Contacts of the strand formed by residues 160 - 163 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G VAL* 4.8 0.7 - - + -
28G ALA* 4.0 18.8 - - + -
34G ILE* 4.4 10.5 - - + -
82G ILE* 4.7 13.9 - - + -
121G ALA* 5.0 4.5 - - + -
122G LEU 3.0 7.1 + - - +
123G ARG* 3.4 33.2 - - + +
124G HIS 3.1 26.2 + - - +
158G ALA* 4.2 0.9 - - - +
159G ASP* 1.3 84.8 - - + +
161G LEU* 1.3 68.7 + - - +
213G ILE* 3.5 28.0 - - + -
215G ALA* 4.1 7.2 - - + -
265G PRO* 4.1 30.7 - - + -
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Residues in contact with LEU 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G HIS 3.7 5.8 - - - +
126G ILE* 5.1 1.6 - - + -
150G PHE* 3.8 37.7 - - + +
153G CYS* 5.0 3.8 - - + -
154G ALA* 4.0 30.7 - - + +
158G ALA* 4.1 22.2 - - + +
160G LEU* 1.3 84.0 - - - +
162G SER* 1.3 64.2 + - - +
200G TRP* 3.6 8.3 - - - -
203G ILE* 4.5 8.1 - - + -
206G ILE* 4.5 7.2 - - + -
207G ALA* 4.4 13.5 - - + -
212G THR* 4.0 11.7 - - - +
213G ILE 2.9 16.0 + - - +
214G SER* 4.8 0.4 - - - -
215G ALA* 3.1 21.0 + - - +
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Residues in contact with SER 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ARG* 3.1 28.6 + - - -
124G HIS 3.2 6.3 + - - -
125G THR* 3.7 15.7 - - - -
126G ILE 2.9 23.6 + - - -
150G PHE* 3.5 9.3 - - - -
161G LEU* 1.3 77.0 + - - +
163G VAL* 1.3 64.8 + - - +
200G TRP* 4.1 2.7 - - - -
215G ALA* 3.5 2.4 - - - +
216G GLY 2.9 20.6 + - - -
267G LYS* 3.6 15.9 - - - -
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Residues in contact with VAL 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G THR* 3.8 3.1 - - - -
126G ILE 3.4 19.3 - - - +
128G ASP* 4.1 9.0 - - + -
146G PHE* 3.8 21.8 - - + -
150G PHE* 3.8 18.8 - - + -
162G SER* 1.3 76.8 - - - +
164G GLU* 1.3 77.1 - - - +
165G SER* 3.9 2.9 - - - +
199G ILE* 4.1 6.7 - - + -
200G TRP* 3.6 14.1 - - + -
203G ILE* 4.0 8.3 - - + -
216G GLY 3.9 1.4 + - - +
217G ASP* 3.1 46.1 - - - +
218G THR* 4.4 0.6 + - - -
267G LYS* 4.8 0.4 - - - +
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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