Contacts of the strand formed by residues 281 - 287 (chain A) in PDB entry 4CCZ
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.4 29.4 + - + +
26A LEU* 3.7 48.7 - - + -
27A GLN* 4.3 8.7 + - - +
254A LEU* 3.0 39.6 + - + +
255A CYS* 3.7 11.7 - - + -
256A ILE* 2.9 26.2 + - - +
279A THR 5.7 0.9 - - - -
280A ALA* 1.3 79.1 - - - +
282A VAL* 1.3 61.1 + - - +
318A ASN* 3.9 21.1 - - + -
343A PRO* 6.4 0.7 - - + -
344A ARG* 3.5 8.7 - - + +
346A PRO* 4.3 22.9 - - + -
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Residues in contact with VAL 282 (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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255A CYS* 3.5 2.9 - - - -
256A ILE 3.0 7.9 - - - +
257A GLY* 4.7 0.4 - - - -
271A ILE* 3.7 25.4 - - + +
274A ILE* 4.8 4.7 - - + -
275A GLY* 3.9 14.4 - - - +
278A THR* 4.5 6.3 - - + -
280A ALA 4.3 0.9 - - - +
281A TYR* 1.3 76.7 - - - +
283A LEU* 1.3 71.7 + - - +
284A CYS* 5.0 0.4 - - + -
316A LEU 3.8 19.1 - - - +
317A VAL* 4.0 1.9 - - - -
318A ASN* 3.0 26.9 + - - +
319A ILE 3.2 5.8 + - - +
344A ARG* 3.4 38.5 - - - +
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Residues in contact with LEU 283 (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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33A LEU* 6.2 1.1 - - + -
192A LEU* 6.3 1.3 - - + -
223A PHE* 5.3 8.7 - - + -
224A ILE 5.4 1.3 - - - +
225A SER* 5.4 3.1 - - - -
255A CYS* 2.9 21.2 - - + -
256A ILE* 2.7 12.4 + - - +
257A GLY* 3.1 25.5 - - - +
271A ILE* 3.6 1.0 - - - +
282A VAL* 1.3 81.4 - - - +
284A CYS* 1.3 64.9 + - - +
285A TYR* 4.8 15.3 - - + -
319A ILE* 3.8 15.5 - - + -
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Residues in contact with CYS 284 (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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258A LEU* 3.5 11.0 - - - -
267A MET* 5.4 4.7 - - - -
271A ILE* 3.9 29.2 - - + -
282A VAL* 5.0 0.2 - - + -
283A LEU* 1.3 79.9 - - - +
285A TYR* 1.3 61.9 + - - +
286A PRO* 3.6 26.0 - - - +
317A VAL* 4.6 14.1 - - + -
319A ILE* 3.1 12.0 + - - +
320A VAL* 3.5 8.7 - - - +
321A GLY 3.3 16.0 + - - -
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Residues in contact with TYR 285 (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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33A LEU* 3.5 27.4 - - + -
94A GLU* 4.0 10.5 - - - -
192A LEU* 3.8 13.8 - - + +
194A GLU* 3.0 39.4 + - - +
225A SER* 3.8 11.8 - - - -
258A LEU 3.2 7.0 + - - -
259A ASN* 3.4 31.9 - - + -
260A CYS* 3.3 18.6 + - - -
283A LEU* 4.8 9.4 - - + -
284A CYS* 1.3 78.6 - - - +
286A PRO* 1.4 66.8 - - - +
319A ILE* 6.4 0.9 - - + -
321A GLY* 3.2 31.6 - - - -
322A GLY 3.4 17.3 - - - +
323A CYS* 3.8 7.0 - - + +
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Residues in contact with PRO 286 (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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259A ASN* 5.2 0.7 - - - -
260A CYS 4.4 4.0 - - - +
262A LEU 3.6 11.2 - - - +
263A GLY 3.7 1.8 - - - +
264A ALA* 3.5 39.5 - - + +
267A MET* 4.9 6.7 - - + -
284A CYS* 3.6 24.9 - - - +
285A TYR* 1.4 90.5 - - - +
287A ASN* 1.3 73.2 + - - +
321A GLY 4.0 7.6 - - - +
322A GLY* 3.6 5.5 - - - -
323A CYS 3.1 10.6 + - - -
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Residues in contact with ASN 287 (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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260A CYS* 3.4 22.8 - - - +
261A ALA* 3.6 9.3 - - - +
262A LEU 3.2 12.1 + - - +
263A GLY* 3.3 18.8 - - - -
264A ALA 4.1 3.1 + - - -
286A PRO* 1.3 77.3 - - - +
288A ALA* 1.3 69.2 + - - +
323A CYS* 2.8 19.1 - - - +
324A CYS* 2.6 52.2 + - - +
326A SER* 6.0 1.1 - - - +
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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