Contacts of the strand formed by residues 363 - 367 (chain E) 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 GLY 363 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300E GLN* 5.4 0.4 - - - -
304E GLN* 3.0 19.1 + - - +
342E TYR* 3.3 12.3 - - - -
343E TRP 4.9 0.2 - - - -
344E ASN* 2.7 23.3 + - - -
360E SER 2.8 31.0 + - - -
362E ASN* 1.3 80.0 - - - +
364E TRP* 1.3 54.8 + - - -
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Residues in contact with TRP 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E ILE* 3.5 16.2 - - + -
300E GLN* 2.8 31.4 + - + -
304E GLN* 3.4 15.8 + - - -
316E MET* 3.4 27.6 - - + +
318E LEU* 3.9 24.5 - - + -
329E TRP* 4.0 12.8 - + - -
335E LEU* 4.1 10.8 - - + -
339E PHE* 3.9 36.1 - + - -
342E TYR* 2.7 38.3 + + + +
343E TRP* 3.6 32.3 - + + -
344E ASN* 2.8 32.0 + - - +
347E GLU* 3.7 1.7 - - - +
358E GLU 3.5 5.4 - - - +
359E PHE* 3.8 2.7 - + - -
363E GLY* 1.3 75.8 - - - -
365E ASN* 1.3 61.1 + - - +
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Residues in contact with ASN 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E TRP* 4.0 7.0 - - - -
344E ASN* 4.0 5.4 - - - +
347E GLU* 2.6 19.5 - - + +
357E ALA* 3.7 0.2 - - - -
358E GLU* 2.9 66.3 + - - +
360E SER* 4.0 12.8 - - - +
364E TRP* 1.3 76.9 - - - +
366E ASP* 1.3 65.3 + - - +
367E ASP* 4.1 3.4 + - - +
802E CA 2.3 28.4 - - - -
1N MAN 4.0 8.6 + - - -
2N MAN 3.0 22.2 + - - -
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Residues in contact with ASP 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E TRP* 3.7 29.2 - - + -
343E TRP* 3.9 3.8 - - + -
347E GLU* 2.6 10.7 - - - +
348E PRO* 3.2 21.3 - - + +
349E ASN 3.2 1.0 + - - -
350E ASN* 2.7 35.2 + - - +
354E GLU* 2.8 17.0 - - - +
356E CYS 3.2 6.5 - - - +
365E ASN* 1.3 73.8 - - - +
367E ASP* 1.3 59.0 + - - +
802E CA 2.5 39.9 - - - -
2N MAN 2.9 4.0 + - - -
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Residues in contact with ASP 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E TRP* 4.5 2.2 - - + -
354E GLU* 3.1 22.6 - - - +
355E ASP 3.5 0.9 + - - -
356E CYS* 2.8 29.8 + - - +
358E GLU* 3.8 9.2 - - - +
365E ASN* 3.8 7.4 + - - +
366E ASP* 1.3 73.0 - - - +
368E LYS* 1.3 89.8 + - - +
369E CYS 3.4 0.3 + - - -
371E LEU* 3.3 12.3 - - - +
373E LYS* 2.8 36.4 + - - +
1N MAN 4.8 3.6 + - - -
2N MAN 3.7 16.5 + - - +
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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