Contacts of the helix formed by residues 165 - 175 (chain H) in PDB entry 2A3W
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 PRO 165 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163H VAL 3.6 6.9 - - - +
164H LEU* 1.3 89.4 - - + +
166H PRO* 1.3 77.6 - - + +
167H GLU* 3.2 23.6 - - + +
168H ASN* 3.0 44.1 + - - +
169H ILE* 3.2 7.5 + - - +
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Residues in contact with PRO 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G VAL* 3.8 29.2 - - + -
106H GLU* 5.8 1.3 - - - +
108H TRP* 3.6 30.7 - - + -
164H LEU 3.9 1.5 - - - +
165H PRO* 1.3 86.5 - - + +
167H GLU* 1.3 66.0 + - - +
169H ILE* 3.1 7.7 + - + +
170H LEU* 2.9 37.8 + - + +
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Residues in contact with GLU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H PRO* 3.5 24.3 - - + +
166H PRO* 1.3 86.8 - - - +
168H ASN* 1.3 68.6 + - - +
170H LEU* 3.3 12.4 + - - +
171H SER* 3.0 28.0 + - - -
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Residues in contact with ASN 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H TRP* 5.9 0.2 - - - -
164H LEU* 3.7 24.9 - - + +
165H PRO* 3.0 36.5 + - - +
167H GLU* 1.3 82.0 - - - +
169H ILE* 1.3 64.7 + - - +
171H SER* 3.3 10.4 + - - -
172H ALA* 3.1 21.0 + - - +
177H PRO* 5.2 1.2 - - - +
178H LEU* 3.5 40.7 + - + +
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Residues in contact with ILE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H THR* 3.8 23.8 - - + -
36H CYS* 4.5 0.4 - - - -
93H HIS* 5.6 0.4 - - + -
95H CYS* 3.7 33.8 - - + -
97H SER* 5.4 2.9 - - - -
106H GLU* 5.4 0.9 - - - +
108H TRP* 3.6 48.2 - - + +
111H GLY* 5.4 2.2 - - - -
164H LEU* 3.9 17.9 - - + +
165H PRO 3.2 15.8 + - - +
166H PRO* 3.2 11.7 - - + +
168H ASN* 1.3 75.8 - - - +
170H LEU* 1.3 65.4 + - + +
172H ALA* 3.1 7.4 + - - +
173H TYR* 3.0 20.5 + - + +
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Residues in contact with LEU 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H TRP* 4.9 8.7 - - + -
111H GLY* 3.5 39.7 - - - +
166H PRO* 2.9 23.5 + - + +
167H GLU* 3.6 11.7 - - - +
168H ASN 3.3 0.2 - - - -
169H ILE* 1.3 76.9 - - + +
171H SER* 1.3 56.9 + - - +
173H TYR* 3.3 10.9 + - + +
174H GLN* 2.9 34.6 + - - +
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Residues in contact with SER 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167H GLU 3.0 14.4 + - - -
168H ASN* 3.4 15.2 + - - -
170H LEU* 1.3 73.8 - - - +
172H ALA* 1.3 64.0 + - - +
174H GLN* 3.2 4.7 + - - +
175H GLY 3.0 5.4 + - - -
176H THR* 2.8 52.9 + - - -
177H PRO* 4.7 0.2 - - - -
178H LEU* 4.5 9.7 - - - +
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Residues in contact with ALA 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H CYS* 4.2 19.5 - - + -
38H ARG* 3.1 12.1 + - - -
93H HIS* 3.7 16.9 + - + +
156H ASP* 5.9 0.9 - - - +
158H TYR* 5.8 1.6 - - + -
160H TRP* 4.5 4.9 - - + -
168H ASN 3.1 13.0 + - - +
169H ILE* 3.1 9.4 + - - +
171H SER* 1.3 73.9 - - - +
173H TYR* 1.3 62.6 + - - +
175H GLY* 3.1 12.1 + - - -
177H PRO* 3.9 28.1 - - + +
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Residues in contact with TYR 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 2.9 23.6 + - - -
93H HIS* 3.5 37.4 - + + +
110H ASN* 3.4 42.9 + - + +
111H GLY* 3.8 17.5 - - - +
169H ILE* 3.0 11.5 + - + +
170H LEU* 3.4 17.0 - - + +
172H ALA* 1.3 77.4 - - - +
174H GLN* 1.3 82.6 + - - +
175H GLY 3.2 0.2 - - - -
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Residues in contact with GLN 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 4.4 0.4 - - - -
170H LEU* 2.9 17.8 + - - +
171H SER* 3.9 6.3 - - - +
172H ALA 3.2 0.4 - - - -
173H TYR* 1.3 104.2 + - - +
175H GLY* 1.3 57.7 + - - +
176H THR* 3.6 7.5 - - - +
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Residues in contact with GLY 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.9 9.2 - - - -
156H ASP* 5.8 2.0 - - - -
171H SER 3.0 2.2 + - - -
172H ALA 3.1 11.8 + - - -
173H TYR 3.2 0.8 - - - -
174H GLN* 1.3 79.3 - - - +
176H THR* 1.3 65.4 - - - +
177H PRO* 3.2 13.1 - - - +
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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