Contacts of the helix formed by residues 164 - 177 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.2 35.9 - - - +
160D GLY 3.2 12.1 + - - -
161D LEU 3.2 4.3 + - - -
162D PRO 3.7 0.2 - - - -
163D GLU* 1.3 76.6 - - - +
165D GLN* 1.3 65.7 + - - +
166D ASP* 3.6 6.9 + - - +
167D VAL* 3.4 24.8 + - - -
168D ALA* 3.2 17.5 + - - +
193D ALA* 3.6 9.0 - - - +
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Residues in contact with GLN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D GLU 3.8 3.6 + - - -
164D SER* 1.3 73.4 + - - +
166D ASP* 1.3 67.7 + - - +
168D ALA* 3.4 7.4 + - - +
169D ALA* 3.3 20.4 + - - +
193D ALA 6.0 0.2 - - - -
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Residues in contact with ASP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 4.4 14.3 - - + +
132D LYS* 5.7 0.7 + - - -
133D LEU* 3.6 25.2 - - + +
134D ALA* 3.1 36.3 + - - +
137D VAL* 3.8 9.2 - - + +
164D SER* 3.2 7.7 + - - +
165D GLN* 1.3 81.2 + - - +
167D VAL* 1.3 59.7 + - - +
169D ALA* 3.2 6.5 + - - +
170D ALA* 3.0 29.8 + - - +
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.0 23.7 - - + +
97D ILE* 4.2 1.6 - - + -
133D LEU* 3.4 21.5 - - + -
161D LEU* 3.7 22.7 - - + +
164D SER* 3.3 25.2 + - - +
166D ASP* 1.3 77.9 - - - +
168D ALA* 1.3 62.9 + - - +
170D ALA* 3.8 3.7 - - - +
171D LEU* 3.1 29.3 + - + +
190D ALA* 3.6 34.8 - - + +
193D ALA* 3.7 2.0 - - + -
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D SER 3.2 9.6 + - - +
165D GLN* 3.5 11.4 - - - +
166D ASP 3.2 0.2 - - - -
167D VAL* 1.3 77.6 - - - +
169D ALA* 1.3 51.0 + - - +
171D LEU* 3.1 4.6 + - - +
172D GLN* 2.6 43.4 + - + +
193D ALA* 3.4 32.1 - - - +
194D LEU* 3.6 14.7 - - + +
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.8 24.1 - - + +
140D LEU* 5.0 0.2 - - - +
165D GLN 3.3 8.8 + - - +
166D ASP* 3.2 9.5 + - - +
168D ALA* 1.3 76.2 - - - +
170D ALA* 1.3 60.6 + - - +
172D GLN* 3.5 10.5 - - - +
173D TRP* 2.8 31.0 + - - +
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.1 2.5 - - + -
54D ILE* 4.3 13.9 - - + -
133D LEU* 4.4 8.5 - - + -
137D VAL* 4.3 9.8 - - + +
140D LEU* 4.5 14.6 - - + -
149D ILE* 3.3 26.8 - - + +
166D ASP 3.0 16.4 + - - +
167D VAL 3.8 5.4 - - - +
169D ALA* 1.3 78.7 - - - +
171D LEU* 1.3 62.4 + - - +
173D TRP* 3.3 4.5 + - - +
174D ALA 3.0 17.0 + - - -
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 5.2 2.2 - - + -
149D ILE* 4.1 24.2 - - + -
151D VAL* 5.1 6.3 - - + -
167D VAL* 3.1 20.8 + - + +
168D ALA* 3.1 7.0 + - - +
170D ALA* 1.3 77.0 - - - +
172D GLN* 1.3 67.2 + - - +
174D ALA* 2.9 15.4 + - - +
175D ILE* 3.0 24.7 + - + +
181D VAL* 4.5 14.1 - - + -
190D ALA* 3.9 18.2 - - + +
191D PHE* 3.7 40.6 - - + -
194D LEU* 3.9 19.7 - - + -
201D LEU* 4.9 2.2 - - + -
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA* 2.6 34.0 + - + +
169D ALA* 3.5 9.0 - - - +
171D LEU* 1.3 71.8 - - - +
173D TRP* 1.3 58.6 + - - +
175D ILE* 3.3 5.6 + - - +
176D LYS* 2.9 33.8 + - - +
194D LEU* 3.9 13.0 - - + +
197D GLY* 4.9 5.5 - - - -
198D ASP* 3.2 40.0 + - - +
199D ASN 4.6 0.4 - - - +
200D PRO* 3.6 23.7 - - - +
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Residues in contact with TRP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.9 1.1 - - + -
140D LEU* 3.7 39.3 - - + -
141D ASN* 3.0 27.4 + - - +
144D SER* 3.4 17.5 - - - -
146D TYR* 3.5 31.2 - + + -
148D ALA 5.7 0.2 - - - -
149D ILE* 4.5 13.2 - - + -
169D ALA 2.8 18.3 + - - +
170D ALA 3.5 8.1 - - - +
172D GLN* 1.3 76.2 - - - +
174D ALA* 1.3 80.4 + - + +
176D LYS* 4.5 11.0 - - - +
177D ASN* 3.1 53.1 + - - +
179D ARG* 3.4 44.2 - - + -
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ILE* 4.0 19.5 - - + -
170D ALA 3.0 11.9 + - - +
171D LEU* 2.9 10.7 + - - +
173D TRP* 1.3 85.8 - - + +
175D ILE* 1.3 61.4 + - - +
177D ASN 3.5 0.5 - - - -
178D ASP 3.0 4.2 + - - -
179D ARG* 2.7 40.8 + - + +
181D VAL* 4.0 23.8 - - + -
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Residues in contact with ILE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.0 28.8 + - + +
172D GLN 3.9 2.7 - - - +
174D ALA* 1.3 72.3 - - - +
176D LYS* 1.3 64.0 + - - +
178D ASP* 2.9 22.9 + - - +
179D ARG 4.9 2.2 - - - +
181D VAL* 4.9 12.3 - - + -
194D LEU* 5.0 0.2 - - + -
200D PRO* 3.7 47.1 - - + +
201D LEU* 3.8 36.6 - - + -
204D TYR* 5.1 9.4 - - + +
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 5.9 1.6 - - - +
172D GLN 2.9 18.4 + - - +
173D TRP* 4.0 11.3 - - - +
175D ILE* 1.3 79.9 - - - +
177D ASN* 1.3 77.8 + - - +
178D ASP* 3.5 1.0 + - - +
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Residues in contact with ASN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 3.3 34.3 - - - +
173D TRP* 3.1 51.6 + - - +
176D LYS* 1.3 96.5 + - - +
178D ASP* 1.3 71.5 + - - +
179D ARG* 3.3 33.1 + - + +
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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