Contacts of the strand formed by residues 377 - 386 (chain F) in PDB entry 1YKN
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 377 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364F LEU* 3.6 27.8 - - + +
372F LEU* 4.3 24.0 - - - +
373F PRO 5.9 2.0 - - - +
375F GLY 3.1 9.1 + - - +
376F GLU* 1.3 73.0 - - - +
378F ILE* 1.3 65.6 + - - +
440F ARG* 3.7 20.4 - - - +
441F THR 3.8 6.5 - - - +
442F ILE* 4.6 4.9 - - + -
517F ASP* 2.8 44.6 + - - +
518F CYS* 3.6 13.4 - - + +
519F LEU* 3.3 17.3 + - - +
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Residues in contact with ILE 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F GLU* 4.2 10.1 - - + +
377F ARG* 1.3 82.2 - - - +
379F ILE* 1.3 66.4 - - - +
380F VAL* 3.6 26.2 - - + -
440F ARG* 3.4 6.8 - - - +
441F THR* 2.7 51.4 + - + +
443F LYS* 3.9 31.0 - - + +
461F ILE* 4.9 0.7 - - + -
480F PHE* 3.8 24.0 - - + -
518F CYS* 4.0 2.4 - - - +
519F LEU* 3.2 26.2 - - + +
521F TYR* 4.0 16.2 - - + -
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Residues in contact with ILE 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F ILE* 1.3 78.0 - - - +
380F VAL* 1.3 70.6 + - - +
381F ALA* 4.3 13.0 - - + -
438F SER* 4.5 8.7 - - - +
439F PHE 3.4 11.0 - - - +
440F ARG* 4.3 14.4 - - + +
512F ASN* 4.1 27.6 - - - +
514F ASN* 4.5 13.5 - - - +
518F CYS* 4.0 23.3 - - - -
519F LEU 2.7 13.3 + - - +
520F ALA* 3.2 6.5 - - + -
521F TYR* 2.7 26.7 + - - +
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Residues in contact with VAL 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F ILE* 3.6 30.5 - - + -
379F ILE* 1.3 73.2 - - - +
381F ALA* 1.4 59.9 + - - +
399F MET* 5.5 0.4 - - + -
437F TYR* 4.0 9.3 - - + +
438F SER* 3.6 0.7 - - - -
439F PHE* 3.0 37.8 + - + +
441F THR* 4.0 6.7 - - + -
461F ILE* 3.9 18.2 - - + -
463F PHE* 4.1 17.9 - - + -
478F LEU* 3.7 27.4 - - + -
480F PHE* 4.9 2.7 - - + -
521F TYR* 3.4 13.5 - - + +
523F PHE* 4.8 1.1 - - + -
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Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F ILE* 4.1 3.3 - - + -
380F VAL* 1.4 72.6 - - - +
382F GLY* 1.4 53.4 + - - +
436F TYR* 6.4 0.2 - - + -
437F TYR* 3.4 22.9 + - - +
438F SER* 3.7 11.9 - - - -
512F ASN* 4.1 23.1 - - - +
521F TYR 2.9 8.1 + - - +
522F ARG* 3.1 9.7 - - - -
523F PHE 2.7 30.0 + - - -
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Residues in contact with GLY 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F ALA* 1.4 78.6 - - - +
383F ARG* 1.3 62.0 + - - -
436F TYR* 3.4 11.6 - - - -
437F TYR* 3.1 33.8 + - - +
522F ARG* 3.8 10.1 - - - -
523F PHE 3.3 12.6 - - - -
524F ASP* 3.5 7.4 - - - -
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Residues in contact with ARG 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F GLY* 1.3 76.7 - - - -
384F VAL* 1.3 62.9 + - - +
385F VAL* 3.9 25.0 + - + +
389F GLY 5.1 4.4 + - - -
391F PRO* 3.6 21.8 - - - +
434F ASP* 3.0 33.1 + - - +
435F GLY* 3.2 15.7 - - - +
436F TYR* 3.6 37.0 + - + -
437F TYR* 4.6 0.8 - - - -
522F ARG* 3.8 3.8 - - - +
523F PHE 4.0 0.6 + - - -
524F ASP* 3.0 20.4 + - - +
525F ILE 3.0 24.6 + - - +
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Residues in contact with VAL 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F ARG* 1.3 75.1 - - - +
385F VAL* 1.4 55.1 + - - +
391F PRO* 3.6 3.6 - - - +
392F VAL* 2.8 37.6 + - + +
395F THR* 4.5 4.0 - - + -
397F VAL* 4.6 6.1 - - + -
431F THR* 3.4 29.2 - - + -
435F GLY* 2.8 14.9 + - - +
437F TYR* 4.3 12.8 - - + -
465F ILE* 4.3 7.6 - - + -
525F ILE* 3.4 19.1 - - + +
527F LEU* 3.7 35.7 - - + -
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Residues in contact with VAL 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.3 10.3 - - + -
383F ARG* 3.9 35.6 - - + +
384F VAL* 1.4 74.1 - - - +
386F ASP* 1.4 70.8 + - - +
389F GLY* 4.0 12.8 - - - +
390F LYS 2.9 16.8 - - - +
391F PRO* 4.2 4.3 - - + -
392F VAL* 3.8 5.2 - - - +
524F ASP* 6.2 3.4 - - + -
525F ILE 3.1 9.0 + - - +
526F VAL* 3.3 19.3 - - + -
527F LEU* 3.1 23.9 + - - +
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Residues in contact with ASP 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 3.8 1.2 - - - +
385F VAL* 1.4 82.6 - - - +
387F GLN* 1.3 60.0 + - - +
388F TYR* 2.8 16.8 + - - -
389F GLY* 2.8 21.7 + - - -
390F LYS* 2.9 35.0 + - - +
392F VAL* 4.3 11.0 - - + -
526F VAL* 3.7 4.3 - - - +
527F LEU* 3.2 9.2 - - + -
528F ARG 3.4 17.5 - - - +
529F GLY* 4.0 2.9 - - - -
530F GLN* 3.2 32.1 + - + +
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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