Contacts of the strand formed by residues 288 - 292 (chain A) in PDB entry 5EWL
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 ILE 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MET* 4.7 6.3 - - + -
160A TRP* 5.2 2.9 - - + -
267A VAL* 5.3 1.3 - - + -
268A TRP 2.9 16.4 + - - +
269A LEU* 3.6 22.9 - - + -
270A VAL* 2.8 32.4 + - - +
286A GLY 4.2 2.5 - - - +
287A ILE* 1.3 72.7 - - - +
289A GLY* 1.3 62.4 + - - +
290A LEU* 5.5 0.2 - - + -
374A ILE* 3.7 26.7 - - + -
375A MET 3.3 3.4 - - - +
376A ASN* 3.4 29.8 - - + +
385A VAL* 4.8 2.5 - - + -
400A ILE* 3.8 29.4 - - + -
402A TRP* 3.9 21.1 - - + -
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.5 16.2 - - - -
275A ILE* 3.7 22.6 - - - +
287A ILE* 4.1 1.6 - - - +
288A ILE* 1.3 76.9 - - - +
290A LEU* 1.3 72.8 + - - +
374A ILE* 3.8 1.0 - - - -
375A MET* 2.8 29.1 + - - +
382A LEU* 6.0 0.4 - - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.6 37.7 - - + +
150A VAL* 3.8 37.0 - - + -
151A TRP* 3.6 24.9 - - + +
154A MET* 4.5 7.2 - - + -
269A LEU* 5.9 0.7 - - + -
270A VAL 3.7 5.6 - - - +
271A GLY 3.3 6.3 + - - -
272A GLU* 3.2 23.1 - - - -
275A ILE* 3.5 5.9 - - - +
288A ILE* 5.5 0.9 - - + -
289A GLY* 1.3 83.1 - - - +
291A GLN* 1.3 68.1 + - - +
372A TYR* 4.3 12.6 - - + -
373A SER 3.3 11.4 - - - +
374A ILE* 4.0 13.0 - - + -
375A MET* 4.5 0.7 - - - -
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 3.6 19.3 - - + +
275A ILE* 3.9 8.7 + - - +
290A LEU* 1.3 77.2 - - - +
292A LEU* 1.3 67.4 + - - +
293A ILE* 3.1 2.6 + - - -
372A TYR* 3.2 2.6 - - - -
373A SER* 2.8 46.5 + - - +
375A MET* 3.9 20.0 - - + +
382A LEU* 3.4 30.5 - - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG* 3.5 31.2 - - - +
141A VAL* 3.8 11.7 - - + -
142A PRO* 3.6 19.5 - - + -
272A GLU* 2.8 25.0 + - - +
291A GLN* 1.3 70.2 - - - +
293A ILE* 1.3 68.9 + - - +
294A ASN 3.4 0.9 + - - -
295A GLY* 3.1 30.6 + - - -
296A LYS* 5.0 0.5 + - - +
370A ALA* 3.7 26.7 - - + -
371A GLN 3.5 16.4 - - - +
372A TYR* 3.8 18.6 - - + -
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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