Contacts of the strand formed by residues 426 - 430 (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 VAL 426 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19K ILE* 3.1 36.6 - - + +
20K GLY* 3.9 18.6 - - - +
23K LEU* 4.5 9.4 - - + -
28K ASN* 5.9 2.2 - - - +
31K ARG* 4.0 24.5 + - - +
363L LEU* 3.3 8.8 - - - +
366L ASN* 2.9 25.1 + - - -
399L MET 3.5 9.9 - - - +
424L GLY* 3.7 5.3 - - - +
425L GLY* 1.3 80.5 - - - +
427L GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 427 (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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31K ARG* 4.6 2.2 + - - -
360L ASP 3.1 14.8 - - - -
363L LEU* 3.7 13.7 - - - +
398L GLU* 3.7 2.8 - - - +
399L MET* 3.1 30.5 + - - +
426L VAL* 1.3 77.9 - - - +
428L ARG* 1.3 66.2 + - - +
439L PHE* 3.6 10.3 - - - -
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Residues in contact with ARG 428 (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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31K ARG* 3.1 55.3 - - - +
33K GLN* 2.8 31.1 + - - +
34K GLU* 3.9 4.9 + - - +
35K ILE* 5.1 4.4 - - - +
354L LEU* 3.8 22.9 - - - +
355L GLY 4.4 10.7 + - - -
356L PHE* 3.2 23.5 - - + -
357L GLY 4.9 0.6 - - - +
360L ASP* 3.1 41.6 + - + +
361L HIS* 3.5 17.3 + - - +
396L LEU* 4.6 3.6 - - + +
397L VAL 3.2 14.1 - - - +
398L GLU* 3.9 18.5 + - + -
427L GLY* 1.3 72.3 - - - +
429L CME 1.3 67.0 + - - +
439L PHE* 3.3 5.2 - - - -
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Residues in contact with CME 429 (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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356L PHE* 4.2 10.0 - - - -
361L HIS* 3.9 24.2 - - + +
396L LEU* 3.8 2.8 - - - +
397L VAL* 2.9 29.9 + - - +
428L ARG* 1.3 81.3 - - - +
430L LEU* 1.3 78.5 + - - -
432L ASP* 4.7 10.2 + - - +
436L TYR 3.6 18.2 + - - -
437L TYR* 3.5 27.5 - - - -
438L SER* 3.2 45.5 - - - +
439L PHE* 3.7 17.9 - - + -
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Residues in contact with LEU 430 (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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351L PHE* 4.0 19.3 - - + +
352L SER* 3.8 29.8 - - - +
356L PHE* 3.6 35.4 - - + -
394L ASN* 4.0 30.3 - - + +
395L THR 3.3 16.8 - - - +
396L LEU* 4.3 2.9 - - - -
429L CME 1.3 96.6 + - - +
431L THR* 1.3 68.2 + - - +
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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