Contacts of the strand formed by residues 259 - 263 (chain A) in PDB entry 3CKM
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 ILE 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A SER 6.2 0.2 - - - +
258A GLN* 1.3 79.6 - - - +
260A GLY* 1.3 74.5 + - - +
261A LEU 4.1 0.9 - - - +
280A PHE* 4.6 5.6 - - + -
289A ILE* 3.8 23.8 - - + -
290A PRO 2.9 6.3 + - - +
291A VAL* 3.2 16.9 - - + -
292A GLN* 2.9 26.9 + - - +
313A ILE* 4.1 6.0 - - - +
315A THR* 3.3 21.3 - - + +
317A VAL* 4.0 20.2 - - + -
524A TRP* 3.9 24.9 - - + -
527A ILE* 4.1 17.9 - - + -
528A ASN* 5.1 1.8 - - - +
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Residues in contact with GLY 260 (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 ILE* 1.3 74.8 - - - +
261A LEU* 1.3 60.0 + - - -
262A LEU* 4.0 5.4 - - - -
292A GLN 3.2 8.1 - - - -
294A PHE* 4.0 11.9 - - - -
313A ILE* 3.6 5.5 - - - +
315A THR 2.9 10.5 + - - -
316A LEU* 3.2 16.8 - - - +
317A VAL 2.8 27.4 + - - +
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Residues in contact with LEU 261 (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 ILE* 4.1 1.0 - - + -
260A GLY* 1.3 71.5 - - - -
262A LEU* 1.3 57.5 + - - +
263A LEU* 3.8 35.5 + - + -
276A ILE* 5.8 1.6 - - + -
277A GLN* 4.2 17.3 - - + +
280A PHE* 3.9 34.5 - - + -
281A ASN* 5.1 1.8 - - - +
291A VAL* 3.9 16.6 - - + -
292A GLN 2.9 10.1 + - - +
293A VAL* 3.6 18.1 - - + +
294A PHE 2.8 32.7 + - - +
317A VAL* 3.4 32.5 - - + +
343A LEU* 5.3 0.7 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLY 4.0 12.1 - - - +
261A LEU* 1.3 75.9 - - - +
263A LEU* 1.3 70.6 + - - +
294A PHE* 3.5 15.7 - - + -
296A THR* 3.8 17.7 - - + -
301A VAL* 4.9 11.7 - - + -
304A ILE* 3.7 35.7 - - + -
305A ILE* 5.0 3.1 - - + -
316A LEU* 4.1 26.5 - - + -
317A VAL 2.8 13.8 + - - +
318A GLY* 3.5 5.9 - - - -
319A PRO* 3.4 44.5 - - + +
320A LEU 4.0 0.5 + - - -
328A ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.8 30.6 + - + -
262A LEU* 1.3 82.6 - - - +
264A PRO* 1.4 77.6 - - + +
265A LEU* 3.4 17.5 + - + +
273A GLY* 3.5 21.1 - - - +
276A ILE* 4.0 16.8 - - + -
277A GLN* 3.8 21.3 - - + +
294A PHE 3.2 5.5 + - - +
295A ASP* 3.3 8.5 - - - -
296A THR* 2.9 23.3 + - - +
320A LEU* 4.4 8.1 - - + -
343A LEU* 3.8 25.6 - - + -
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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