Contacts of the helix formed by residues 162 - 173 (chain H) in PDB entry 2WWA
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 THR 162 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160H GLN 3.6 2.9 + - - -
161H LYS* 1.4 71.8 - - - +
163H LYS* 1.4 76.9 + - + +
164H GLU 3.2 0.2 - - - -
165H ALA* 3.2 26.3 + - + +
166H VAL* 3.8 9.6 + - + +
218H ALA* 6.1 0.5 - - - +
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Residues in contact with LYS 163 (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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161H LYS* 3.4 1.9 - - + +
162H THR* 1.4 94.4 - - + +
164H GLU* 1.4 72.6 + - - +
165H ALA 3.3 0.4 - - - -
166H VAL* 3.7 13.3 + - + +
167H ALA* 3.5 18.0 + - - +
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Residues in contact with GLU 164 (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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159H ILE* 3.6 18.3 - - + +
161H LYS* 3.4 47.2 + - + +
162H THR 3.2 0.6 - - - -
163H LYS* 1.4 88.9 - - - +
165H ALA* 1.4 58.7 + - - +
166H VAL 3.4 0.7 - - - -
167H ALA* 3.7 12.8 - - + +
168H ALA* 3.2 24.3 + - - +
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Residues in contact with ALA 165 (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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159H ILE* 3.4 20.6 - - + +
161H LYS 3.6 0.6 + - - +
162H THR* 3.2 17.6 + - + +
164H GLU* 1.4 76.9 - - - +
166H VAL* 1.4 60.8 + - + +
168H ALA* 3.3 6.2 + - - +
169H LEU* 3.1 38.1 + - + +
222H VAL* 4.3 22.9 - - + -
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Residues in contact with VAL 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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162H THR* 3.8 15.9 - - + +
163H LYS* 3.7 13.7 + - + +
164H GLU 3.4 0.2 - - - -
165H ALA* 1.4 77.1 - - + +
167H ALA* 1.4 58.6 + - - +
169H LEU* 3.3 9.9 + - + +
170H LYS* 3.2 25.1 + - + +
175H HIS* 3.9 22.1 + - + -
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Residues in contact with ALA 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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11H LEU* 4.2 11.4 - - + +
163H LYS 3.5 11.9 + - - +
164H GLU* 3.7 17.5 - - + +
165H ALA 3.3 0.2 - - - -
166H VAL* 1.4 78.2 - - - +
168H ALA* 1.4 60.8 + - - +
170H LYS* 3.4 30.8 - - - +
171H ALA* 4.1 1.4 + - - +
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Residues in contact with ALA 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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11H LEU* 4.5 30.7 - - + +
152H VAL* 5.9 2.0 - - + -
156H LEU* 4.8 14.1 - - + -
159H ILE* 5.7 1.8 - - + -
164H GLU 3.2 12.3 + - - +
165H ALA* 3.6 10.1 - - - +
166H VAL 3.3 0.2 - - - -
167H ALA* 1.4 78.5 - - - +
169H LEU* 1.4 63.2 + - + +
171H ALA* 3.4 18.2 + - - +
172H VAL* 3.6 13.0 + - - +
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Residues in contact with LEU 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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165H ALA* 3.1 27.0 + - + +
166H VAL* 3.3 6.2 + - + +
168H ALA* 1.4 76.8 - - + +
170H LYS* 1.4 65.0 + - - +
172H VAL* 3.4 16.2 - - + +
173H GLY 3.2 16.5 + - - -
174H ALA* 5.2 0.4 - - + -
175H HIS* 3.6 31.9 + - + +
178H LEU* 3.8 44.0 - - + -
205H PRO* 5.6 3.6 - - + -
207H VAL* 6.4 1.3 - - + -
222H VAL* 4.3 16.4 - - + -
223H PRO* 6.1 0.2 - - + -
225H VAL* 5.7 4.3 - - + -
249H ILE* 5.9 2.2 - - + -
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Residues in contact with LYS 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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11H LEU 5.2 3.6 - - - -
12H THR 4.9 5.4 + - - -
13H GLY 5.0 1.4 - - - +
14H GLU* 3.9 27.7 + - - -
166H VAL* 3.2 12.5 + - + +
167H ALA* 3.4 25.1 - - - +
169H LEU* 1.4 75.7 - - - +
171H ALA* 1.4 73.9 + - - +
173H GLY* 3.5 12.1 + - - -
175H HIS* 3.9 18.5 + - + +
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Residues in contact with ALA 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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10H SER 4.5 2.9 - - - +
11H LEU* 4.4 16.4 - - - +
13H GLY 4.1 20.0 - - - +
144H LYS* 3.4 24.6 + - - +
167H ALA 4.3 7.2 - - - +
168H ALA 3.4 11.1 + - - +
169H LEU 3.3 0.2 - - - -
170H LYS* 1.4 93.6 - - - +
172H VAL* 1.4 62.9 + - + +
173H GLY* 3.6 0.3 + - - -
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Residues in contact with VAL 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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11H LEU* 6.6 0.7 - - + -
142H VAL* 4.8 0.2 - - - +
144H LYS* 3.7 10.6 - - - +
150H LEU* 3.2 39.5 - - + +
151H VAL 5.1 1.8 - - - +
152H VAL* 3.9 28.0 - - + -
168H ALA 3.6 13.7 - - - +
169H LEU* 3.4 25.8 - - + +
171H ALA* 1.4 78.0 - - + +
173H GLY* 1.4 65.1 - - - +
174H ALA* 3.4 13.1 + - + +
247H PHE* 4.4 0.9 - - - -
249H ILE* 4.2 17.0 - - + -
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Residues in contact with GLY 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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142H VAL* 3.9 1.4 - - - +
143H GLU* 3.6 9.6 + - - +
144H LYS* 3.2 32.7 + - - +
169H LEU 3.2 10.3 + - - -
170H LYS 3.5 11.4 + - - -
171H ALA 3.3 3.0 - - - -
172H VAL* 1.4 76.6 - - - +
174H ALA* 1.4 64.9 + - - +
175H HIS* 4.6 1.8 - - - -
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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