Contacts of the strand formed by residues 377 - 386 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364L LEU* 3.9 26.6 - - + +
372L LEU* 4.4 26.1 - - - +
373L PRO 5.8 2.7 - - - +
375L GLY 3.3 8.5 + - - +
376L GLU* 1.3 72.4 - - - +
378L ILE* 1.4 61.7 + - - +
440L ARG* 3.6 21.4 - - - +
441L THR 3.7 6.3 - - - -
442L ILE* 4.5 5.2 - - + -
517L ASP* 2.8 42.7 + - - +
518L CYS* 3.4 13.8 - - + -
519L LEU* 3.3 20.3 + - - +
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Residues in contact with ILE 378 (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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376L GLU* 3.9 13.7 - - + +
377L ARG* 1.4 78.6 - - - +
379L ILE* 1.3 62.9 + - - +
380L VAL* 3.6 25.1 - - + -
440L ARG* 3.4 6.9 - - - +
441L THR* 2.7 54.1 + - + +
443L LYS* 4.0 25.1 - - + +
461L ILE* 4.9 0.4 - - + -
480L PHE* 3.8 27.8 - - + -
518L CYS* 4.1 0.9 - - - +
519L LEU* 3.2 20.0 - - + +
521L TYR* 3.9 23.3 - - + -
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Residues in contact with ILE 379 (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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378L ILE* 1.3 76.0 - - - +
380L VAL* 1.3 71.0 + - - +
381L ALA* 4.0 11.2 - - + -
438L SER* 4.6 7.4 - - - -
439L PHE 3.2 13.5 - - - +
440L ARG* 4.4 10.5 - - + +
512L ASN* 4.0 24.5 - - - +
514L ASN* 4.6 13.7 - - - +
518L CYS* 3.8 26.7 - - - -
519L LEU 3.1 8.3 + - - +
520L ALA* 3.1 11.5 - - + -
521L TYR* 2.8 25.6 + - - +
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Residues in contact with VAL 380 (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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378L ILE* 3.6 29.8 - - + -
379L ILE* 1.3 73.1 - - - +
381L ALA* 1.3 60.8 + - - +
399L MET* 5.5 1.3 - - + -
437L TYR* 3.9 10.4 - - + +
438L SER* 3.5 1.7 - - - -
439L PHE* 2.9 40.1 + - + +
441L THR* 4.3 6.1 - - + -
461L ILE* 4.1 17.0 - - + -
463L PHE* 4.1 16.4 - - + -
478L LEU* 3.5 28.9 - - + -
480L PHE* 5.0 1.8 - - + -
521L TYR* 3.6 13.5 - - + +
523L PHE* 4.5 4.0 - - + -
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Residues in contact with ALA 381 (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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379L ILE* 4.4 4.3 - - + -
380L VAL* 1.3 73.7 - - - +
382L GLY* 1.3 61.0 + - - +
436L TYR* 6.2 1.1 - - + -
437L TYR* 3.4 20.5 + - - +
438L SER* 4.0 10.3 - - - -
509L ASP* 6.1 0.2 - - - +
512L ASN* 3.8 25.4 - - - +
521L TYR 2.9 13.1 + - - +
522L ARG* 3.3 8.5 - - - +
523L PHE 2.9 21.1 + - - -
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Residues in contact with GLY 382 (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 ALA* 1.3 78.6 - - - +
383L ARG* 1.3 60.1 + - - -
436L TYR* 3.5 10.8 - - - -
437L TYR* 3.1 34.5 + - - -
522L ARG* 3.9 11.6 - - - +
523L PHE 3.3 14.6 - - - -
524L ASP* 3.6 7.9 - - - -
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Residues in contact with ARG 383 (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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382L GLY* 1.3 73.9 - - - -
384L VAL* 1.3 62.7 + - - +
385L VAL* 3.8 25.1 + - + +
389L GLY 5.2 3.4 + - - -
391L PRO* 3.9 20.5 - - - +
434L ASP* 2.8 38.4 + - - +
435L GLY 3.3 11.7 - - - +
436L TYR* 3.5 38.7 + - + -
437L TYR* 4.7 0.6 - - - -
522L ARG* 3.9 7.9 - - - +
523L PHE 4.0 0.7 + - - +
524L ASP* 3.0 19.1 + - - +
525L ILE 2.8 26.9 + - - +
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Residues in contact with VAL 384 (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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383L ARG* 1.3 74.8 - - - +
385L VAL* 1.3 63.2 + - - +
391L PRO* 3.8 2.3 - - - +
392L VAL* 3.0 29.9 + - + +
395L THR* 4.3 3.6 - - + -
397L VAL* 4.4 8.7 - - + -
431L THR* 3.6 26.5 - - + -
435L GLY* 2.8 14.8 + - - +
437L TYR* 4.2 13.0 - - + -
465L ILE* 4.2 8.1 - - + -
525L ILE* 3.2 20.9 - - + +
527L LEU* 3.7 34.8 - - + -
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Residues in contact with VAL 385 (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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5K LEU* 4.3 10.5 - - + -
383L ARG* 3.8 33.0 - - + +
384L VAL* 1.3 79.8 - - - +
386L ASP* 1.3 70.2 + - - +
389L GLY* 4.1 13.0 - - - +
390L LYS 3.0 18.8 - - - +
391L PRO* 4.3 2.2 - - + -
392L VAL* 3.8 6.3 - - - +
524L ASP* 6.2 2.9 - - + -
525L ILE 3.0 8.1 + - - +
526L VAL* 3.4 24.2 - - + -
527L LEU* 2.8 26.7 + - - +
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Residues in contact with ASP 386 (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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5K LEU* 4.1 1.0 - - - +
385L VAL* 1.3 83.1 - - - +
387L GLN* 1.3 57.6 + - - +
388L TYR* 2.7 33.2 + - - +
389L GLY* 2.8 25.8 + - - -
390L LYS* 3.1 32.9 + - - +
392L VAL* 4.4 11.0 - - + -
526L VAL* 3.8 4.5 - - - +
527L LEU* 3.2 7.9 - - + +
528L ARG 3.6 16.2 - - - +
529L GLY* 3.9 4.3 - - - -
530L GLN* 3.4 27.4 + - + +
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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