Contacts of the strand formed by residues 211 - 215 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E TYR* 4.2 15.3 - - + +
210E HIS* 1.3 76.1 - - - +
212E ILE* 1.4 61.9 + - - +
213E GLN* 3.5 31.1 + - + +
228E THR* 3.7 20.2 - - + +
230E PHE 3.5 3.6 - - - -
231E ARG* 3.5 38.1 - - + -
260E GLN 3.3 2.6 - - - +
261E LEU* 3.3 4.0 - - - -
262E ALA* 2.8 38.2 + - + +
264E PRO* 3.8 26.2 - - + -
27K LEU 5.5 2.2 - - - +
28K LEU* 4.3 3.8 - - + -
30K ARG* 4.6 7.4 - - - +
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Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E ILE* 3.6 24.5 - - + -
196E TYR* 3.8 10.5 - - - +
197E GLY* 3.7 29.8 - - - +
210E HIS* 4.3 13.6 + - + +
211E LEU* 1.4 71.3 - - - +
213E GLN* 1.3 54.3 + - - +
228E THR 3.7 0.5 - - - -
229E LEU* 2.8 43.2 + - + +
230E PHE* 2.8 38.5 + - + +
247E SER* 3.9 13.9 - - - +
259E LEU* 5.0 2.5 - - + -
260E GLN 3.5 3.4 - - - -
261E LEU* 4.6 4.0 - - + -
279E PHE* 4.1 20.0 - - + -
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Residues in contact with GLN 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E TYR* 5.2 7.6 + - - -
211E LEU* 3.7 33.1 - - + +
212E ILE* 1.3 76.3 - - - +
214E ARG* 1.3 61.1 + - - +
215E LYS 4.1 0.4 - - - -
226E LEU* 3.5 27.4 - - + +
227E VAL 3.2 6.9 - - - +
228E THR* 3.4 22.6 + - - +
229E LEU* 4.7 0.4 - - - -
258E GLU 3.7 0.5 - - - +
259E LEU* 3.3 11.4 - - - +
260E GLN* 2.7 72.3 + - + +
262E ALA* 3.5 11.4 - - - +
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Residues in contact with ARG 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ILE 4.4 0.2 + - - -
213E GLN* 1.3 73.4 - - - +
215E LYS* 1.4 60.3 + - - +
216E LYS* 3.4 31.0 + - - +
225E SER 3.3 6.2 - - - +
226E LEU* 3.4 3.9 - - - -
227E VAL* 2.8 46.5 + - + +
229E LEU* 3.9 22.0 - - + +
252E LYS 3.9 19.3 + - - -
253E LEU* 3.8 20.1 - - + +
254E GLU* 3.5 24.2 + - - +
257E ASP* 2.8 35.5 + - + +
258E GLU 3.5 5.8 - - - +
259E LEU* 4.2 2.0 - - + -
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LYS* 6.4 0.4 - - + -
213E GLN 4.1 0.6 - - - -
214E ARG* 1.4 70.1 - - - +
216E LYS* 1.3 69.9 + - - +
217E VAL* 4.6 0.3 - - - -
225E SER* 3.5 13.5 - - - +
226E LEU* 3.8 19.9 - - + +
256E GLY 4.6 0.7 - - - +
257E ASP* 3.4 4.5 - - - -
258E GLU* 2.7 52.9 + - + +
260E GLN* 5.8 3.6 - - + +
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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