Contacts of the strand formed by residues 377 - 386 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364D LEU* 3.7 26.2 - - + +
372D LEU* 4.2 27.5 - - - +
373D PRO* 5.9 2.4 - - - +
375D GLY 3.2 8.7 + - - +
376D GLU* 1.3 71.0 - - - +
378D ILE* 1.3 65.5 + - - +
440D ARG* 3.7 20.6 - - - +
441D THR 3.7 4.7 - - - -
442D ILE* 4.6 6.7 - - + -
517D ASP* 3.1 41.7 + - - +
518D CYS* 3.6 14.3 - - + +
519D LEU* 3.3 17.5 + - - +
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Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D GLU* 3.9 12.6 - - + +
377D ARG* 1.3 83.7 - - - +
379D ILE* 1.3 67.5 + - - +
380D VAL* 3.8 22.7 - - + -
440D ARG* 3.2 6.4 - - - +
441D THR* 2.7 64.9 + - + +
443D LYS* 4.0 25.6 - - + +
461D ILE* 5.0 0.4 - - + -
480D PHE* 3.9 25.1 - - + -
518D CYS* 4.2 1.1 - - - +
519D LEU* 3.3 16.8 - - + +
521D TYR* 4.0 23.8 - - + -
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Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D ILE* 1.3 78.1 - - - +
380D VAL* 1.3 70.5 + - - +
381D ALA* 4.2 13.0 - - + -
438D SER* 4.7 7.6 - - - -
439D PHE 3.4 11.0 - - - +
440D ARG* 4.4 12.3 - - + -
512D ASN* 4.1 27.1 - - - +
514D ASN* 4.6 11.9 - - - +
518D CYS* 3.7 28.0 - - - -
519D LEU 3.0 9.7 + - - +
520D ALA* 3.1 7.9 - - + -
521D TYR* 2.9 27.0 + - - +
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D ILE* 3.8 25.8 - - + -
379D ILE* 1.3 77.0 - - - +
381D ALA* 1.3 59.6 + - - +
399D MET* 5.2 1.1 - - + -
437D TYR* 3.9 11.7 - - + +
438D SER* 3.5 1.0 - - - -
439D PHE* 2.9 39.1 + - + +
441D THR* 3.9 13.9 - - + -
461D ILE* 4.0 12.1 - - + -
463D PHE* 3.9 18.2 - - + -
478D LEU* 3.6 28.3 - - + -
480D PHE* 5.0 1.3 - - + -
521D TYR* 3.4 12.6 - - + +
523D PHE* 4.6 4.0 - - + -
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ILE* 4.1 5.1 - - + -
380D VAL* 1.3 76.6 - - - +
382D GLY* 1.3 60.6 + - - +
436D TYR* 6.3 0.7 - - + -
437D TYR* 3.4 23.0 + - - +
438D SER* 3.8 11.0 - - - -
512D ASN* 3.8 25.4 - - - +
521D TYR 3.0 7.1 + - - +
522D ARG* 3.2 12.0 - - - +
523D PHE 2.8 23.2 + - - -
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Residues in contact with GLY 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ALA* 1.3 78.6 - - - +
383D ARG* 1.3 59.4 + - - -
436D TYR* 3.3 12.7 - - - -
437D TYR* 3.0 33.6 + - - +
522D ARG* 4.1 11.2 - - - +
523D PHE 3.5 8.5 - - - -
524D ASP* 3.3 13.0 - - - -
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Residues in contact with ARG 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D GLY* 1.3 74.3 - - - -
384D VAL* 1.3 62.9 + - - +
385D VAL* 3.9 22.3 + - + +
389D GLY 4.9 4.2 + - - -
391D PRO* 3.6 24.4 - - - +
434D ASP* 2.9 38.9 + - - +
435D GLY* 3.2 11.4 - - - +
436D TYR* 3.5 37.7 + - + -
437D TYR* 4.0 1.5 - - - -
522D ARG* 3.9 5.4 - - - +
523D PHE 4.0 0.4 + - - -
524D ASP* 2.8 18.1 + - - +
525D ILE 2.9 24.8 + - - +
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ARG* 1.3 73.5 - - - +
385D VAL* 1.3 64.7 + - - +
391D PRO* 3.8 1.2 - - - +
392D VAL* 2.9 33.3 + - + +
395D THR* 4.3 3.8 - - + -
397D VAL* 4.5 7.2 - - + -
431D THR* 3.5 27.8 - - + -
435D GLY* 2.9 12.7 + - - +
437D TYR* 4.1 15.3 - - + -
465D ILE* 4.2 10.1 - - + -
525D ILE* 3.4 19.1 - - + +
527D LEU* 3.5 35.4 - - + -
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.5 9.4 - - + -
383D ARG* 4.1 31.4 - - + +
384D VAL* 1.3 80.1 - - - +
386D ASP* 1.3 68.1 + - - +
389D GLY* 4.0 14.8 - - - +
390D LYS 3.1 14.4 - - - +
391D PRO* 4.1 5.6 - - + -
392D VAL* 3.7 6.5 - - - -
524D ASP* 6.1 2.2 - - + -
525D ILE 3.0 10.7 + - - +
526D VAL* 3.2 20.6 - - + -
527D LEU* 2.8 25.5 + - - +
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Residues in contact with ASP 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.1 1.7 - - - +
385D VAL* 1.3 76.6 - - - +
387D GLN* 1.3 60.7 + - - +
388D TYR* 2.8 23.1 + - - +
389D GLY* 2.9 18.0 + - - -
390D LYS* 2.9 43.6 + - - +
392D VAL* 4.5 9.6 - - + -
526D VAL* 3.7 8.3 - - - +
527D LEU* 3.1 9.6 - - + +
528D ARG 3.5 16.8 - - - +
529D GLY* 3.7 2.5 - - - -
530D GLN* 3.1 29.4 + - + +
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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