Contacts of the strand formed by residues 314 - 321 (chain A) in PDB entry 3RC3
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 ALA 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A MSE 3.3 5.1 - - - +
200A ARG* 3.3 24.3 - - - +
285A TYR* 3.0 14.1 - - + +
287A VAL 4.1 2.2 - - - -
288A ALA* 3.6 30.3 - - + +
312A LEU* 2.9 6.0 + - + +
313A CYS* 1.3 75.6 - - - +
315A GLU* 1.3 64.2 + - - +
316A GLU 3.4 18.5 + - - +
317A VAL* 3.9 8.0 - - + +
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Residues in contact with GLU 315 (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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198A MSE 3.4 17.5 - - + +
199A GLN 4.1 5.9 - - - +
200A ARG* 3.5 2.6 - - - -
201A LYS* 3.0 23.6 + - - +
285A TYR 3.1 10.4 + - - +
286A GLU* 3.3 34.7 + - - +
314A ALA* 1.3 71.9 - - - +
316A GLU* 1.3 66.2 + - + +
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Residues in contact with GLU 316 (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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201A LYS* 3.3 21.9 + - + +
203A ILE* 3.5 17.7 - - + +
220A LYS* 3.4 23.5 + - - -
286A GLU 3.1 10.1 + - - +
287A VAL* 3.5 6.4 - - + -
288A ALA 3.0 25.8 + - - +
314A ALA* 3.6 1.8 - - - +
315A GLU* 1.3 83.8 - - + +
317A VAL* 1.3 62.5 + - - +
318A HIS* 2.9 29.8 + - + +
343A ARG* 5.4 2.6 + - - -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 3.7 31.9 - - + +
201A LYS 2.8 7.9 + - - -
202A ILE* 3.4 23.0 - - + +
203A ILE 3.0 24.3 + - - +
288A ALA* 3.8 10.5 - - + -
290A ILE* 3.8 31.4 - - + -
309A LEU* 4.7 4.0 - - + +
312A LEU* 4.3 3.6 - - + +
314A ALA* 3.9 23.3 - - + +
316A GLU* 1.3 73.7 - - - +
318A HIS* 1.3 61.2 + - - +
319A LEU* 3.8 11.5 + - + -
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Residues in contact with HIS 318 (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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203A ILE* 3.3 25.2 - - + +
205A HIS* 2.8 31.7 + + + +
217A ALA* 4.1 16.9 - - + -
220A LYS* 3.8 25.4 - - + +
287A VAL* 3.9 13.1 - - + +
288A ALA 2.8 17.9 + - - +
289A VAL* 3.3 5.1 - - + +
290A ILE* 2.9 25.6 + - - +
316A GLU* 2.9 43.0 + - + +
317A VAL* 1.3 71.7 - - - +
319A LEU* 1.3 62.0 + - - +
343A ARG* 4.2 9.6 - - - -
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Residues in contact with LEU 319 (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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202A ILE* 3.8 15.3 - - + -
203A ILE 2.7 15.0 + - - +
204A PHE* 3.9 13.2 - - + -
205A HIS* 2.8 30.5 + - - -
290A ILE* 3.6 34.1 - - + -
293A ILE* 4.1 18.2 - - + -
309A LEU* 4.0 11.4 - - + -
317A VAL* 3.9 10.3 - - + +
318A HIS* 1.3 79.5 - - - +
320A CYS* 1.3 62.3 + - - +
329A VAL* 3.7 40.4 - - + -
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Residues in contact with CYS 320 (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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205A HIS* 3.6 6.7 - - - +
213A LYS* 3.9 25.6 - - + -
214A THR* 3.9 15.0 - - - +
217A ALA* 3.6 31.9 - - - -
289A VAL* 4.2 12.1 - - - -
290A ILE 3.1 9.2 + - - +
291A ASP* 3.8 15.0 - - - +
292A GLU 2.9 12.6 + - - -
293A ILE* 2.9 26.3 + - - -
319A LEU* 1.3 78.2 - - - +
321A GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 321 (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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204A PHE* 3.6 3.9 - - - -
205A HIS 3.3 6.9 + - - +
206A SER* 3.4 6.6 - - - -
207A GLY 3.4 20.6 + - - -
213A LYS* 3.6 16.4 - - - +
292A GLU* 4.7 1.1 - - - -
293A ILE* 4.1 5.0 - - - +
294A GLN* 3.2 14.4 - - - -
320A CYS* 1.3 77.2 - - - +
322A GLU* 1.3 67.1 + - - -
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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