Contacts of the strand formed by residues 481 - 488 (chain L) in PDB entry 1KFX
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 GLU 481 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388L LEU* 3.8 22.9 - - + +
389L ILE 3.7 5.8 - - - +
390L LYS* 3.1 41.5 + - - +
436L VAL* 3.0 51.6 + - + +
438L GLU* 4.6 0.7 - - - -
439L GLU 2.7 38.4 + - - +
480L GLY* 1.3 71.5 - - - -
482L TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 482 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387L TYR 4.1 0.5 - - - +
389L ILE* 3.1 37.9 + - + +
391L LEU* 3.4 29.8 - - + -
407L PHE* 4.7 2.5 - + + -
433L ILE* 3.2 29.2 - - + -
434L TYR 3.6 2.7 - - - -
435L GLU* 4.6 15.0 - - + -
459L ARG* 4.9 16.6 - - + -
477L LEU* 3.6 26.0 - - + -
478L PRO* 2.5 46.7 + - + +
480L GLY* 3.0 30.6 - - - -
481L GLU* 1.3 78.8 - - - +
483L ILE* 1.3 64.3 + - - +
484L LEU* 4.2 0.7 - - - +
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Residues in contact with ILE 483 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386L GLN* 4.5 11.2 - - + -
387L TYR 3.7 7.0 - - - +
388L LEU* 3.3 42.2 - - + -
433L ILE* 2.6 12.7 - - - +
434L TYR* 2.3 53.3 + - + +
436L VAL* 3.4 21.8 - - + -
448L LEU* 3.8 31.6 - - + -
452L PHE* 5.2 2.7 - - + -
453L PHE* 5.3 0.2 - - + -
482L TYR* 1.3 73.3 - - - +
484L LEU* 1.3 62.6 + - - +
485L VAL* 4.7 4.7 - - + -
512L VAL* 4.3 13.0 - - + -
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Residues in contact with LEU 484 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386L GLN* 4.1 0.5 - - - -
387L TYR* 3.0 41.4 + - + +
389L ILE* 3.3 42.2 - - + -
409L VAL* 4.5 19.7 - - + -
431L PHE* 4.4 11.4 - - + -
432L GLY 3.0 10.3 - - - +
433L ILE* 3.9 11.9 - - + -
482L TYR 4.2 0.4 - - - +
483L ILE* 1.3 80.0 - - - +
485L VAL* 1.3 67.3 + - - +
486L PRO* 3.3 8.8 - - + +
499L ILE* 4.4 28.3 - - + -
509L TYR* 4.9 0.7 - - + -
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Residues in contact with VAL 485 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381L PHE* 3.8 33.0 - - + +
384L ASN* 3.4 33.9 - - + +
385L PRO 4.0 1.6 - - - +
386L GLN* 3.7 23.1 - - + +
431L PHE* 3.8 3.2 - - - -
432L GLY 2.6 25.7 + - - +
434L TYR* 4.4 4.3 - - + -
453L PHE* 3.9 24.5 - - + -
483L ILE* 4.7 2.0 - - + -
484L LEU* 1.3 78.2 - - - +
486L PRO* 1.3 65.7 - - - +
487L SER* 3.6 6.4 + - - -
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Residues in contact with PRO 486 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365L TRP* 3.5 9.6 + - + -
384L ASN* 3.4 11.8 - - - +
385L PRO* 3.5 13.0 - - + +
387L TYR* 3.7 14.4 - - + -
411L LEU* 3.1 34.3 - - + -
431L PHE* 3.9 8.9 - - + -
484L LEU 3.3 12.1 - - - +
485L VAL* 1.3 84.7 - - - +
487L SER* 1.3 67.4 + - - +
497L PHE* 3.7 25.1 - - + -
499L ILE* 3.5 11.0 - - + -
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Residues in contact with SER 487 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365L TRP* 3.1 24.2 - - - -
373L GLY* 3.1 19.5 - - - -
374L CYS 3.4 8.5 + - - -
381L PHE* 4.9 1.9 - - - -
384L ASN* 2.9 23.1 + - - -
411L LEU* 4.6 0.2 - - - +
429L ILE* 3.5 4.7 - - - +
430L GLY 3.1 28.4 + - - +
465L PHE* 4.1 8.1 - - - -
485L VAL* 3.7 7.8 + - - +
486L PRO* 1.3 77.8 - - - +
488L THR* 1.3 60.8 + - - +
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Residues in contact with THR 488 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365L TRP* 3.4 34.8 - - + +
371L ALA* 5.6 1.9 - - - +
372L GLY 5.2 0.3 - - - -
373L GLY* 3.1 15.9 + - - -
384L ASN* 4.7 0.4 + - - -
427L HIS* 4.3 20.9 - - + -
428L THR 3.4 8.7 - - - -
429L ILE* 4.1 2.9 - - + +
465L PHE* 3.2 10.9 - - - -
487L SER* 1.3 75.1 - - - +
489L PHE* 1.3 72.9 + - - +
490L GLU 3.3 13.2 + - - -
491L PRO* 4.8 1.0 - - - +
493L LYS* 3.5 35.7 + - + +
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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