Contacts of the helix formed by residues 152 - 162 (chain C) in PDB entry 2I6A
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 LEU 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C GLU 4.1 18.6 - - - +
148C LYS* 4.2 14.1 - - - +
149C HIS* 3.3 15.6 + - + +
151C ASP* 1.3 79.8 - - + +
153C GLU* 1.3 60.5 + - - +
154C LYS* 3.4 25.6 - - + +
155C ASN* 3.2 19.0 + - - +
156C TRP* 2.8 27.0 + - - +
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ASP 3.7 2.6 + - - -
152C LEU* 1.3 72.7 - - - +
154C LYS* 1.3 66.2 + - - +
156C TRP* 4.5 5.2 - - - +
157C MET* 2.9 37.7 + - + +
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C HIS* 6.1 2.0 - - + +
152C LEU* 3.8 26.5 - - + +
153C GLU* 1.3 80.1 - - - +
155C ASN* 1.3 79.9 + - - +
157C MET* 2.8 30.8 - - + +
158C LEU* 3.5 12.6 - - - +
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 3.6 23.0 - - + -
111C HIS* 4.1 20.6 + - - +
149C HIS* 3.1 53.8 + - + +
150C LEU 4.4 0.7 - - - +
152C LEU* 3.2 20.2 + - - +
153C GLU 3.1 0.2 - - - -
154C LYS* 1.3 95.4 + - - +
156C TRP* 1.3 62.5 + - - +
157C MET 3.0 1.6 - - - -
158C LEU* 2.8 28.9 + - - +
159C VAL 3.5 3.3 + - - -
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 3.2 39.6 + - + +
151C ASP 4.6 2.7 - - - +
152C LEU 2.8 18.6 + - - +
153C GLU* 4.4 3.8 - - - +
155C ASN* 1.3 73.2 - - - +
157C MET* 1.3 62.2 + - - +
158C LEU 3.2 0.2 - - - -
159C VAL* 3.3 27.3 + - + +
160C GLU* 3.2 40.5 + - + +
181C LYS* 3.1 52.0 - - + +
182C VAL* 4.4 6.7 - - + -
185C HIS* 3.5 39.3 - + + -
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Residues in contact with MET 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU* 2.9 28.2 + - + +
154C LYS* 2.8 45.1 - - + +
155C ASN 3.0 0.2 - - - -
156C TRP* 1.3 79.1 - - - +
158C LEU* 1.3 73.1 + - + +
160C GLU* 3.2 17.6 + - + +
161C LYS* 3.1 26.4 + - + +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASN* 4.1 20.9 - - - +
10C PHE* 5.0 2.4 - - - +
85C THR* 4.2 11.2 + - + -
87C PHE* 4.1 12.8 - - + -
109C ASP* 3.9 6.1 - - - +
111C HIS* 3.0 47.3 - - + +
154C LYS 3.5 18.2 - - - +
155C ASN* 2.8 10.3 + - - +
157C MET* 1.3 85.7 - - + +
159C VAL* 1.3 61.4 + - - +
161C LYS* 3.3 35.8 + - + +
162C ALA* 3.8 5.2 + - - +
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Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.4 46.0 - - + -
87C PHE* 3.7 13.0 - - + -
150C LEU* 4.0 13.5 - - + -
155C ASN 4.2 1.8 - - - +
156C TRP* 3.3 39.7 + - + +
158C LEU* 1.3 76.6 - - - +
160C GLU* 1.3 63.5 + - - +
161C LYS 3.1 0.6 + - - -
162C ALA* 3.4 17.2 + - - +
165C CYS* 4.9 3.3 - - - -
182C VAL* 4.7 13.7 - - + -
185C HIS* 4.5 12.4 + - + -
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C TRP* 3.4 38.6 + - + +
157C MET* 3.2 13.9 + - + +
159C VAL* 1.3 78.6 - - - +
161C LYS* 1.3 60.2 + - + +
162C ALA 3.4 2.0 + - - +
185C HIS* 2.9 35.7 + - + -
191C ARG* 3.6 23.2 + - - -
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Residues in contact with LYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 5.7 6.9 - - - +
6C GLU* 3.6 26.2 + - - +
7C ASN* 3.3 32.7 + - + +
8C ILE* 4.3 4.5 - - - +
157C MET* 3.1 27.1 - - + +
158C LEU* 3.4 24.3 - - + +
159C VAL 3.1 0.6 - - - -
160C GLU* 1.3 79.0 - - + +
162C ALA* 1.3 63.7 + - - +
163C ARG* 3.7 4.9 + - - +
191C ARG* 5.5 0.7 + - - -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASN 3.2 12.9 + - - +
8C ILE 3.5 0.7 - - - -
10C PHE* 3.5 35.9 - - + +
158C LEU 3.8 1.2 + - - +
159C VAL 3.4 12.0 + - - +
160C GLU 3.4 2.4 - - - +
161C LYS* 1.3 79.6 - - - +
163C ARG* 1.3 60.3 - - - +
164C VAL 3.5 13.2 - - - +
165C CYS* 4.2 7.4 - - - -
191C ARG* 3.5 26.9 + - - +
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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