Contacts of the strand formed by residues 283 - 290 (chain A) in PDB entry 1K1S
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 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PRO* 3.3 4.7 - - - +
282A MET* 1.3 81.7 - - - +
284A ILE* 1.3 70.3 + - - +
285A THR* 4.1 15.2 + - - +
299A GLY* 3.5 12.9 + - - +
300A LYS* 3.0 28.7 - - - +
301A LYS* 3.8 35.5 - - + +
306A ILE* 4.0 0.7 - - - -
337A LYS 5.4 0.4 - - - +
338A LEU* 3.7 4.2 - - - -
339A ASP* 3.3 42.4 + - + +
340A ASN* 4.7 8.0 - - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 5.8 1.1 - - + -
274A TYR* 4.0 3.6 - - - +
281A PRO* 4.9 0.9 - - + -
283A ARG* 1.3 80.3 - - - +
285A THR* 1.3 68.1 + - - +
286A VAL* 4.3 3.8 - - + -
299A GLY* 2.9 2.9 - - - -
300A LYS 2.8 32.5 + - - +
306A ILE* 3.2 44.2 - - + -
311A ALA* 3.9 24.5 - - + +
314A VAL* 4.8 11.9 - - + -
315A ALA* 5.2 8.5 - - + -
318A LEU* 3.9 13.7 - - + +
336A VAL* 3.8 23.3 - - + -
337A LYS 3.9 2.5 - - - -
338A LEU* 3.9 11.4 - - + -
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 4.1 17.0 + - - +
284A ILE* 1.3 80.1 + - - +
286A VAL* 1.3 64.2 + - - +
287A ILE* 3.2 21.9 - - + +
297A SER* 4.0 11.2 - - - -
298A LYS 3.5 19.1 - - - +
299A GLY* 4.1 4.4 - - - +
336A VAL* 3.3 5.7 - - - +
337A LYS* 2.8 51.8 + - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.0 28.3 - - + -
284A ILE* 5.0 3.4 - - + -
285A THR* 1.3 72.2 - - - +
287A ILE* 1.3 62.0 + - - +
288A ALA* 5.6 0.2 - - + -
297A SER* 3.2 22.0 - - - -
298A LYS 2.9 12.9 + - - +
315A ALA* 3.7 23.1 - - + +
318A LEU* 3.4 39.0 - - + -
319A LEU* 4.6 7.6 - - - -
322A LEU* 3.7 17.5 - - + +
334A ILE* 4.3 11.2 - - + -
335A GLY 3.8 4.7 - - - +
336A VAL* 5.5 1.8 - - + -
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 3.5 37.2 - - + +
285A THR* 3.2 35.4 - - + +
286A VAL* 1.3 75.0 - - - +
288A ALA* 1.3 67.5 + - - +
289A ILE* 4.4 6.5 - - + -
295A ILE* 3.9 26.7 - - + -
297A SER* 3.6 14.6 - - - -
334A ILE* 3.3 6.4 - - - +
335A GLY 2.8 35.6 + - - +
336A VAL 4.5 1.6 - - - -
337A LYS* 3.8 28.5 - - + +
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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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286A VAL* 4.1 0.4 + - + -
287A ILE* 1.3 76.3 - - - +
289A ILE* 1.3 61.8 + - - +
290A MET* 3.3 15.1 + - + +
294A ASP 3.8 0.2 - - - +
296A LEU* 3.1 38.0 + - + +
319A LEU* 5.5 3.6 - - + -
322A LEU* 4.2 14.6 - - + -
331A VAL* 4.0 23.3 - - + -
333A ARG 3.5 4.0 - - - -
334A ILE* 4.4 6.7 - - + +
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 4.0 16.8 - - + -
287A ILE* 4.4 13.2 - - + +
288A ALA* 1.3 69.2 - - - +
290A MET* 1.3 54.1 + - - +
293A LEU* 3.9 32.1 - - + +
294A ASP 3.9 3.8 - - - -
295A ILE* 5.0 10.1 - - + +
331A VAL* 4.6 0.4 - - - -
332A ARG* 2.8 36.7 + - + +
333A ARG* 2.7 74.8 + - + +
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Residues in contact with MET 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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288A ALA* 3.7 15.7 - - + +
289A ILE* 1.3 72.8 - - - +
291A GLU* 1.3 51.8 + - - +
292A ASP* 2.4 9.3 + - - +
293A LEU* 2.3 35.9 + - - -
294A ASP* 3.3 25.7 + - - +
296A LEU* 3.2 49.1 - - + -
326A ASP* 3.5 13.7 - - - +
329A ARG* 2.7 46.4 - - + +
330A ASN 3.8 10.8 - - - +
331A VAL* 4.9 6.5 - - + -
332A ARG* 4.1 2.0 - - - +
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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