Contacts of the strand formed by residues 265 - 270 (chain C) in PDB entry 1EJI
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 GLY 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C VAL 4.3 5.7 - - - +
117C PRO* 3.1 32.9 + - - +
119C SER* 3.8 16.3 - - - +
123C ALA* 4.7 1.6 - - - -
253C THR 3.0 12.6 - - - -
254C THR* 4.2 0.2 - - - -
255C THR* 4.6 1.6 - - - -
264C ALA* 1.3 79.9 - - - +
266C MSE 1.3 68.8 + - - +
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Residues in contact with MSE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ALA* 4.1 15.7 - - - -
104C TYR* 4.9 2.7 - - + -
113C VAL* 4.2 6.3 - - + -
114C ASN 3.4 12.3 - - - +
115C VAL* 4.3 17.5 - - + -
117C PRO* 4.5 0.9 - - - -
123C ALA* 4.2 2.2 - - - +
251C VAL 4.1 0.8 - - - +
252C THR* 3.3 5.2 - - - -
253C THR* 2.9 49.6 + - + +
255C THR* 3.6 27.4 - - + -
259C LEU* 4.3 15.7 - - + -
265C GLY* 1.3 79.7 - - - +
267C ILE* 1.3 67.0 + - - +
268C PHE* 4.1 26.0 - - + -
312C VAL* 4.6 12.3 - - + -
316C LEU* 4.7 11.7 - - + -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.4 5.5 - - - -
114C ASN* 3.1 33.5 + - + -
117C PRO* 3.9 13.2 - - + -
123C ALA* 3.2 41.3 - - + +
126C ALA* 3.9 12.1 - - + -
127C VAL* 3.7 22.2 - - + -
250C VAL* 4.1 9.0 - - + -
251C VAL 3.8 2.2 - - - -
252C THR* 4.3 4.3 - - + +
266C MSE 1.3 80.6 - - - +
268C PHE* 1.3 60.3 + - - +
269C TYR* 3.5 5.1 - - + -
292C ILE* 3.8 32.5 - - + -
296C VAL* 4.3 4.7 - - + -
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Residues in contact with PHE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ALA* 3.9 24.0 - - + -
101C LEU* 3.9 2.0 - - + -
104C TYR* 3.9 18.2 - + - -
106C LEU* 3.7 24.0 - - + -
111C TRP* 4.1 3.8 - + + -
112C GLY 3.4 2.9 - - - -
113C VAL* 3.6 36.6 - - + -
229C MSE 4.5 5.8 - - + -
245C PHE* 3.5 30.7 - + + -
250C VAL* 3.3 8.8 - - - +
251C VAL* 2.7 47.9 + - + +
253C THR* 4.3 8.7 - - + -
266C MSE 4.1 28.7 - - + -
267C ILE* 1.3 73.7 - - - +
269C TYR* 1.3 59.8 + - - +
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Residues in contact with TYR 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C TRP* 3.4 9.3 - - - -
112C GLY* 3.0 47.2 + - - -
113C VAL 3.5 20.4 + - - -
114C ASN* 4.3 3.6 - - + -
249C HIS 3.7 5.2 - - - -
250C VAL* 4.2 3.4 - - + -
267C ILE* 3.5 18.2 - - + -
268C PHE* 1.3 75.0 - - - +
270C ARG* 1.3 67.6 + - - +
271C LYS* 4.7 3.1 - - - -
288C LEU* 4.0 8.1 - - + -
289C GLU* 3.2 50.5 + - + -
292C ILE* 3.7 35.2 - - + -
293C ASN* 3.4 26.9 + - - -
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Residues in contact with ARG 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C CYS* 3.2 31.2 + - - +
111C TRP* 3.5 29.2 - - + +
215C ARG* 5.7 0.9 - - - +
248C CYS 4.2 6.1 - - - -
249C HIS* 3.1 25.9 + - - +
269C TYR* 1.3 79.1 - - - +
271C LYS* 1.3 77.9 + - - +
272C GLY 3.9 4.4 + - - -
274C ARG* 2.6 55.0 - - - +
286C TYR* 3.6 30.2 - - + +
288C LEU* 3.4 26.3 - - + +
289C GLU 4.6 0.7 + - - -
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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