Contacts of the helix formed by residues 158 - 163 (chain R) in PDB entry 1H2I
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 PHE 158 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q ASN* 3.3 15.9 + - - +
81Q TYR* 3.8 22.7 - + - +
43R LEU* 3.5 28.8 - - + +
79R PHE* 4.0 20.6 - + + -
113R VAL* 4.0 34.1 - - + -
115R LEU* 3.2 47.6 - - + -
119R SER* 4.6 2.5 - - - -
120R TYR* 4.7 7.2 - - - -
121R HIS* 3.6 27.4 - + - -
154R ALA 4.6 0.7 - - - -
155R LEU* 3.0 30.5 + - + +
156R ARG 3.0 0.8 + - - -
157R SER* 1.3 77.4 - - - +
159R GLY* 1.3 56.7 + - - +
162R LEU* 4.8 3.1 - - + -
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Residues in contact with GLY 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q ASN* 4.4 4.3 - - - -
76Q ASN* 3.9 9.4 - - - -
43R LEU* 3.9 9.0 - - - -
155R LEU 4.3 0.4 + - - -
156R ARG 3.0 8.1 + - - +
157R SER 3.3 1.4 - - - -
158R PHE* 1.3 80.8 - - - +
160R ASN* 1.3 66.7 + - - -
161R ALA 3.2 2.9 - - - -
162R LEU* 3.0 13.7 + - - +
163R GLY 3.4 0.3 + - - -
164R ASN* 3.1 21.6 + - - +
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Residues in contact with ASN 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q ASN* 3.1 33.6 + - - +
43R LEU 3.0 3.8 + - - -
44R ARG* 2.9 25.9 + - - +
45R GLN 3.1 16.6 - - - +
46R ARG* 4.2 17.3 + - - +
47R LEU* 3.0 13.7 - - - +
159R GLY* 1.3 71.4 - - - -
161R ALA* 1.3 58.5 + - - +
163R GLY 2.8 18.2 + - - -
164R ASN* 3.6 11.2 + - - +
165R CYS* 3.6 28.4 + - + +
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Residues in contact with ALA 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q LYS* 4.5 11.4 - - + +
42R ALA 3.4 25.8 - - - +
43R LEU* 2.8 19.4 + - - +
45R GLN* 3.0 11.5 + - + +
47R LEU* 3.8 9.3 - - - +
74R LEU* 3.5 26.2 - - - +
78R MET* 3.8 16.6 - - + -
160R ASN* 1.3 71.1 - - - +
162R LEU* 1.3 62.2 + - + +
163R GLY 3.4 0.7 - - - -
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Residues in contact with LEU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R LEU* 3.6 24.5 - - + -
66R ILE* 5.1 2.1 - - - +
71R VAL* 4.3 13.4 - - + +
74R LEU* 4.1 16.8 - - + +
75R ALA* 4.0 26.0 - - + +
78R MET* 4.1 23.3 - - + -
79R PHE* 4.6 8.7 - - + -
152R LYS 4.8 1.0 - - - +
155R LEU* 3.5 44.9 - - + +
156R ARG* 3.8 14.9 + - - +
158R PHE* 4.8 1.8 - - + -
159R GLY 3.0 11.7 + - - +
160R ASN 3.0 1.4 - - - -
161R ALA* 1.3 83.9 - - - +
163R GLY* 1.3 56.6 + - - +
164R ASN 3.8 0.2 - - - -
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Residues in contact with GLY 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R LEU* 4.3 3.6 - - - +
66R ILE* 3.9 22.6 - - - +
156R ARG* 3.9 15.1 - - - -
160R ASN 2.8 6.8 + - - -
161R ALA 3.4 1.2 + - - -
162R LEU* 1.3 81.9 - - - +
164R ASN* 1.3 64.6 + - - +
165R CYS 2.9 4.7 + - - -
166R ILE* 3.0 25.7 + - - +
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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