Contacts of the strand formed by residues 314 - 320 (chain A) in PDB entry 5N4D
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 TYR 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.5 8.6 - - - -
285A ASN* 2.9 42.7 + - - +
287A LEU* 4.1 14.6 - - + -
307A VAL* 3.6 41.8 - - + +
311A ALA* 5.6 2.4 - - + +
312A ALA* 3.4 32.8 - - + -
313A ASP* 1.3 75.4 + - - +
315A ASN* 1.3 62.2 + - - +
326A ILE* 3.9 19.3 - - + -
327A LYS 3.5 3.1 - - - -
328A THR* 3.6 18.2 - - - -
330A LEU* 3.4 30.2 - - + +
338A ILE* 4.3 15.7 - - + -
340A ILE* 5.1 3.6 - - + -
349A ILE* 6.3 1.1 - - + -
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Residues in contact with ASN 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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265A ASP* 4.2 4.3 + - - +
276A TYR* 3.6 18.5 + - - -
313A ASP* 4.4 7.6 - - - +
314A TYR* 1.3 76.2 - - - +
316A ILE* 1.3 75.5 + - - +
317A ILE* 3.5 2.5 + - - +
326A ILE* 3.5 4.7 - - - +
327A LYS* 2.9 55.8 + - + +
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Residues in contact with ILE 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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265A ASP* 4.4 8.9 - - + +
274A TYR* 3.7 52.3 - - + +
276A TYR* 2.9 28.3 + - + +
287A LEU* 3.7 27.1 - - + -
289A VAL* 5.9 0.2 - - + -
315A ASN* 1.3 85.3 + - - +
317A ILE* 1.3 65.6 + - - +
318A THR* 3.7 17.0 - - - +
324A VAL* 3.7 22.2 - - + -
325A TYR 3.9 5.2 - - - +
326A ILE* 3.8 6.3 - - + -
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Residues in contact with ILE 317 (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 ASN* 4.2 2.5 - - - +
316A ILE* 1.3 77.2 - - - +
318A THR* 1.3 63.0 + - + +
325A TYR* 2.9 15.9 + - + +
326A ILE 3.9 2.0 - - - +
327A LYS* 3.6 31.4 - - + +
337A VAL* 3.8 35.4 - - + -
364A VAL* 3.8 31.2 - - + +
365A ASN* 4.4 0.2 - - - -
366A CYS* 3.8 26.6 + - - +
372A PHE* 3.9 21.5 - - + -
411A GLN* 4.4 4.2 - - - +
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Residues in contact with THR 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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267A SER* 6.1 0.7 - - - +
268A GLU* 5.5 0.7 - - - +
274A TYR* 5.0 0.2 - - - -
316A ILE* 3.7 7.9 - - - +
317A ILE* 1.3 84.4 - - + +
319A ASN* 1.3 74.8 + - - +
320A HIS* 4.6 5.3 - - - +
324A VAL* 3.7 4.7 - - - +
325A TYR* 2.8 35.7 + - + +
366A CYS* 3.8 23.1 - - + -
372A PHE* 3.9 21.5 - - + -
411A GLN* 2.7 34.7 + - - -
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Residues in contact with ASN 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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267A SER* 3.3 27.9 - - - -
268A GLU* 4.7 2.9 + - - +
269A ASP* 2.9 32.0 + - - +
271A LYS* 4.7 0.4 - - - +
272A TYR* 3.9 8.4 - - - -
274A TYR* 4.0 11.6 + - - +
318A THR* 1.3 86.0 + - - +
320A HIS* 1.4 75.4 + - - +
321A GLY 2.9 23.4 + - - +
323A LEU 3.2 13.5 - - - +
324A VAL* 4.1 8.1 - - + -
325A TYR* 4.4 0.9 - - - -
411A GLN* 5.0 2.8 + - - -
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Residues in contact with HIS 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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318A THR* 4.6 11.2 - - + +
319A ASN* 1.4 78.7 + - - +
321A GLY* 1.3 64.2 - - - +
322A SER 3.3 0.5 + - - -
323A LEU* 2.8 28.2 + - + +
325A TYR* 3.7 34.5 - + + +
366A CYS* 5.0 0.4 - - - -
369A GLU* 3.1 31.1 + - + -
370A GLU* 4.3 14.0 + - + +
372A PHE* 4.8 6.2 - + - -
389A LYS* 6.1 2.1 - - + +
411A GLN* 5.2 3.1 - - - -
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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