Contacts of the strand formed by residues 252 - 256 (chain A) in PDB entry 6KSF
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 ALA 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A SER* 1.3 76.4 - - - +
253A ILE* 1.3 64.3 + - - +
269A PHE* 3.5 8.8 - - - -
270A MET* 2.9 46.0 + - + -
289A VAL* 3.9 6.5 - - + -
291A ARG 3.4 15.3 - - - +
292A VAL* 4.3 3.4 - - + +
293A LEU* 4.4 4.0 - - - +
338A ARG* 3.6 27.8 - - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.9 33.9 - - + +
33A SER* 5.3 0.9 - - - +
40A LEU* 3.9 28.9 - - + -
43A VAL* 4.4 4.7 - - + -
252A ALA* 1.3 78.7 - - - +
254A PHE* 1.3 67.0 + - - +
255A LEU* 4.4 4.9 - - + -
267A ALA* 4.3 17.0 - - + -
268A MET 3.5 7.9 - - - +
269A PHE* 4.1 18.8 - - + -
289A VAL* 3.3 13.6 - - - +
290A PRO* 3.1 24.5 - - + +
291A ARG* 3.1 13.9 + - + +
293A LEU* 4.3 19.1 - - + -
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Residues in contact with PHE 254 (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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99A PHE* 4.4 4.7 - + - -
253A ILE* 1.3 73.9 - - - +
255A LEU* 1.3 62.6 - - - +
256A LEU* 3.9 23.8 - - + -
266A THR 3.5 1.4 - - - +
267A ALA* 3.4 4.2 - - - -
268A MET* 2.9 50.0 + - + +
270A MET* 3.8 29.4 - - + -
276A MET* 3.5 31.2 - - + -
278A MET* 4.2 16.2 - - + -
287A HIS* 3.7 37.9 - + + -
288A ALA 3.6 12.8 - - - -
289A VAL* 3.9 15.0 - - + -
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Residues in contact with LEU 255 (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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23A PHE* 3.6 30.3 - - + -
26A LEU* 4.2 4.7 - - + +
27A PHE* 3.8 22.0 - - + +
30A TYR* 4.0 13.9 - - + -
253A ILE* 4.4 3.1 - - + -
254A PHE* 1.3 75.9 - - - +
256A LEU* 1.3 60.0 + - - +
257A GLY 4.0 0.2 - - - -
265A PRO* 4.1 14.1 - - + -
266A THR 3.4 3.1 - - - +
267A ALA* 3.5 33.4 - - + +
287A HIS* 3.1 10.4 - - - +
288A ALA 2.8 32.4 + - - +
290A PRO* 3.5 28.5 - - + -
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Residues in contact with LEU 256 (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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93A LEU* 5.0 0.9 - - + -
96A TYR* 3.5 42.6 + - + -
99A PHE* 3.7 38.4 - - + -
254A PHE* 3.9 16.5 - - + -
255A LEU* 1.3 72.5 - - - +
257A GLY* 1.3 60.8 + - - +
265A PRO* 3.4 2.5 - - - +
266A THR* 2.9 35.8 + - - +
268A MET* 4.3 9.0 - - + -
278A MET* 4.7 11.9 - - - -
282A SER* 4.7 2.9 - - - +
285A LEU* 4.1 19.1 - - + -
286A ASN 3.9 7.0 - - - +
287A HIS* 4.2 12.1 - - + +
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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