Contacts of the strand formed by residues 160 - 163 (chain C) in PDB entry 2I2X
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 160 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.9 0.9 - - + -
28C ALA* 3.9 24.2 - - + -
34C ILE* 4.4 11.2 - - + -
82C ILE* 4.3 17.9 - - + -
121C ALA* 4.8 4.3 - - + -
122C LEU 3.0 8.3 + - - +
123C ARG* 3.4 28.3 - - + +
124C HIS 3.0 26.7 + - - +
158C ALA* 4.4 0.9 - - - +
159C ASP* 1.3 87.1 - - + +
161C LEU* 1.3 64.9 + - - +
213C ILE* 3.6 18.8 - - + -
215C ALA* 4.0 13.2 - - + -
265C PRO* 4.2 27.4 - - + -
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C HIS* 3.6 6.3 - - + +
126C ILE* 4.7 5.2 - - + -
150C PHE* 4.0 40.4 - - + +
153C CYS* 4.8 0.7 - - + -
154C ALA* 4.0 17.3 - - + +
158C ALA* 4.2 17.3 - - + +
160C LEU* 1.3 81.6 - - - +
162C SER* 1.3 62.0 + - - +
200C TRP* 3.7 6.7 - - - -
203C ILE* 4.5 10.1 - - + -
206C ILE* 4.4 9.0 - - + -
207C ALA* 4.2 15.5 - - + -
212C THR* 3.6 22.0 - - - +
213C ILE 3.0 14.4 + - - +
215C ALA* 3.1 21.7 + - - +
216C GLY 3.7 1.7 + - - -
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Residues in contact with SER 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 3.0 33.4 + - - -
124C HIS 3.2 6.7 + - - +
125C THR* 3.3 21.0 - - - -
126C ILE 3.1 22.2 + - - -
150C PHE* 3.5 10.7 - - - -
161C LEU* 1.3 75.5 + - - +
163C VAL* 1.3 64.3 + - - +
200C TRP* 4.1 2.7 - - - -
215C ALA* 3.8 1.9 - - - +
216C GLY 3.2 18.6 + - - -
267C LYS* 3.7 10.9 - - - +
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Residues in contact with VAL 163 (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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125C THR* 3.9 3.8 - - - -
126C ILE 3.4 20.6 - - - +
128C ASP* 4.0 10.5 - - + +
146C PHE* 3.9 23.1 - - + -
150C PHE* 3.9 7.2 - - + -
162C SER* 1.3 77.4 - - - +
164C GLU* 1.3 75.2 + - - +
165C SER* 3.9 2.7 - - - +
199C ILE* 4.0 8.7 - - + -
200C TRP* 3.7 14.8 - - + -
203C ILE* 4.0 16.6 - - + -
216C GLY 3.8 1.8 + - - +
217C ASP* 3.1 46.2 - - - +
267C LYS* 4.6 2.0 - - - +
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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