Contacts of the helix formed by residues 159 - 167 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.6 14.5 - - - +
62A TRP 2.9 16.4 + - - -
63A THR* 3.2 12.8 + - - -
158A PHE* 1.3 76.1 - - - +
160A PRO* 1.3 76.5 - - - +
161A TRP* 3.3 26.3 - - - -
162A MET* 3.2 23.6 + - - +
163A VAL* 3.2 19.1 + - - +
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Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 3.4 43.7 - - + +
106A ALA* 4.0 15.5 - - + -
107A THR 5.8 0.2 - - - +
158A PHE 3.4 3.3 - - - +
159A SER* 1.3 89.8 - - - +
161A TRP* 1.3 63.7 + - + +
163A VAL* 3.5 7.7 + - + +
164A MET* 3.1 36.3 + - - +
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Residues in contact with TRP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 4.4 23.1 - - - -
58A TRP* 3.5 53.4 - + + -
63A THR* 3.3 19.1 + - - -
64A ASN* 3.5 10.9 - - - +
67A CYS* 3.6 13.8 - - - -
102A PHE* 4.0 5.4 - - + -
104A PHE* 3.7 35.2 - + + -
159A SER* 3.3 21.1 - - - -
160A PRO* 1.3 82.7 - - + +
162A MET* 1.3 79.2 + - - +
163A VAL 3.2 0.2 - - - -
164A MET* 3.8 9.5 - - - +
165A GLN* 2.9 48.8 + - - +
186A EIP 3.5 30.1 - - + -
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Residues in contact with MET 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TRP* 3.9 25.8 - - + -
48A VAL* 3.8 21.3 - - + -
63A THR* 3.7 15.5 - - - -
64A ASN* 3.8 24.7 - - - +
147A VAL* 3.7 30.1 - - + -
151A ILE* 3.9 10.1 - - + -
158A PHE* 3.8 29.8 - - + -
159A SER* 3.2 20.7 + - - +
161A TRP* 1.3 85.1 - - - +
163A VAL* 1.3 62.3 + - - +
165A GLN* 3.2 1.8 + - - +
166A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.0 21.5 - - + +
155A PRO* 3.5 49.1 - - + +
158A PHE* 4.2 8.5 - - + +
159A SER 3.2 12.7 + - - +
160A PRO* 3.6 9.9 - - + +
162A MET* 1.3 78.4 - - - +
164A MET* 1.3 65.7 + - + +
166A ALA 3.2 0.3 + - - -
167A THR* 2.9 37.9 + - + +
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.4 2.3 - - - -
102A PHE* 3.6 25.6 - - + -
103A ARG 4.3 4.3 - - - +
104A PHE* 3.7 36.1 - - + -
105A ARG 5.8 1.6 - - - +
106A ALA* 6.2 1.1 - - - -
160A PRO* 3.1 23.2 + - - +
161A TRP* 3.8 3.8 - - - +
163A VAL* 1.3 76.2 - - + +
165A GLN* 1.3 64.7 + - - +
167A THR* 3.4 6.8 + - - -
168A ASN* 3.3 18.9 + - - +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER* 2.8 30.5 + - - -
38A TRP* 2.7 37.4 + - + +
64A ASN* 4.2 2.1 + - - -
98A ILE* 5.8 1.3 - - + -
99A TYR* 4.3 10.8 - - + -
102A PHE* 3.6 24.2 - - + -
118A CYS* 4.8 0.6 - - - -
120A VAL* 3.2 26.6 - - + +
161A TRP* 2.9 36.9 + - - +
162A MET* 3.2 3.3 + - - +
164A MET* 1.3 76.9 - - - +
166A ALA* 1.3 57.4 + - - +
168A ASN* 3.0 23.6 + - - +
171A ALA* 3.6 14.5 - - + +
172A ARG 4.5 0.2 + - - -
175A LEU* 5.5 0.9 - - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TRP* 3.9 12.5 - - + -
148A LEU* 3.7 16.6 - - + -
151A ILE* 3.5 35.7 - - + -
162A MET 3.0 11.9 + - - +
163A VAL 3.8 2.5 - - - +
165A GLN* 1.3 76.8 - - - +
167A THR* 1.3 61.3 + - - +
168A ASN 3.2 1.4 + - - -
172A ARG* 3.0 33.2 + - - +
175A LEU* 4.9 6.5 - - - -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.1 16.6 - - + +
152A ASP* 4.2 5.2 - - - +
163A VAL* 2.9 28.5 + - + +
164A MET* 3.7 8.0 + - - -
165A GLN 3.1 0.2 - - - -
166A ALA* 1.3 78.5 - - - +
168A ASN* 1.3 63.5 + - - +
169A ARG* 3.3 3.3 + - - -
172A ARG* 3.9 17.9 - - - +
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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