Contacts of the strand formed by residues 310 - 317 (chain A) in PDB entry 4XX1
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 GLU 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A PHE* 5.8 1.2 - - - -
204A ASP* 4.1 23.1 + - - +
205A GLY* 4.5 2.8 - - - -
206A PHE* 2.7 36.9 + - - +
309A VAL* 1.3 74.6 - - - +
311A VAL* 1.3 58.1 + - - +
312A TYR* 3.0 36.7 + - + -
365A GLN* 3.8 5.5 - - + +
366A PRO* 3.5 36.6 - - + +
368A HIS* 3.6 14.9 + - + -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 3.2 22.4 - - + +
208A SER* 4.8 5.4 - - - +
213A TRP* 5.9 0.7 - - + -
307A PRO* 3.6 31.0 - - + -
309A VAL* 3.8 3.8 - - + +
310A GLU* 1.3 81.2 - - - +
312A TYR* 1.3 64.2 + - - +
313A CYS* 4.0 20.6 - - + +
356A CYS* 5.4 0.2 - - + -
359A TRP* 4.4 16.8 - - + -
363A GLN* 4.5 2.7 - - - +
366A PRO 3.1 10.5 + - - +
367A VAL* 3.5 14.8 - - + -
368A HIS* 2.7 36.2 + - - +
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 4.2 14.0 - + - -
205A GLY* 4.9 2.7 - - - -
206A PHE 2.7 19.5 + - - +
207A ILE* 3.6 13.7 - - + +
208A SER 3.0 28.1 + - - +
310A GLU* 3.0 37.0 + - + -
311A VAL* 1.3 74.8 - - - +
313A CYS* 1.3 61.2 + - - +
314A LEU* 3.4 1.1 + - + +
368A HIS* 3.6 29.8 + + + -
370A LEU* 4.0 11.2 - - + -
393A ILE* 3.5 60.0 + - + +
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Residues in contact with CYS 313 (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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208A SER* 3.4 16.4 - - - +
211A ALA* 5.7 1.8 - - - -
213A TRP* 3.8 10.1 - - - -
311A VAL* 3.9 7.9 - - + -
312A TYR* 1.3 70.0 - - - +
314A LEU* 1.3 61.6 + - - +
315A TYR* 3.6 10.3 - - + -
353A THR 3.9 9.6 - - - -
356A CYS* 2.0 50.3 - - + -
367A VAL* 5.5 0.4 - - + -
368A HIS 2.7 15.9 + - - +
369A LEU* 4.3 4.0 - - - -
370A LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 314 (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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207A ILE* 4.1 11.7 - - + -
208A SER* 3.2 14.5 + - - +
209A LEU* 3.5 27.0 + - + -
210A GLY 2.6 31.0 + - - -
211A ALA 4.5 0.9 + - - -
312A TYR 4.5 0.7 - - - +
313A CYS* 1.3 72.8 - - - +
315A TYR* 1.3 59.0 + - - +
370A LEU* 3.6 41.3 - - + +
372A LEU* 3.7 25.1 - - + -
380A MET* 5.0 2.5 - - - -
386A THR* 4.3 6.7 - - + -
389A HIS* 3.9 16.4 - - + -
390A ILE* 4.0 20.0 - - + -
393A ILE* 4.9 4.9 - - + -
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Residues in contact with TYR 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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210A GLY* 4.0 8.1 - - - +
211A ALA 5.2 0.2 - - - +
313A CYS* 3.6 25.4 - - - -
314A LEU* 1.3 80.6 - - - +
316A GLY* 1.3 59.0 + - - +
317A VAL* 3.7 24.9 - - + -
353A THR* 3.6 43.3 - - + +
354A GLU* 3.2 40.4 + - + +
369A LEU* 3.5 18.7 - - + +
370A LEU 3.9 9.5 + - - -
371A PRO* 3.4 25.5 - - + +
372A LEU* 2.8 27.1 + - - +
380A MET* 4.1 11.2 - - - -
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Residues in contact with GLY 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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315A TYR* 1.3 76.7 - - - +
317A VAL* 1.3 65.9 + - - +
344A GLY 3.5 3.8 - - - +
345A ASP* 3.3 28.8 - - - +
348A VAL 5.2 0.5 - - - +
349A ALA 5.7 0.2 - - - +
350A THR* 4.5 1.2 + - - -
353A THR* 4.8 4.3 + - - +
372A LEU* 3.2 16.8 - - - -
375A ILE* 4.3 9.6 - - - -
380A MET* 3.6 14.0 - - - +
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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
----------------------------------------------------------
315A TYR* 3.7 27.1 - - + -
316A GLY* 1.3 78.0 - - - +
318A GLY* 1.3 61.2 + - - +
319A LEU* 3.4 2.8 + - - +
343A ASP* 4.0 3.6 - - - +
344A GLY 3.2 11.0 - - - -
350A THR* 3.3 26.7 - - + +
354A GLU* 5.1 2.7 - - - +
371A PRO* 4.2 16.2 - - + -
372A LEU 3.6 3.4 + - - -
373A HIS* 3.7 31.8 - - + +
374A GLY* 2.8 27.1 + - - +
375A ILE 4.5 0.2 + - - -
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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
------------------------------------------------------------
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