Contacts of the strand formed by residues 165 - 169 (chain D) in PDB entry 2OTD
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 ARG 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D LEU* 4.4 0.2 - - - -
145D LEU* 3.1 11.9 - - + +
153D LEU* 3.8 41.5 + - + -
156D ALA* 4.1 5.6 - - + -
157D GLN* 3.6 26.6 - - - +
160D ALA 4.1 2.2 + - - +
161D PRO* 3.1 26.1 + - - +
163D LEU 2.9 26.0 + - - +
164D PRO* 1.3 79.3 - - - +
166D GLY* 1.3 58.3 + - - +
183D LEU* 2.7 31.2 + - + +
184D GLY* 3.2 19.2 + - - -
185D CYS* 3.3 15.4 - - - -
186D VAL* 3.1 27.8 + - - +
187D SER* 3.3 6.5 + - - -
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 4.3 1.0 - - - +
145D LEU 2.8 9.7 + - - -
146D SER* 3.2 24.8 - - - -
147D SER 3.6 3.6 + - - -
153D LEU* 3.7 7.4 - - - +
165D ARG* 1.3 75.2 - - - +
167D LEU* 1.3 59.5 + - - -
185D CYS* 4.3 3.4 - - - -
187D SER* 3.2 24.8 + - - -
189D HIS* 3.6 10.5 - - - -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D SER 3.9 6.7 - - - +
148D PHE 5.1 3.4 - - - +
150D ILE* 4.4 14.8 - - + -
153D LEU* 3.3 22.7 - - + -
166D GLY* 1.3 72.6 - - - -
168D LEU* 1.3 63.9 + - - +
169D LEU* 3.6 25.7 - - + +
173D ARG* 5.3 0.4 - - - -
176D TRP* 5.6 2.5 - - + +
179D LEU* 3.5 33.2 - - + -
180D THR* 4.8 12.6 - - + -
183D LEU* 4.3 10.3 - - + -
185D CYS* 4.1 12.5 - - - -
187D SER 3.3 8.9 + - - +
188D ILE* 3.6 10.6 - - + +
189D HIS* 2.9 28.1 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C PO4 4.1 13.0 - - - +
114D GLU* 4.2 13.7 - - - +
146D SER* 3.2 39.0 - - - +
147D SER* 3.1 25.2 + - - +
148D PHE* 3.5 48.3 - - + +
167D LEU* 1.3 76.7 - - - +
169D LEU* 1.3 66.6 + - - +
189D HIS* 3.0 34.8 - - + +
211D LEU* 5.3 1.3 - - + -
213D TYR* 3.8 20.6 - - + -
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 3.8 2.2 - - - -
167D LEU* 3.6 33.0 - - + +
168D LEU* 1.3 77.5 - - - +
170D ASP* 1.3 59.7 + - - +
171D GLU* 3.3 23.3 - - + +
173D ARG* 3.3 42.6 - - + +
176D TRP* 5.2 5.6 - - + -
188D ILE* 4.1 21.8 - - + -
189D HIS 2.9 9.1 + - - +
190D LEU* 3.6 18.0 - - + +
191D ASN 3.2 17.5 + - - -
213D TYR* 3.2 11.2 + - - -
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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