Contacts of the strand formed by residues 210 - 215 (chain E) in PDB entry 5IJ7
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 THR 210 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E TRP* 3.4 8.5 - - - +
205E ASN* 2.8 38.8 + - - +
208E THR* 2.8 27.0 + - - +
209E ASP* 1.3 76.3 - - - +
211E LEU* 1.3 60.5 + - - +
212E VAL 3.6 0.4 + - - -
263E SER* 3.4 10.4 - - - +
266E TYR* 3.6 35.4 - - + -
275E PHE* 3.8 27.4 - - + -
572S LEU* 6.2 0.4 - - - -
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Residues in contact with LEU 211 (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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202E ARG* 3.6 46.7 - - + +
203E LEU 3.4 17.0 - - - +
204E TRP* 3.9 17.0 - - + -
210E THR* 1.3 72.7 - - - +
212E VAL* 1.3 62.7 + - - +
213E ALA 3.5 16.4 - - - +
214E ILE* 3.8 22.2 - - + -
275E PHE* 3.5 11.6 - - - -
277E SER* 2.7 37.8 + - - +
570S THR* 4.0 4.7 - - - -
572S LEU* 3.8 25.7 - - + +
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Residues in contact with VAL 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E LEU* 4.5 9.9 - - + -
203E LEU* 2.8 27.4 + - + +
204E TRP 4.2 2.5 - - - -
205E ASN* 3.9 21.5 - - + +
211E LEU* 1.3 72.8 - - - +
213E ALA* 1.3 57.3 + - - +
256E MET* 4.1 3.8 - - + -
259E ALA* 3.8 34.9 - - + +
260E ILE* 3.8 15.3 - - + +
263E SER* 3.6 26.5 - - - +
275E PHE* 4.2 7.9 - - - -
276E ILE 4.7 0.2 - - - +
277E SER* 3.7 1.2 - - - -
278E GLN* 3.1 23.4 + - - +
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Residues in contact with ALA 213 (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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202E ARG* 3.6 1.0 - - - -
203E LEU* 3.0 26.6 + - + -
211E LEU* 3.5 11.0 - - - +
212E VAL* 1.3 79.9 - - - +
214E ILE* 1.3 64.2 + - - +
215E PHE* 3.9 15.7 - - + -
256E MET* 3.9 32.5 - - + -
277E SER* 4.8 0.4 - - - -
278E GLN* 3.3 16.4 - - + +
280E ILE* 4.2 4.0 - - + -
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Residues in contact with ILE 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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112A SER* 5.7 1.6 - - - +
200E ALA* 3.9 24.2 - - + -
201E LEU 3.5 5.4 - - - +
202E ARG* 4.2 16.2 - - + +
211E LEU* 3.8 27.6 - - + -
213E ALA* 1.3 75.6 - - - +
215E PHE* 1.3 61.5 + - - +
216E GLY* 3.5 8.9 + - - +
277E SER* 4.8 1.8 - - - -
278E GLN 2.8 11.3 + - - +
279E LYS* 3.8 19.7 - - + -
280E ILE 2.9 27.2 + - - +
569S ASP 3.3 26.9 - - - +
570S THR* 4.0 11.2 - - + -
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Residues in contact with PHE 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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193E LEU* 4.4 4.9 - - + -
199E HIS 4.4 0.5 - - - +
200E ALA* 3.4 3.1 - - - -
201E LEU* 2.8 65.3 + - + +
203E LEU* 3.8 24.0 - - + -
213E ALA* 3.9 7.4 - - + -
214E ILE* 1.3 68.6 - - - +
216E GLY* 1.3 57.8 + - - +
221E HIS 5.8 0.2 + - - -
237E ILE* 4.3 13.0 - - + -
249E TRP* 3.6 52.8 - + + -
250E ARG 5.0 1.8 - - - -
251E ILE* 3.9 16.8 - - + -
256E MET* 3.9 27.8 - - + -
280E ILE* 3.6 29.4 - - + -
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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