Contacts of the strand formed by residues 153 - 159 (chain C) in PDB entry 2I3T
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 ILE 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C CYS* 3.4 9.4 - - - -
118C ALA* 4.0 23.1 - - + -
119C SER 3.4 11.7 - - - +
120C TRP* 3.1 31.0 + - - -
122C GLY* 3.9 16.4 - - - -
123C LEU 4.2 0.4 - - - +
124C ILE* 3.8 24.9 - - + -
142C LEU* 3.6 30.5 - - + -
152C LYS* 1.3 78.8 - - - +
154C PHE* 1.3 62.7 + - - +
155C THR 3.5 19.7 - - - +
165C VAL* 4.0 17.0 - - + -
166C GLY 3.7 2.7 - - - -
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Residues in contact with PHE 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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105C CYS* 4.1 12.9 - - - +
106C ARG* 3.8 12.1 + - - -
120C TRP* 4.5 7.1 + + - +
152C LYS* 3.8 20.8 - - + -
153C ILE* 1.3 79.5 - - - +
155C THR* 1.3 64.1 + - + +
166C GLY 2.8 11.1 + - - +
167C MET 3.7 13.5 - - - -
168C ASN* 3.7 24.9 - - + -
195C GLN* 3.8 9.6 - - + -
196C ILE 3.8 23.1 - - - +
197C ARG* 4.8 3.1 - - - +
378D GLU* 3.4 28.7 - - + -
379D PHE 4.4 0.2 - - - -
380D SER* 3.7 27.6 - - - -
382D GLU* 5.6 5.9 - - + +
383D GLU* 3.0 25.1 - - - -
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Residues in contact with THR 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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105C CYS* 4.9 0.9 - - - -
106C ARG* 3.2 15.9 + - - +
153C ILE* 3.5 8.2 - - - +
154C PHE* 1.3 80.7 - - + +
156C MET* 1.3 73.8 + - - +
165C VAL* 3.4 2.8 - - - -
166C GLY* 2.8 35.1 + - - +
196C ILE* 4.1 6.3 - - + -
197C ARG 3.8 9.2 - - - +
198C ASP* 2.7 42.9 + - - +
199C VAL* 3.5 21.4 + - + +
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Residues in contact with MET 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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106C ARG* 3.7 25.9 + - + +
108C CYS* 3.5 28.0 - - + -
116C ILE* 3.4 29.4 - - + +
117C ALA 3.9 1.6 - - - -
118C ALA* 3.4 36.1 - - + +
124C ILE* 5.1 3.8 - - - -
155C THR* 1.3 85.5 + - - +
157C ASP* 1.3 72.3 + - - +
163C LEU* 4.1 21.8 - - + -
164C ILE 3.3 15.3 - - - +
165C VAL* 4.0 15.3 - - + -
198C ASP* 5.3 0.2 - - - +
199C VAL* 4.1 6.3 - - - +
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Residues in contact with ASP 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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108C CYS* 3.9 6.3 - - - -
156C MET* 1.3 78.4 - - - +
158C THR* 1.3 82.6 + - - +
163C LEU* 3.6 0.2 - - - -
164C ILE* 3.0 40.1 + - + +
199C VAL 3.8 16.2 - - - +
200C ALA* 3.5 6.2 - - - +
201C LEU* 2.7 37.6 + - - +
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Residues in contact with THR 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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108C CYS* 3.6 23.2 - - + +
109C LYS* 2.6 33.1 + - - +
116C ILE* 4.2 4.5 - - + -
156C MET* 4.8 0.9 - - + -
157C ASP* 1.3 93.6 + - - +
159C ASN* 1.3 65.6 + - - +
162C ARG 3.3 8.1 - - - -
163C LEU* 3.8 30.1 - - + -
177C LEU* 4.3 8.1 - - + -
201C LEU* 3.4 6.1 - - - +
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Residues in contact with ASN 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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109C LYS 5.6 0.2 - - - +
158C THR* 1.3 76.8 - - - +
160C SER* 1.3 67.7 + - - +
161C SER* 3.0 6.6 + - - -
162C ARG* 2.8 39.4 + - - +
177C LEU* 3.6 10.4 - - - +
201C LEU* 3.8 29.2 - - + +
202C LEU 4.4 1.8 + - - -
204C LYS* 3.9 35.9 - - + +
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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