Contacts of the helix formed by residues 164 - 177 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ILE* 3.2 40.7 - - - +
160G GLY 3.2 1.8 + - - -
161G LEU 3.1 14.5 + - - -
162G PRO 3.5 0.6 - - - -
163G GLU* 1.3 76.4 - - - +
165G GLN* 1.3 59.3 + - - +
166G ASP* 3.5 9.5 + - - +
167G VAL* 3.5 18.8 + - - -
168G ALA* 2.9 26.2 + - - +
193G ALA* 3.4 9.0 - - - +
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Residues in contact with GLN 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G GLU 3.5 5.8 + - - +
164G SER* 1.3 71.6 + - - +
166G ASP* 1.3 63.2 + - - +
168G ALA* 3.5 7.2 - - + +
169G ALA* 2.9 30.1 + - - +
193G ALA 5.7 0.2 - - - -
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Residues in contact with ASP 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ILE* 4.6 13.2 - - + +
132G LYS* 5.9 0.9 - - - -
133G LEU* 4.1 22.4 - - + -
134G ALA* 3.3 36.2 + - - +
137G VAL* 3.7 9.1 - - + +
164G SER* 3.1 10.2 + - - +
165G GLN* 1.3 79.9 + - - +
167G VAL* 1.3 60.0 + - - +
169G ALA* 3.7 5.0 - - - +
170G ALA* 2.8 31.5 + - - +
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ILE* 3.9 22.0 - - + -
97G ILE* 4.5 1.1 - - + -
133G LEU* 3.7 22.9 - - + -
161G LEU* 3.8 22.2 - - + +
164G SER* 3.3 24.6 + - - +
166G ASP* 1.3 76.6 - - - +
168G ALA* 1.3 67.1 + - - +
170G ALA* 3.2 3.9 + - - +
171G LEU* 2.9 36.0 + - + +
190G ALA* 3.6 33.0 - - + +
193G ALA* 3.8 1.3 - - + -
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Residues in contact with ALA 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G SER 2.9 14.8 + - - +
165G GLN* 3.5 8.7 - - + +
167G VAL* 1.3 80.4 - - - +
169G ALA* 1.3 54.1 + - - +
171G LEU* 2.9 3.7 + - - +
172G GLN* 2.8 41.1 + - + +
193G ALA* 3.4 32.5 - - - +
194G LEU* 3.6 14.6 - - + +
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Residues in contact with ALA 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G VAL* 4.2 20.2 - - + -
165G GLN 2.9 22.2 + - - +
166G ASP* 3.7 4.5 - - - +
168G ALA* 1.3 72.9 - - - +
170G ALA* 1.3 57.8 + - - +
172G GLN* 3.1 13.3 + - - +
173G TRP* 2.9 28.4 + - - +
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Residues in contact with ALA 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 5.3 1.6 - - + -
54G ILE* 4.5 13.2 - - + -
133G LEU* 4.6 6.5 - - + -
137G VAL* 3.9 17.4 - - + +
140G LEU* 4.4 11.7 - - + -
149G ILE* 3.4 26.1 - - + +
166G ASP 2.8 21.3 + - - +
167G VAL 3.7 3.6 - - - +
169G ALA* 1.3 73.0 - - - +
171G LEU* 1.3 58.2 + - - +
173G TRP* 3.4 3.3 + - - +
174G ALA 2.9 23.0 + - - -
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Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ILE* 5.6 2.5 - - + -
149G ILE* 4.1 24.5 - - + -
151G VAL* 5.3 4.3 - - + -
167G VAL* 2.9 33.6 + - + +
168G ALA* 3.3 7.2 - - - +
170G ALA* 1.3 74.7 - - + +
172G GLN* 1.3 64.9 - - - +
174G ALA* 3.0 3.0 + - + +
175G ILE* 2.9 38.5 + - + +
181G VAL* 4.2 25.6 - - + -
190G ALA* 4.3 2.5 - - + +
191G PHE* 3.6 38.1 - - + -
194G LEU* 4.3 16.4 - - + -
201G LEU* 4.9 1.1 - - + -
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Residues in contact with GLN 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ALA* 2.8 31.8 + - - +
169G ALA* 3.3 11.2 - - - +
171G LEU* 1.3 72.1 - - - +
173G TRP* 1.3 63.5 + - - +
175G ILE* 3.8 7.0 - - - +
176G LYS* 2.9 26.8 + - - +
194G LEU* 3.8 19.8 - - + +
197G GLY* 4.7 11.3 - - - -
198G ASP* 3.5 27.5 + - - +
200G PRO* 3.8 14.5 - - - +
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Residues in contact with TRP 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 5.9 0.4 - - + -
140G LEU* 3.8 42.4 - - + -
141G ASN* 3.1 29.1 + - - +
144G SER* 3.6 24.2 - - - -
146G TYR* 3.6 42.2 - - + -
148G ALA 5.8 0.2 - - - -
149G ILE* 4.3 13.5 - - + -
169G ALA 2.9 12.6 + - - +
170G ALA 3.5 11.0 - - - +
172G GLN* 1.3 76.2 - - - +
174G ALA* 1.3 89.2 - - + +
175G ILE 3.2 0.2 + - - -
176G LYS* 3.2 7.5 + - - -
177G ASN* 3.1 48.4 + - + +
179G ARG* 3.9 19.7 - - + -
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Residues in contact with ALA 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ILE* 3.8 23.8 - - + -
170G ALA 2.9 14.3 + - - +
171G LEU* 3.0 11.2 + - - +
173G TRP* 1.3 89.7 - - + +
175G ILE* 1.3 60.8 + - - +
177G ASN 3.6 0.3 + - - -
178G ASP 3.5 1.7 + - - -
179G ARG* 2.9 37.4 + - + +
181G VAL* 4.1 20.4 - - + -
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G LEU* 2.9 34.3 + - + +
172G GLN 3.8 2.2 - - - +
174G ALA* 1.3 72.7 - - - +
176G LYS* 1.3 69.2 + - - +
177G ASN 3.0 2.2 - - - -
178G ASP* 2.9 15.9 + - - -
179G ARG 5.0 2.9 - - - +
181G VAL* 4.8 12.1 - - + -
194G LEU* 4.9 0.4 - - + -
200G PRO* 3.6 44.4 - - + +
201G LEU* 3.6 28.7 - - + -
204G TYR* 5.1 11.2 - - + +
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Residues in contact with LYS 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ALA* 5.8 3.4 - - - +
172G GLN 2.9 19.2 + - - +
173G TRP* 3.8 7.6 - - - +
175G ILE* 1.3 79.2 - - - +
177G ASN* 1.3 81.4 + - - +
178G ASP* 3.4 1.3 + - - +
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Residues in contact with ASN 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ALA* 3.3 34.0 - - - +
173G TRP* 3.1 48.2 + - - +
175G ILE 3.0 1.4 + - - -
176G LYS* 1.3 98.3 + - - +
178G ASP* 1.3 71.6 + - - +
179G ARG* 3.1 32.4 + - + +
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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