.4 - - - -
198B ASP* 3.3 45.9 + - - +
199B ASN 4.0 0.7 + - - -
200B PRO* 3.6 22.9 - - + +
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Residues in contact with TRP 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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52B LEU* 6.2 0.2 - - + -
137B VAL* 5.9 0.2 - - + -
140B LEU* 3.6 36.8 - - + -
141B ASN* 3.4 24.7 - - - +
144B SER* 3.4 26.0 - - - -
146B TYR* 3.6 41.3 - + + -
148B ALA 5.8 0.4 - - - -
149B ILE* 4.3 13.5 - - + -
169B ALA 2.8 14.1 + - - +
170B ALA 3.4 10.3 - - - +
172B GLN* 1.3 72.2 - - - +
174B ALA* 1.3 95.3 + - + +
176B LYS* 3.4 5.5 + - - +
177B ASN* 3.0 50.2 + - + +
179B ARG* 4.1 25.6 - - + -
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Residues in contact with ALA 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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149B ILE* 3.6 30.5 - - + -
170B ALA 3.0 8.0 + - - +
171B LEU* 3.4 10.1 - - - +
172B GLN 3.1 0.4 + - - -
173B TRP* 1.3 91.7 - - + +
175B ILE* 1.3 62.9 + - - +
177B ASN 3.4 0.3 + - - -
178B ASP 3.2 2.4 + - - -
179B ARG* 2.8 34.3 + - + +
180B PHE 4.7 0.2 - - - +
181B VAL* 3.8 17.5 - - + -
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Residues in contact with ILE 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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171B LEU* 3.2 10.3 + - + +
174B ALA* 1.3 76.4 - - - +
176B LYS* 1.3 70.6 + - - +
178B ASP* 2.9 16.6 + - - +
179B ARG 4.5 8.3 - - - +
181B VAL* 3.6 29.2 - - + -
200B PRO* 3.3 34.3 - - + +
201B LEU* 3.7 27.6 - - + -
204B TYR* 4.2 19.1 - - + +
256B LYS* 6.1 2.0 - - + +
257B LEU* 5.5 4.9 - - + +
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Residues in contact with LYS 176 (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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172B GLN* 2.9 21.9 + - + +
173B TRP* 3.7 4.7 - - - +
175B ILE* 1.3 83.5 - - - +
177B ASN* 1.3 74.8 + - - +
178B ASP* 3.4 2.8 + - - +
200B PRO* 6.3 0.7 - - + -
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Residues in contact with ASN 177 (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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141B ASN 3.8 17.0 + - - +
173B TRP* 3.0 55.1 + - + +
174B ALA 4.3 0.9 - - - +
176B LYS* 1.3 92.5 - - - +
178B ASP* 1.3 69.2 + - - +
179B ARG* 3.0 39.1 + - - +
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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