Contacts of the helix formed by residues 164 - 177 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E ILE* 3.7 37.9 - - - +
160E GLY 3.4 0.6 + - - -
161E LEU 3.0 12.9 + - - -
162E PRO 3.6 0.6 - - - -
163E GLU* 1.3 76.7 - - - +
165E GLN* 1.3 58.1 + - - +
166E ASP* 3.5 14.2 + - - +
167E VAL* 3.5 19.0 + - - -
168E ALA* 3.0 23.2 + - - +
193E ALA* 3.4 10.8 - - - +
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Residues in contact with GLN 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLU 3.6 7.5 + - - +
164E SER* 1.3 73.1 + - - +
166E ASP* 1.3 57.6 + - - +
168E ALA* 3.4 8.8 + - - +
169E ALA* 2.8 34.0 + - - +
193E ALA 5.7 0.2 - - - -
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Residues in contact with ASP 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ILE* 4.5 13.1 - - + +
132E LYS* 5.5 0.7 + - - -
133E LEU* 4.0 21.9 - - + +
134E ALA* 3.4 35.0 + - - +
137E VAL* 3.6 9.8 - - + +
164E SER* 3.6 10.7 + - - +
165E GLN* 1.3 80.1 + - - +
167E VAL* 1.3 59.9 + - - +
169E ALA* 3.3 7.0 + - - +
170E ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ILE* 3.9 20.9 - - + -
97E ILE* 4.6 1.8 - - + -
133E LEU* 3.7 22.4 - - + -
151E VAL* 6.1 0.2 - - + -
161E LEU* 3.9 19.7 - - + +
164E SER* 3.2 24.1 + - - +
166E ASP* 1.3 74.7 - - - +
168E ALA* 1.3 67.4 + - - +
170E ALA* 3.3 3.2 + - - +
171E LEU* 2.9 43.4 + - + +
190E ALA* 3.9 16.2 - - + +
193E ALA* 3.9 11.9 - - + -
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Residues in contact with ALA 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E SER 3.0 11.4 + - - +
165E GLN* 3.4 12.8 - - - +
167E VAL* 1.3 79.7 - - - +
169E ALA* 1.3 57.3 + - - +
171E LEU* 3.2 0.4 + - - -
172E GLN* 2.8 35.1 + - + +
193E ALA* 3.4 30.5 - - - +
194E LEU* 3.5 17.6 - - + +
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Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E VAL* 3.8 24.9 - - + -
140E LEU* 5.2 0.4 - - - +
165E GLN 2.8 20.8 + - - +
166E ASP* 3.6 7.0 - - - +
167E VAL 3.3 0.2 - - - -
168E ALA* 1.3 71.9 - - - +
170E ALA* 1.3 63.8 + - - +
172E GLN* 3.3 8.5 + - - +
173E TRP* 3.0 23.6 + - - +
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Residues in contact with ALA 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.2 1.6 - - + -
54E ILE* 3.9 24.7 - - + -
133E LEU* 4.6 5.2 - - + -
137E VAL* 3.9 16.0 - - + +
140E LEU* 4.7 3.8 - - + -
149E ILE* 4.1 11.8 - - + +
166E ASP 2.9 17.6 + - - +
167E VAL* 3.5 4.9 - - - +
169E ALA* 1.3 75.2 - - - +
171E LEU* 1.3 62.9 + - - +
173E TRP* 3.2 10.9 + - - +
174E ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ILE* 5.5 0.9 - - + -
149E ILE* 4.2 19.3 - - + -
151E VAL* 4.9 6.1 - - + -
167E VAL* 2.9 37.6 + - + +
168E ALA 3.6 3.1 - - - +
170E ALA* 1.3 76.4 - - + +
172E GLN* 1.3 65.3 + - - +
174E ALA* 3.2 4.9 + - - +
175E ILE* 3.1 31.4 + - + +
181E VAL* 4.1 28.9 - - + -
190E ALA* 4.1 2.5 - - + +
191E PHE* 3.8 38.4 - - + +
193E ALA* 5.2 0.2 - - + -
194E LEU* 4.0 22.4 - - + -
201E LEU* 5.4 0.4 - - + -
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Residues in contact with GLN 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ALA* 2.8 24.7 + - + +
169E ALA* 3.4 11.7 - - - +
171E LEU* 1.3 73.2 - - - +
173E TRP* 1.3 64.6 + - - +
175E ILE* 3.9 0.7 - - - +
176E LYS* 2.8 31.7 + - - +
194E LEU* 3.8 12.4 - - + +
197E GLY* 4.9 5.5 - - - -
198E ASP* 2.6 36.1 + - - +
199E ASN 4.8 0.4 - - - +
200E PRO* 3.4 26.0 - - - +
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Residues in contact with TRP 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.5 36.5 - - + +
141E ASN* 2.6 30.1 + - - +
144E SER* 3.4 20.9 - - - -
146E TYR* 3.5 37.2 - + + -
148E ALA 5.8 0.4 - - - -
149E ILE* 4.5 11.4 - - + -
169E ALA 3.0 9.9 + - - +
170E ALA 3.3 11.0 - - - +
172E GLN* 1.3 79.9 - - - +
174E ALA* 1.3 89.0 + - + +
176E LYS* 3.1 4.4 + - + -
177E ASN* 2.9 48.7 + - - +
179E ARG* 3.4 44.6 - - + -
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Residues in contact with ALA 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ILE* 3.6 30.7 - - + -
170E ALA 3.0 5.2 + - - +
171E LEU* 3.2 9.8 + - - +
173E TRP* 1.3 92.2 - - + +
175E ILE* 1.3 58.0 + - - +
177E ASN 3.3 0.7 + - - -
178E ASP 3.2 2.8 + - - -
179E ARG* 2.8 43.3 + - + +
180E PHE 4.7 0.4 - - - +
181E VAL* 4.2 15.9 - - + -
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Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU* 3.1 29.8 + - + +
172E GLN 4.1 0.7 - - - +
174E ALA* 1.3 72.8 - - - +
176E LYS* 1.3 66.1 + - - +
178E ASP* 3.1 15.1 + - - +
179E ARG 4.7 4.7 - - - +
181E VAL* 3.8 22.0 - - + -
194E LEU* 4.7 1.3 - - + -
200E PRO* 3.8 38.6 - - + +
201E LEU* 3.6 35.0 - - + +
204E TYR* 4.4 14.6 - - + +
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Residues in contact with LYS 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E GLN* 2.8 21.6 + - - +
173E TRP* 3.7 5.2 - - - +
175E ILE* 1.3 76.7 - - - +
177E ASN* 1.3 83.4 + - - +
178E ASP 3.4 0.7 + - - -
200E PRO* 5.5 2.6 - - + +
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Residues in contact with ASN 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASN 4.3 1.4 + - - -
142E ALA* 3.6 29.5 - - - +
173E TRP* 2.9 52.1 + - + +
174E ALA 4.2 1.6 - - - +
176E LYS* 1.3 97.9 - - - +
178E ASP* 1.3 71.5 + - - +
179E ARG* 3.2 35.2 + - + +
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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