Contacts of the strand formed by residues 319 - 325 (chain A) in PDB entry 4WTM
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 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ARG* 5.8 0.7 + - - -
219A TYR 3.6 3.2 - - - +
220A ASP* 2.9 14.6 - - - +
314A LEU 4.0 0.2 - - - +
315A VAL* 3.5 2.4 - - - +
316A CYS* 2.9 36.3 + - - +
318A ASP* 1.3 78.4 + - - +
320A LEU* 1.3 63.6 + - - +
365A SER* 3.6 13.9 + - - +
366A CYS* 3.0 33.5 + - - -
367A SER 4.8 0.3 + - - -
601A MN 1.9 35.0 + - - -
2P C 2.6 18.0 + - - +
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Residues in contact with LEU 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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200A ARG* 6.2 0.2 - - - +
217A PHE* 4.6 2.9 - - + -
218A SER* 3.1 8.5 - - - -
219A TYR* 2.9 67.6 + - + +
295A CYS* 3.4 28.3 - - - -
299A ALA* 3.8 15.0 - - + -
313A MET* 4.3 8.3 - - + -
314A LEU 3.3 9.6 - - - +
315A VAL* 4.4 11.7 - - + -
318A ASP 4.6 1.1 - - - +
319A ASP* 1.3 74.1 - - - +
321A ILE* 1.3 63.1 + - - +
322A VAL* 3.6 29.2 - - + -
339A PHE* 4.3 11.0 - - + -
343A MET* 4.7 2.2 - - + -
365A SER* 3.7 3.2 + - - -
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Residues in contact with ILE 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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200A ARG* 4.3 10.5 - - - +
204A LEU* 4.1 33.2 - - + -
217A PHE 3.4 10.1 - - - +
218A SER* 4.4 1.1 - - - -
312A THR 3.8 0.6 - - - +
313A MET* 3.2 5.2 - - - +
314A LEU* 2.9 40.8 + - + +
320A LEU* 1.3 75.9 - - - +
322A VAL* 1.3 74.8 + - - +
323A ILE* 4.2 15.3 - - + -
360A LEU* 6.2 1.6 - - + -
363A ILE* 4.0 28.7 - - + +
365A SER* 3.5 32.8 - - - +
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Residues in contact with VAL 322 (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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215A MET 3.9 0.3 - - - +
216A GLY* 3.2 4.0 - - - -
217A PHE* 3.0 61.6 + - + -
303A CYS* 4.1 10.8 - - - -
308A ILE* 4.1 11.4 - - + -
311A PRO* 3.9 27.1 - - + -
312A THR 3.4 4.3 - - - +
313A MET* 4.0 15.7 - - + -
320A LEU* 3.6 22.4 - - + -
321A ILE* 1.3 79.0 - - - +
323A ILE* 1.3 68.7 + - - +
324A SER* 4.2 1.6 + - - -
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Residues in contact with ILE 323 (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 LEU* 3.7 48.0 - - + +
207A ALA* 3.8 34.1 - - + +
208A TRP* 3.9 36.3 - - + +
211A LYS* 3.6 12.7 - - + -
214A PRO* 4.7 1.1 - - + -
215A MET 3.4 4.9 - - - +
216A GLY* 4.4 2.2 - - - -
310A ALA 3.5 2.1 - - - +
311A PRO 3.5 0.3 - - - -
312A THR 2.7 39.6 + - - +
321A ILE* 4.2 9.6 - - + -
322A VAL* 1.3 77.8 - - - +
324A SER* 1.3 62.1 + - - +
360A LEU* 4.6 4.5 - - + -
363A ILE* 5.3 0.9 - - + -
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Residues in contact with SER 324 (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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211A LYS* 3.6 9.6 - - - +
214A PRO* 3.3 7.8 - - - +
215A MET* 2.8 54.6 + - - +
308A ILE* 3.4 28.3 - - - +
309A VAL 3.2 14.8 - - - -
310A ALA 3.7 5.2 - - - -
311A PRO* 4.1 1.1 - - - -
322A VAL* 4.1 3.9 + - - +
323A ILE* 1.3 75.9 - - - +
325A GLU* 1.3 64.7 + - - +
326A SER 3.7 0.2 - - - -
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Residues in contact with GLU 325 (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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210A GLU 4.5 0.7 - - - +
211A LYS* 3.3 13.2 - - + +
212A LYS* 2.7 31.7 + - - +
213A ASP* 3.1 27.0 + - - +
215A MET* 5.4 0.7 - - - +
309A VAL* 2.9 33.2 + - + +
310A ALA* 4.1 19.7 - - + -
324A SER* 1.3 78.9 + - - +
326A SER* 1.3 65.7 + - - +
327A GLN* 3.2 16.0 + - - +
332A ASP* 4.6 1.0 - - - +
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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