Contacts of the strand formed by residues 356 - 360 (chain B) in PDB entry 1K9I
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 CYS 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B TRP* 3.2 39.3 - - + -
315B TRP* 3.3 26.1 - - + -
318B LEU 3.6 3.1 - - - -
319B SER* 4.2 0.9 - - - -
321B LEU* 4.1 2.9 - - - -
327B TRP* 3.9 4.3 - - - -
355B ASP* 1.3 82.4 - - - +
357B ALA* 1.3 59.7 + - - +
366B ASP* 3.2 2.4 - - - -
367B ASP 2.8 28.6 + - - +
369B CYS* 2.0 45.3 - - - -
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B TRP* 3.3 9.2 - - - -
316B MET* 3.2 34.5 + - + +
318B LEU* 3.0 39.8 + - + +
327B TRP* 3.6 13.6 - - + -
343B TRP* 4.2 10.1 - - + -
356B CYS* 1.3 73.8 - - - +
358B GLU* 1.3 60.8 - - - +
364B TRP* 5.2 0.4 - - + -
365B ASN 3.4 7.6 - - - +
366B ASP* 4.4 0.4 - - - +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PHE* 3.2 20.4 - - - +
314B THR 3.0 18.4 - - - +
315B TRP* 4.1 9.9 - - + -
316B MET* 3.7 8.6 - - - +
357B ALA* 1.3 75.5 - - - +
359B PHE* 1.3 59.9 + - - +
360B SER* 3.6 16.0 + - - -
364B TRP* 3.3 6.9 - - - -
365B ASN* 2.9 70.0 + - + +
367B ASP* 3.9 7.2 - - + +
373B LYS* 2.9 31.1 + - + +
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B VAL* 4.4 9.9 - - + -
294B ILE* 3.7 12.6 - - + -
300B GLN* 3.8 19.7 - - - -
303B LEU* 3.7 28.9 - - + -
304B GLN* 3.3 30.5 - - - +
307B SER* 3.4 30.1 - - - +
312B ARG 3.7 3.4 - - - +
313B PHE* 3.4 10.2 - - - +
314B THR* 2.7 44.7 + - + +
315B TRP 4.4 0.7 - - - -
316B MET* 3.7 37.0 - - + -
358B GLU* 1.3 70.5 - - - +
360B SER* 1.3 59.7 + - - +
363B GLY 3.7 2.9 - - - -
376B ILE* 4.4 10.5 - - + -
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B GLN* 4.1 0.2 - - - +
312B ARG 5.6 0.2 - - - -
313B PHE* 3.1 25.1 - - - -
344B ASN* 2.8 35.3 + - - -
358B GLU* 3.6 20.3 + - - -
359B PHE* 1.3 76.0 - - - +
361B GLY* 1.3 64.8 + - - +
362B ASN 3.2 0.5 + - - -
363B GLY 2.8 17.8 + - - +
365B ASN* 4.0 11.5 + - - +
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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