Contacts of the strand formed by residues 314 - 321 (chain A) in PDB entry 3CX5
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 ASN 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 4.8 3.5 + - - -
288A TYR* 3.1 20.9 - - - +
289A ASN* 4.3 7.3 + - + +
312A CYS* 3.4 7.7 - - - -
313A ASP* 1.3 92.8 - - - +
315A PHE* 1.3 65.6 + - - +
316A ASN* 5.2 4.4 + - - -
331A SER 5.9 0.2 - - - -
332A THR* 2.8 22.2 + - - +
333A ALA* 3.2 34.0 + - - +
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE 3.2 26.0 - - - -
286A GLY 3.4 9.4 - - - -
287A SER* 3.3 1.7 - - - -
288A TYR* 2.8 69.3 + + + +
300A ILE* 4.9 4.5 - - + -
302A LEU* 3.9 23.8 - - + -
303A LEU* 4.0 17.0 - - + -
306A ILE* 4.6 6.5 - - + -
312A CYS* 3.9 10.8 - - - -
314A ASN* 1.3 77.8 - - - +
316A ASN* 1.3 67.1 + - - +
317A HIS* 3.6 19.3 - + - -
330A PHE* 4.0 10.5 - + + -
331A SER 3.2 13.7 - - - +
332A THR* 3.7 11.4 - - - +
343A LEU* 5.6 3.1 - - + -
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 3.6 5.6 - - - -
287A SER* 3.4 16.6 - - - +
314A ASN* 5.2 4.3 + - - -
315A PHE* 1.3 78.5 - - - +
317A HIS* 1.3 64.8 + - - +
318A PHE* 3.9 16.4 - - - +
330A PHE* 3.2 4.9 - - - -
331A SER* 3.0 47.9 + - - +
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Residues in contact with HIS 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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282A ALA* 3.4 28.6 - - + +
285A PHE* 3.4 31.1 - + + +
286A GLY* 2.9 29.3 + - - +
287A SER* 4.7 3.5 + - - -
302A LEU* 4.4 3.6 - - + +
315A PHE* 3.6 23.0 - + - -
316A ASN* 1.3 78.2 + - - +
318A PHE* 1.3 61.4 + - - +
328A TRP* 4.4 3.6 - - + -
329A GLY 3.3 8.5 + - - +
330A PHE* 3.7 20.0 - - + +
347A THR* 3.9 9.4 - - + +
351A TRP* 3.0 37.5 + + - -
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.1 11.7 - - + -
164A LEU* 3.9 21.8 - - + -
262A SER* 5.3 0.2 - - - -
264A ALA* 4.1 9.2 - - + -
282A ALA* 3.9 7.2 - - - +
316A ASN* 3.9 20.9 - - - +
317A HIS* 1.3 75.1 - - - +
319A SER* 1.3 62.9 + - - +
320A LEU* 3.8 31.2 - - + -
327A LEU* 3.5 19.1 - - + -
328A TRP* 3.5 7.4 - - - -
329A GLY* 2.8 38.2 + - - +
330A PHE* 3.5 35.0 - - - -
331A SER* 3.5 11.7 - - - -
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Residues in contact with SER 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 GLY* 5.9 0.2 - - - -
268A GLU 5.3 3.6 + - - -
275A TYR 4.8 0.5 + - - -
278A ALA* 3.4 34.7 - - - +
279A LYS* 3.3 40.2 + - - +
282A ALA* 4.3 2.8 - - - +
318A PHE* 1.3 75.8 - - - +
320A LEU* 1.3 66.5 + - - +
321A SER* 3.6 10.3 + - - -
327A LEU 3.6 5.6 - - - -
328A TRP* 3.6 15.3 - - - +
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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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161A LEU* 4.5 14.8 - - + -
165A HIS* 3.8 28.5 - - + +
268A GLU 3.7 2.3 + - - +
318A PHE* 3.8 39.3 - - + -
319A SER* 1.3 76.1 - - - +
321A SER* 1.3 61.5 + - - +
322A TYR* 3.8 21.5 - - + +
326A GLY* 3.1 5.1 - - - -
327A LEU* 2.9 40.9 + - + +
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Residues in contact with SER 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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268A GLU* 2.8 25.8 + - - +
270A VAL* 3.5 19.9 - - - +
275A TYR* 3.5 35.5 + - - -
279A LYS* 5.3 1.6 - - - +
319A SER* 3.6 12.2 + - - -
320A LEU* 1.3 73.8 + - - +
322A TYR* 1.3 72.2 + - - +
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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
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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