Contacts of the strand formed by residues 396 - 400 (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 LEU 396 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35K ILE* 4.2 14.4 - - + -
94K ARG* 4.8 1.6 - - - +
351L PHE* 3.6 34.6 - - + -
354L LEU* 5.1 4.0 - - + -
356L PHE* 3.7 36.1 - - + -
394L ASN 4.3 0.6 + - - -
395L THR* 1.3 71.1 - - - +
397L VAL* 1.3 64.1 + - - +
398L GLU* 3.4 40.3 - - + +
428L ARG* 4.6 3.8 - - + +
429L CME 3.9 3.6 - - - +
430L LEU* 4.3 2.6 - - + +
464L GLY 3.5 1.6 - - - +
465L ILE* 3.4 5.9 - - - +
466L SER* 2.9 45.7 + - - +
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Residues in contact with VAL 397 (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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384L VAL* 4.4 11.0 - - + -
395L THR* 4.3 2.7 - - + +
396L LEU* 1.3 77.7 - - - +
398L GLU* 1.3 62.3 + - - +
428L ARG* 3.2 4.0 - - - +
429L CME 2.9 37.2 + - - +
431L THR* 3.9 28.0 - - + -
437L TYR* 4.4 12.6 - - + -
439L PHE* 3.7 17.7 - - + -
463L PHE* 3.6 36.3 - - + -
464L GLY 3.4 4.7 - - - +
465L ILE* 4.5 8.7 - - + +
525L ILE* 5.2 0.7 - - + -
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Residues in contact with GLU 398 (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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20K GLY 4.7 5.9 - - - +
21K LEU* 3.3 25.6 - - + +
31K ARG* 5.3 5.9 + - - +
35K ILE* 4.7 1.4 - - - +
94K ARG* 2.6 41.0 + - - -
396L LEU* 3.4 26.1 - - + +
397L VAL* 1.3 80.0 - - - +
399L MET* 1.3 63.4 + - - +
400L TRP* 4.7 3.1 - - + -
427L GLY 3.7 6.5 - - - +
428L ARG* 3.9 18.5 + - + +
463L PHE* 3.3 8.0 - - - +
464L GLY* 2.7 39.9 + - - +
473L LYS* 4.8 4.3 + - - -
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Residues in contact with MET 399 (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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20K GLY* 4.7 0.5 - - - -
363L LEU* 3.7 28.3 - - + -
380L VAL* 5.5 2.0 - - + -
398L GLU* 1.3 75.3 - - - +
400L TRP* 1.3 67.5 + - - +
401L GLN* 4.0 13.2 - - - +
426L VAL* 3.5 4.7 - - - +
427L GLY 3.1 28.7 + - - +
439L PHE* 3.6 53.6 - - + -
441L THR* 4.4 5.6 - - + -
461L ILE* 3.9 29.2 - - + -
462L HIS 3.2 13.0 - - - +
463L PHE* 4.3 11.4 - - + -
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Residues in contact with TRP 400 (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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13K ALA* 3.6 21.4 + - - -
16K TYR* 3.7 15.4 + - - +
17K VAL* 3.8 18.1 - - + +
19K ILE* 3.8 25.4 - - + -
20K GLY* 3.6 27.1 - - - -
21K LEU* 3.6 34.5 - - + -
398L GLU 4.7 1.6 - - - -
399L MET* 1.3 82.2 - - - +
401L GLN* 1.3 64.9 + - - +
408L GLU* 5.1 4.0 - - - -
425L GLY 3.0 14.4 - - - +
426L VAL* 4.5 0.2 - - + -
461L ILE* 3.8 1.0 - - - -
462L HIS* 2.9 70.2 + + + +
463L PHE 4.4 11.2 - - - -
464L GLY* 4.6 2.5 - - - -
475L ILE* 4.3 17.3 - - + -
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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