Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 4IE6
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 ASP 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.6 7.6 - - + -
52A ARG 4.5 1.1 - - - +
53A GLU* 3.3 11.8 - - - +
54A ALA* 2.7 32.1 + - - +
244A VAL 3.8 0.2 - - - +
245A TYR* 3.7 0.5 - - - -
246A SER* 2.7 34.6 + - - -
288A PRO 4.3 2.3 - - - +
289A LEU* 3.6 23.7 - - + -
290A HIS* 2.7 46.9 + - - +
292A GLY* 1.3 78.1 - - - +
294A CYS* 1.3 57.1 + - - +
295A TYR 4.5 0.2 + - - -
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Residues in contact with CYS 294 (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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51A LEU* 3.3 6.7 - - - +
52A ARG* 2.8 43.1 + - + +
57A VAL* 4.3 15.3 - - - -
142A LEU* 5.7 0.2 - - - -
145A TYR* 5.9 0.4 - - - -
146A LEU* 4.1 16.6 - - + -
244A VAL 3.1 8.5 - - - +
245A TYR* 3.5 38.1 - - - -
292A GLY 4.2 4.0 - - - -
293A ASP* 1.3 75.0 - - - +
295A TYR* 1.3 60.6 + - - +
296A PHE* 3.8 20.4 - - + -
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Residues in contact with TYR 295 (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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49A LEU* 4.3 18.4 - - + -
50A ILE 3.2 11.4 - - - +
51A LEU* 4.3 10.3 - - + -
242A VAL 4.1 0.2 - - - +
243A ALA* 3.6 0.2 - - - -
244A VAL* 2.9 67.7 + - + +
246A SER* 5.4 0.7 - - - -
272A VAL* 3.5 31.3 - - + +
274A PHE* 4.3 9.4 - + - -
287A ILE* 6.1 1.8 - - + -
289A LEU* 3.9 34.8 - - + -
294A CYS* 1.3 73.8 - - - +
296A PHE* 1.3 71.1 + - - +
297A MET* 4.6 15.5 - - + -
307A HIS* 4.9 2.6 - + - -
602A UN9 2.9 32.6 + - - -
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Residues in contact with PHE 296 (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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48A LYS 3.5 5.2 - - - +
49A LEU* 3.5 4.7 - - - +
50A ILE* 2.8 51.3 + - + +
52A ARG* 3.9 20.9 - - + -
146A LEU* 3.9 29.6 - - + -
149A GLU* 4.0 18.8 - - + -
150A THR* 3.4 33.4 - - - -
153A ALA* 5.9 2.5 - - + -
199A TYR* 4.7 0.2 - - - -
242A VAL 3.3 6.7 - - - +
243A ALA* 3.8 18.4 - - + -
294A CYS* 3.8 23.1 - - + -
295A TYR* 1.3 80.6 - - - +
297A MET* 1.3 63.5 + - - +
298A LEU* 4.0 15.4 - - + +
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Residues in contact with MET 297 (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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233A ASP* 3.6 15.7 - - - +
240A SER 4.4 1.4 - - - +
241A ALA* 3.1 8.0 - - - +
242A VAL* 2.9 66.7 + - + +
274A PHE* 4.0 22.9 - - + -
295A TYR* 4.6 12.6 - - + -
296A PHE* 1.3 72.4 - - - +
298A LEU* 1.3 60.4 + - - +
299A ASP 5.5 0.2 - - - -
301A LEU* 3.6 28.0 - - + -
302A ASN* 3.7 27.1 - - + +
307A HIS* 3.8 25.4 - - - -
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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