Contacts of the helix formed by residues 159 - 167 (chain B) in PDB entry 2G73
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 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B VAL* 3.5 11.8 - - - +
62B TRP 2.9 13.7 + - - -
63B THR* 2.9 28.2 + - - -
158B PHE* 1.3 74.7 - - - +
160B PRO* 1.3 71.8 - - - +
161B TRP* 3.4 27.9 - - - -
162B MET* 3.1 24.6 + - - +
163B VAL* 3.4 10.7 + - - +
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.6 37.0 - - + +
104B PHE* 5.2 0.9 - - + -
106B ALA* 4.9 13.2 - - + -
107B THR 5.8 0.7 - - - +
155B PRO 5.7 0.4 - - - +
158B PHE 3.3 4.9 - - - +
159B SER* 1.3 86.0 - - - +
161B TRP* 1.3 61.1 + - + +
163B VAL* 3.2 9.6 + - + +
164B MET* 3.0 43.0 + - + +
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Residues in contact with TRP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 4.2 22.9 - - - -
58B TRP* 3.6 46.9 - + + -
63B THR* 3.1 27.4 + - + -
64B ASN* 3.5 10.9 - - - +
67B CYS* 3.3 23.6 - - - -
102B PHE* 4.4 9.9 - - + -
104B PHE* 3.8 22.8 - + + -
159B SER* 3.4 19.1 - - - -
160B PRO* 1.3 83.8 - - + +
162B MET* 1.3 63.6 + - - +
164B MET* 4.0 9.6 - - - +
165B GLN* 3.0 49.4 + - - +
186B EIP 3.1 32.8 - - + +
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Residues in contact with MET 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 5.3 0.2 - - + -
38B TRP* 3.8 22.1 - - + -
48B VAL* 4.1 15.3 - - + -
63B THR* 3.6 32.3 - - - +
64B ASN* 3.5 22.7 - - - +
147B VAL* 3.8 28.5 - - + -
151B ILE* 4.0 7.9 - - + -
158B PHE* 3.8 31.4 - - + -
159B SER* 3.1 21.9 + - - +
161B TRP* 1.3 79.2 - - - +
163B VAL* 1.3 63.0 + - - +
166B ALA* 3.0 26.7 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 3.9 32.1 - - + -
155B PRO* 3.5 39.7 - - + +
158B PHE* 4.3 8.7 - - + -
159B SER 3.6 12.8 - - - +
160B PRO* 3.5 9.2 - - + +
162B MET* 1.3 77.0 - - - +
164B MET* 1.3 65.2 + - + +
166B ALA* 3.3 1.0 + - - +
167B THR* 3.0 36.1 + - + +
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TYR* 4.6 2.6 + - - -
102B PHE* 3.9 30.7 - - + -
104B PHE* 4.5 15.9 - - + -
105B ARG 5.6 4.3 - - - +
160B PRO* 3.0 32.6 + - + +
161B TRP* 4.0 3.8 - - - +
163B VAL* 1.3 79.6 - - + +
165B GLN* 1.3 64.8 + - - +
167B THR* 3.4 15.2 + - - -
168B ASN* 3.4 10.7 + - - +
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 2.9 33.2 + - - -
38B TRP* 2.9 33.4 + - + +
64B ASN* 4.2 1.6 + - - -
99B TYR* 4.3 9.0 - - + -
102B PHE* 3.6 34.4 - - + -
118B CYS* 4.3 1.6 - - - -
120B VAL* 3.4 22.9 - - + +
161B TRP* 3.0 28.7 + - - +
162B MET 4.1 1.8 - - - +
164B MET* 1.3 77.0 - - - +
166B ALA* 1.3 63.0 + - - +
168B ASN* 3.1 11.8 + - - +
171B ALA* 3.4 22.5 - - + +
175B LEU* 5.5 0.4 - - - -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TRP* 4.0 9.8 - - + -
148B LEU* 3.8 15.0 - - + -
151B ILE* 3.8 22.4 - - + -
162B MET 3.0 19.6 + - - +
163B VAL 3.7 3.8 - - - +
165B GLN* 1.3 77.0 - - - +
167B THR* 1.3 54.8 + - + +
168B ASN 3.3 0.2 - - - -
172B ARG* 2.6 42.8 + - - +
175B LEU* 4.5 12.1 - - - -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 4.5 8.5 - - + -
163B VAL* 3.0 30.6 + - + +
164B MET* 3.4 10.0 + - - -
165B GLN 3.2 0.2 - - - -
166B ALA* 1.3 76.2 - - - +
168B ASN* 1.3 62.3 + - - +
169B ARG* 3.4 3.7 + - - +
172B ARG* 3.7 20.6 - - - +
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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