Contacts of the strand formed by residues 314 - 321 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258L LYS* 4.8 3.3 + - - -
288L TYR* 3.1 19.1 - - - +
289L ASN* 4.3 7.5 + - + +
312L CYS* 3.5 7.3 - - - -
313L ASP* 1.3 93.1 - - - +
315L PHE* 1.3 59.8 + - - +
316L ASN* 5.1 5.7 + - - -
332L THR* 2.7 29.6 + - - +
333L ALA* 3.1 34.0 + - - +
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Residues in contact with PHE 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285L PHE 3.3 26.2 - - - -
286L GLY 3.4 10.5 - - - -
287L SER* 3.2 2.5 - - - -
288L TYR* 2.7 63.5 + + + +
300L ILE* 4.8 3.6 - - + -
302L LEU* 4.0 20.0 - - + -
303L LEU* 3.8 10.3 - - + -
306L ILE* 3.5 29.6 - - + -
312L CYS* 4.0 5.4 - - - -
314L ASN* 1.3 77.6 - - - +
316L ASN* 1.3 66.0 + - - +
317L HIS* 3.5 19.1 - + - -
330L PHE* 4.0 11.2 - + + -
331L SER 3.1 14.1 - - - +
332L THR* 3.8 10.1 - - - +
343L LEU* 5.5 2.2 - - + -
347L THR* 5.9 0.2 - - - -
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Residues in contact with ASN 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L LEU* 6.4 0.6 - - - +
286L GLY 3.7 4.5 - - - -
287L SER* 3.7 14.1 - - - -
314L ASN* 5.1 5.2 + - - -
315L PHE* 1.3 79.1 - - - +
317L HIS* 1.3 65.1 + - - +
318L PHE* 3.9 12.6 - - - +
330L PHE* 3.2 5.4 - - - -
331L SER* 3.0 47.0 + - - +
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Residues in contact with HIS 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282L ALA* 3.4 26.0 - - + +
285L PHE* 3.4 31.0 - + + +
286L GLY* 2.8 32.1 + - - +
287L SER* 5.7 0.5 - - - -
302L LEU* 4.4 4.4 - - + +
315L PHE* 3.5 22.5 - + - -
316L ASN* 1.3 78.3 + - - +
318L PHE* 1.3 62.1 + - - +
328L TRP* 4.5 4.2 - - + -
329L GLY 3.2 8.1 + - - +
330L PHE* 3.6 21.8 - - + +
347L THR* 4.0 8.6 - - + +
351L TRP* 3.0 35.4 + + - -
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Residues in contact with PHE 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L LEU* 4.1 12.3 - - + -
164L LEU* 3.9 22.4 - - + -
264L ALA* 4.1 8.5 - - + -
282L ALA* 3.9 7.5 - - - +
316L ASN* 3.9 18.6 - - - +
317L HIS* 1.3 75.3 - - - +
319L SER* 1.3 62.0 + - - +
320L LEU* 3.8 32.5 - - + -
327L LEU* 3.4 19.3 - - + -
328L TRP* 3.5 7.3 - - - -
329L GLY* 2.8 47.3 + - - +
330L PHE* 3.5 34.5 - - - -
331L SER* 3.5 13.7 - - - -
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Residues in contact with SER 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268L GLU 5.3 3.6 + - - -
275L TYR 4.9 0.3 + - - -
278L ALA* 3.4 34.9 - - - +
279L LYS* 3.8 38.8 + - - +
282L ALA* 4.2 2.6 - - - +
318L PHE* 1.3 76.9 - - - +
320L LEU* 1.3 65.2 + - - +
321L SER* 3.6 11.5 + - - -
327L LEU 3.6 4.4 - - - -
328L TRP* 3.6 14.8 - - - +
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Residues in contact with LEU 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L LEU* 4.4 15.0 - - + -
165L HIS* 3.8 27.4 - - + +
268L GLU 3.8 1.7 + - - +
318L PHE* 3.8 41.3 - - + -
319L SER* 1.3 75.2 + - - +
321L SER* 1.3 61.1 + - - +
322L TYR* 3.7 22.4 - - + +
326L GLY* 3.0 6.1 - - - -
327L LEU* 2.8 42.8 + - + +
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Residues in contact with SER 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268L GLU* 2.6 25.5 + - - +
270L VAL* 3.7 19.1 - - - +
275L TYR* 3.6 35.9 + - - -
279L LYS* 5.9 0.6 - - - +
319L SER* 3.6 11.9 + - - -
320L LEU* 1.3 74.5 - - - +
322L TYR* 1.3 72.3 + - - +
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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