Contacts of the strand formed by residues 416 - 421 (chain E) in PDB entry 1KXT
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 GLN 416 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410E TRP* 3.8 17.8 - - + -
411E ASP* 3.0 6.1 - - - +
412E ASN* 2.9 57.3 + - - +
414E SER 3.7 0.2 - - - -
415E ASN* 1.3 76.7 - - - +
417E VAL* 1.3 64.8 + - - +
429E PHE 3.3 9.4 - - - +
430E ASN* 3.0 26.1 + - - +
432E ASP* 3.2 7.1 - - - +
434E TRP* 3.3 23.9 + - - +
435E GLN 3.5 4.3 + - - +
436E LEU* 3.1 38.0 - - + +
437E SER 4.7 1.0 + - - -
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Residues in contact with VAL 417 (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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274E MET* 3.6 27.0 - - + +
275E SER* 3.5 33.7 - - - +
327E PHE* 5.5 3.6 - - + -
409E TRP* 2.9 37.0 - - + -
410E TRP* 3.3 11.6 - - - +
411E ASP* 3.7 5.4 - - + -
416E GLN* 1.3 80.2 - - - +
418E ALA* 1.3 75.5 + - - +
419E PHE* 4.9 3.1 - - + -
428E VAL* 3.7 2.3 - - - +
429E PHE* 2.8 41.4 + - + +
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Residues in contact with ALA 418 (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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408E ASN 4.2 1.6 - - - -
409E TRP* 3.3 2.9 - - - -
410E TRP* 2.8 36.2 + - + +
417E VAL* 1.3 83.5 - - - +
419E PHE* 1.3 67.5 + - - +
426E PHE* 3.7 6.5 - - + -
427E ILE 3.2 15.0 - - - +
428E VAL* 4.0 4.7 - - + +
429E PHE* 5.1 1.3 - - - -
440E LEU* 3.5 31.6 - - + -
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Residues in contact with PHE 419 (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 PHE* 3.5 31.0 - + - -
330E ALA* 3.7 29.2 - - + -
331E HIS* 3.7 31.9 - + + -
332E PRO* 4.7 1.6 - - + -
397E PHE* 5.9 0.6 - + - -
406E PHE* 3.8 23.6 - + + -
407E ALA 3.6 9.6 - - - +
408E ASN 3.7 5.4 - - - -
409E TRP* 3.8 30.3 - + + -
417E VAL* 4.9 1.6 - - + -
418E ALA* 1.3 78.6 - - - +
420E GLY* 1.3 74.3 + - - +
421E ARG* 4.7 2.0 - - + -
426E PHE* 3.7 6.6 - - - -
427E ILE* 3.0 41.5 + - + +
429E PHE* 4.6 1.6 - + - -
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Residues in contact with GLY 420 (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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397E PHE* 6.0 0.4 - - - -
406E PHE* 3.4 5.7 - - - -
407E ALA* 2.6 39.1 + - - -
408E ASN* 5.0 1.8 - - - -
419E PHE* 1.3 81.9 - - - +
421E ARG* 1.3 65.6 + - - -
422E GLY 3.8 3.8 - - - -
425E GLY 3.2 12.6 - - - -
426E PHE* 3.8 10.5 - - - -
442E THR 5.0 1.8 - - - -
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Residues in contact with ARG 421 (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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330E ALA 2.9 22.6 + - - +
331E HIS 3.8 4.4 + - - -
332E PRO* 2.9 49.1 + - - +
397E PHE* 4.2 6.5 - - + -
398E ARG* 4.3 13.7 - - - +
401E VAL* 3.0 64.7 + - + +
402E ASP* 4.6 2.6 + - - +
403E GLY 4.3 5.1 - - - +
404E GLN* 2.9 40.3 + - + +
405E PRO 3.6 1.8 - - - -
406E PHE* 4.3 5.2 - - - +
419E PHE* 4.7 3.6 - - + -
420E GLY* 1.3 78.3 - - - -
422E GLY* 1.3 65.9 + - - +
424E ARG* 3.1 13.0 + - - -
425E GLY 2.8 10.2 + - - +
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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