Contacts of the strand formed by residues 287 - 292 (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 HIS 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.9 3.8 - - - -
228A LEU* 5.6 1.6 - - + -
231A HIS* 3.1 57.7 + + - -
233A ASP* 3.7 16.4 - - - -
254A PHE* 3.7 28.7 - + + -
255A LEU 3.1 14.8 - - - +
256A LEU* 4.2 8.6 - - + +
278A MET* 4.9 12.0 - - + +
283A ARG 5.4 3.4 - - - -
285A LEU 2.9 24.0 + - - -
286A ASN* 1.3 74.9 - - - +
288A ALA* 1.3 61.5 + - - +
403A SIN 2.5 38.6 + - + +
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Residues in contact with ALA 288 (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* 4.0 10.5 - - + -
27A PHE* 3.7 20.2 - - + -
228A LEU* 3.3 19.3 - - - +
229A GLY 3.6 11.7 - - - +
230A ILE* 3.8 5.2 - - - +
231A HIS* 5.1 0.2 - - - -
254A PHE* 3.6 6.7 - - - -
255A LEU* 2.8 31.8 + - + -
287A HIS* 1.3 79.1 - - - +
289A VAL* 1.3 63.8 + - - +
290A PRO* 3.7 2.0 - - - +
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Residues in contact with VAL 289 (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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222A TYR* 5.9 0.9 - - + -
226A SER 4.7 0.5 - - - +
227A THR* 3.6 2.9 - - - -
228A LEU* 2.9 58.3 + - + +
252A ALA* 3.9 22.4 - - + -
253A ILE 3.3 14.4 - - - +
254A PHE* 3.9 18.4 - - + -
270A MET* 4.0 11.9 - - + -
288A ALA* 1.3 78.9 - - - +
290A PRO* 1.3 64.1 - - - +
291A ARG 3.4 5.8 + - - +
292A VAL* 5.4 2.9 - - + -
338A ARG* 4.0 15.5 - - - +
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Residues in contact with PRO 290 (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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27A PHE* 3.5 41.5 - - + +
30A TYR* 4.1 10.5 - - + -
31A ARG* 3.4 19.0 - - - +
227A THR* 3.3 21.5 - - - +
253A ILE* 3.1 19.3 - - + +
255A LEU* 3.5 35.4 - - + -
288A ALA 3.7 5.8 - - - +
289A VAL* 1.3 85.6 - - - +
291A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 291 (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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30A TYR 3.2 22.9 - - - +
31A ARG* 3.6 11.7 + - - +
33A SER* 2.6 33.7 + - - -
34A ARG* 4.2 19.5 - - - +
35A PRO* 3.8 9.7 - - - +
224A LEU 4.3 10.1 + - - -
225A ASP* 5.8 1.0 - - - +
226A SER 4.5 4.3 - - - -
252A ALA* 3.4 6.2 - - - +
253A ILE* 3.1 34.7 + - + +
289A VAL* 3.3 4.7 + - - +
290A PRO* 1.3 84.3 - - + +
292A VAL* 1.3 77.9 + - - +
293A LEU* 4.0 20.1 + - + +
294A PRO* 3.6 23.0 - - - +
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Residues in contact with VAL 292 (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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222A TYR* 4.1 19.7 - - + -
223A ARG 3.5 26.5 - - - +
224A LEU* 3.5 31.1 + - + +
226A SER 4.3 9.7 + - - +
250A GLN* 4.0 14.6 - - + -
251A SER 3.6 12.6 - - - +
252A ALA* 4.3 1.1 - - + -
289A VAL* 5.4 3.6 - - + -
291A ARG* 1.3 83.4 - - - +
293A LEU* 1.3 71.2 + - - +
294A PRO* 3.7 4.7 - - - +
338A ARG* 4.3 25.1 - - + +
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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