Contacts of the strand formed by residues 315 - 318 (chain A) in PDB entry 1CK7
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 ARG 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A THR 5.4 0.6 - - - -
133A PRO* 3.7 30.0 - - + +
277A GLU* 3.6 10.1 + - - -
305A CYS* 3.6 29.2 - - + +
306A THR* 3.3 8.1 - - - +
307A THR* 4.1 9.0 - - + -
313A GLY 3.6 3.7 + - - +
314A TYR* 1.3 74.9 - - - +
316A TRP* 1.3 62.8 + - - +
331A PHE* 3.6 8.1 - - - +
332A CYS* 2.3 58.4 + - + +
333A PRO* 4.0 8.5 + - - +
334A GLU 3.8 4.9 - - - -
335A THR* 2.5 37.0 + - - -
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Residues in contact with TRP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 3.8 18.3 - + - -
297A PHE* 4.4 20.6 - + - -
302A TYR* 6.1 0.2 - + - -
305A CYS* 2.9 23.3 - - - +
306A THR* 2.8 46.1 + - - -
308A GLU* 2.8 27.3 + - + -
309A GLY* 5.8 0.4 - - - -
310A ARG* 3.7 25.8 - - + +
314A TYR 4.3 0.4 - - - +
315A ARG* 1.3 77.1 - - - +
317A CYS* 1.3 97.8 + - - +
318A GLY 3.8 3.4 - - - -
323A TYR* 3.9 39.9 - + - -
329A TYR* 4.0 15.7 - + + -
330A GLY 3.8 11.9 - - - +
331A PHE* 4.2 16.2 - - + -
332A CYS* 4.2 2.2 - - - -
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Residues in contact with CYS 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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281A THR* 4.2 4.7 - - - -
291A CYS* 2.2 58.8 - - + -
293A PHE* 4.5 0.9 - - + -
295A PHE* 3.5 16.2 - - + -
305A CYS* 4.0 7.2 - - - -
316A TRP* 1.3 93.0 - - - +
318A GLY* 1.3 63.8 + - - +
319A THR* 3.4 3.1 + - - -
329A TYR* 3.4 17.0 - - - -
330A GLY 3.3 12.0 + - - -
332A CYS* 4.0 1.8 - - - -
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Residues in contact with GLY 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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291A CYS* 3.5 1.2 - - - -
292A LYS* 2.7 36.2 + - - +
295A PHE* 3.2 30.1 - - - -
316A TRP* 3.8 2.4 - - - -
317A CYS* 1.3 75.5 - - - +
319A THR* 1.3 52.5 + - - -
320A THR 3.2 11.1 + - - -
323A TYR* 4.1 11.9 - - - -
328A LYS 3.4 8.1 - - - -
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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