Contacts of the strand formed by residues 160 - 163 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28O ALA* 3.9 23.6 - - + -
34O ILE* 4.3 16.4 - - + -
82O ILE* 4.6 15.7 - - + -
121O ALA* 4.9 5.6 - - + -
122O LEU 3.0 11.9 + - - +
123O ARG* 4.0 28.3 - - + +
124O HIS* 3.0 27.9 + - - +
158O ALA* 4.5 0.2 - - - +
159O ASP* 1.3 88.7 + - + +
161O LEU* 1.3 65.5 + - - +
213O ILE* 3.6 19.3 - - + -
215O ALA* 4.2 8.1 - - + -
265O PRO* 4.0 25.4 - - + -
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Residues in contact with LEU 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124O HIS* 3.7 5.4 - - + +
126O ILE* 4.8 3.8 - - + -
150O PHE* 4.0 41.3 - - + +
153O CYS* 5.0 1.1 - - + -
154O ALA* 4.2 21.8 - - + +
158O ALA* 4.5 9.2 - - + +
160O LEU* 1.3 80.6 - - - +
162O SER* 1.3 64.9 + - - +
200O TRP* 3.8 5.4 - - - -
203O ILE* 4.5 11.4 - - + -
206O ILE* 4.5 9.9 - - + -
207O ALA* 4.2 20.2 - - + +
212O THR* 3.9 20.2 - - - +
213O ILE 2.8 16.6 + - - +
214O SER 4.1 0.2 - - - -
215O ALA* 3.0 21.5 + - - +
216O GLY 3.6 2.3 + - - -
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Residues in contact with SER 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123O ARG* 3.1 27.9 + - - -
124O HIS 3.0 8.5 + - - +
125O THR* 3.6 21.8 - - - -
126O ILE 2.9 22.9 + - - -
150O PHE* 3.3 10.9 - - - -
160O LEU 4.2 0.2 - - - -
161O LEU* 1.3 74.7 + - - +
163O VAL* 1.3 65.4 + - - +
200O TRP* 4.1 2.9 - - - -
215O ALA* 3.7 1.2 - - - +
216O GLY 2.9 20.2 + - - -
267O LYS* 3.8 10.8 - - - -
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Residues in contact with VAL 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O THR* 3.7 4.5 - - - -
126O ILE 3.3 20.9 - - - +
128O ASP* 4.0 13.9 - - + -
146O PHE* 3.9 19.3 - - + -
150O PHE* 3.9 6.5 - - + -
162O SER* 1.3 78.9 - - - +
164O GLU* 1.3 74.6 + - - +
165O SER* 4.0 1.8 - - - +
199O ILE* 4.2 7.6 - - + -
200O TRP* 3.7 12.6 - - + -
203O ILE* 4.0 16.8 - - + -
216O GLY 3.7 1.3 + - - +
217O ASP* 3.1 46.5 - - - +
218O THR* 4.3 0.3 + - - -
267O LYS* 4.6 0.5 - - - +
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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