Contacts of the strand formed by residues 211 - 215 (chain D) in PDB entry 3V56
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 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D TYR* 4.2 15.5 - - + +
210D HIS* 1.3 76.1 - - - +
212D ILE* 1.3 61.7 + - - +
213D GLN* 3.6 30.3 + - + +
228D THR* 3.8 20.9 - - + +
230D PHE 3.5 4.0 - - - -
231D ARG* 3.6 37.2 - - + -
260D GLN 3.3 2.4 - - - +
261D LEU* 3.3 5.2 - - - -
262D ALA* 2.8 37.1 + - + +
264D PRO* 3.8 26.0 - - + -
27J LEU* 5.4 4.5 - - + +
28J LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 3.6 25.8 - - + -
196D TYR* 3.9 10.1 - - - +
197D GLY* 3.8 29.2 - - - +
210D HIS* 4.6 13.9 - - + +
211D LEU* 1.3 71.7 - - - +
213D GLN* 1.3 55.4 + - - +
228D THR* 3.7 1.0 - - - -
229D LEU* 2.7 42.5 + - + +
230D PHE* 2.8 38.9 + - + +
247D SER* 3.9 14.6 - - - +
259D LEU* 5.0 2.5 - - + -
260D GLN 3.5 2.9 - - - -
261D LEU* 4.6 3.6 - - + -
279D PHE* 4.0 20.4 - - + -
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Residues in contact with GLN 213 (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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163D TYR* 5.4 5.8 + - - -
211D LEU* 3.7 34.0 - - + +
212D ILE* 1.3 76.9 - - - +
214D ARG* 1.3 60.1 + - - +
226D LEU* 3.6 27.8 - - + +
227D VAL 3.1 8.2 - - - +
228D THR* 3.4 22.2 + - - +
229D LEU* 4.8 0.7 - - - -
258D GLU 3.8 0.5 - - - +
259D LEU* 3.2 11.1 - - - +
260D GLN* 2.7 73.3 + - + +
262D ALA* 3.6 10.5 - - - +
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Residues in contact with ARG 214 (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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212D ILE 4.4 0.2 + - - -
213D GLN* 1.3 72.7 - - - +
215D LYS* 1.3 60.9 + - - +
216D LYS* 3.5 16.1 + - - +
225D SER 3.3 6.9 - - - +
226D LEU* 3.4 4.0 - - - -
227D VAL* 2.8 51.6 + - + +
229D LEU* 3.9 21.4 - - + +
252D LYS 3.8 19.9 + - - -
253D LEU* 3.7 19.4 - - + +
254D GLU* 3.5 24.7 + - - +
257D ASP* 2.8 36.1 + - + +
258D GLU 3.4 6.3 - - - +
259D LEU* 4.2 2.5 - - + -
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Residues in contact with LYS 215 (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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184D LYS* 6.5 0.2 - - + -
213D GLN 4.2 0.4 - - - -
214D ARG* 1.3 70.3 - - - +
216D LYS* 1.3 68.2 + - - +
217D VAL* 4.6 0.2 - - - -
225D SER* 3.6 10.1 - - - +
226D LEU* 3.8 19.4 - - + +
256D GLY 4.6 1.2 - - - +
257D ASP* 3.4 4.0 - - - -
258D GLU* 2.7 50.4 + - + +
260D GLN* 5.9 3.3 - - + +
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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