Contacts of the strand formed by residues 377 - 386 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364J LEU* 3.7 24.9 - - + +
372J LEU* 4.2 25.3 - - - +
373J PRO 6.0 1.8 - - - +
375J GLY 3.2 12.0 + - - +
376J GLU* 1.3 72.9 - - - +
378J ILE* 1.3 66.2 + - - +
440J ARG* 3.4 24.0 - - - +
441J THR 3.6 6.5 - - - +
442J ILE* 4.2 6.3 - - + -
517J ASP* 3.0 44.0 + - - +
518J CYS* 3.6 12.5 - - + -
519J LEU* 3.3 16.3 + - - +
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Residues in contact with ILE 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376J GLU* 4.1 14.1 - - + +
377J ARG* 1.3 83.5 - - - +
379J ILE* 1.3 66.6 + - - +
380J VAL* 3.7 22.4 - - + -
440J ARG* 3.4 5.1 - - - +
441J THR* 2.7 63.4 + - + +
443J LYS* 4.0 21.3 - - + +
444J PRO* 5.0 0.4 - - + -
461J ILE* 5.0 0.2 - - + -
480J PHE* 3.9 25.8 - - + -
518J CYS* 4.0 2.0 - - - +
519J LEU* 3.2 19.7 - - + +
521J TYR* 4.0 22.4 - - + -
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Residues in contact with ILE 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378J ILE* 1.3 79.9 - - - +
380J VAL* 1.3 72.4 + - - +
381J ALA* 4.3 11.2 - - + -
438J SER* 4.6 8.3 - - - -
439J PHE 3.3 11.0 - - - +
440J ARG* 4.3 13.7 - - + +
512J ASN* 4.1 22.9 - - - +
514J ASN* 4.5 13.7 - - - +
518J CYS* 3.7 25.6 - - - -
519J LEU 2.8 12.6 + - - +
520J ALA* 3.2 10.9 - - + -
521J TYR* 2.8 27.2 + - - +
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Residues in contact with VAL 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378J ILE* 3.7 25.5 + - + -
379J ILE* 1.3 77.2 - - - +
381J ALA* 1.3 62.0 + - - +
399J MET* 5.2 1.3 - - + -
437J TYR* 4.0 10.3 - - + +
438J SER* 3.5 0.9 - - - -
439J PHE* 2.9 40.6 + - + +
441J THR* 4.1 12.8 - - + -
461J ILE* 4.1 11.9 - - + -
463J PHE* 4.1 17.3 - - + -
478J LEU* 3.8 26.9 - - + -
480J PHE* 5.1 0.9 - - + -
521J TYR* 3.4 12.8 - - + +
523J PHE* 4.7 2.2 - - + -
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Residues in contact with ALA 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379J ILE* 4.3 4.5 - - + -
380J VAL* 1.3 76.3 - - - +
382J GLY* 1.4 59.3 + - - +
437J TYR* 3.5 23.4 + - - +
438J SER* 3.9 9.2 - - - -
512J ASN* 4.1 23.6 - - - +
521J TYR 2.9 9.3 + - - +
522J ARG* 3.3 9.2 - - - -
523J PHE 2.8 22.9 + - - -
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Residues in contact with GLY 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381J ALA* 1.4 77.8 - - - +
383J ARG* 1.3 59.9 + - - -
436J TYR* 3.4 12.5 - - - -
437J TYR* 3.2 35.4 + - - +
522J ARG* 3.4 11.4 - - - +
523J PHE 3.3 13.2 - - - -
524J ASP* 3.4 8.1 - - - -
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Residues in contact with ARG 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382J GLY* 1.3 74.6 - - - -
384J VAL* 1.3 65.5 + - - +
385J VAL* 3.9 23.2 + - + +
389J GLY 5.2 3.8 + - - -
391J PRO* 3.7 19.6 - - - +
434J ASP* 3.0 50.2 + - - +
435J GLY 3.3 6.3 - - - +
436J TYR* 3.5 38.0 + - + -
437J TYR* 4.7 0.7 - - - -
522J ARG* 4.2 4.3 - - - +
524J ASP* 2.8 18.9 + - - +
525J ILE 2.9 23.9 + - - +
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Residues in contact with VAL 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J ARG* 1.3 75.3 - - - +
385J VAL* 1.4 63.3 + - - +
391J PRO* 3.7 1.7 - - - +
392J VAL* 2.9 34.9 + - + -
395J THR* 4.3 5.4 - - + -
397J VAL* 4.4 7.4 - - + -
431J THR* 3.5 27.4 - - + -
435J GLY* 2.7 17.4 + - - +
437J TYR* 3.9 17.7 - - + -
465J ILE* 4.4 6.3 - - + -
525J ILE* 3.5 19.5 - - + +
527J LEU* 3.6 34.1 - - + -
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Residues in contact with VAL 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.6 10.5 - - + -
383J ARG* 3.9 33.9 - - + +
384J VAL* 1.4 79.8 - - - +
386J ASP* 1.3 68.5 + - - +
389J GLY* 4.2 14.6 - - - +
390J LYS 3.2 13.9 - - - +
391J PRO* 4.4 4.0 - - + -
392J VAL* 3.8 5.2 - - - -
524J ASP* 6.3 2.0 - - + -
525J ILE 3.2 10.3 + - - +
526J VAL* 3.3 16.8 - - + -
527J LEU* 2.9 24.1 + - - +
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Residues in contact with ASP 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.3 1.0 - - - +
385J VAL* 1.3 79.4 - - - +
387J GLN* 1.3 60.3 + - - +
388J TYR* 2.8 27.3 + - - +
389J GLY* 2.9 22.0 + - - -
390J LYS* 2.9 32.8 + - - +
392J VAL* 3.9 11.2 - - + +
468J PRO* 6.6 0.4 - - + -
526J VAL* 3.8 4.6 - - - +
527J LEU* 3.3 9.2 - - + +
528J ARG 3.5 16.6 - - - +
530J GLN* 2.9 32.8 + - + +
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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