Contacts of the strand formed by residues 430 - 435 (chain D) in PDB entry 5Y7K
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 ASN 430 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ILE* 3.3 10.9 - - - +
419D SER 3.1 29.5 + - - +
422D TYR* 3.7 30.5 - - + +
428D GLY* 5.1 2.0 - - - -
429D ARG* 1.3 84.1 + - - +
431D LEU* 1.3 60.2 + - - +
432D TYR* 3.5 21.9 - - + +
444D CYS* 3.9 5.6 - - - -
446D SER* 2.6 25.7 + - - +
447D CYS* 3.1 22.7 + - - +
454D CYS 5.3 0.7 - - - +
455D GLN* 4.5 9.9 + - - +
457D TYR* 3.6 8.7 - - - -
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Residues in contact with LEU 431 (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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408D GLU* 4.6 0.4 - - + -
416D TYR* 4.0 17.5 - - + -
417D TYR 3.3 18.4 - - - +
418D ILE* 3.6 18.3 - - + +
430D ASN* 1.3 71.4 - - - +
432D TYR* 1.3 64.8 + - - +
444D CYS* 3.6 6.2 - - - -
445D LEU* 2.7 49.6 + - + -
446D SER* 2.9 13.7 + - - +
457D TYR* 4.7 1.7 - - + +
459D VAL* 3.9 20.6 - - + -
461D PHE* 4.1 8.3 - - + -
468D TYR* 4.0 14.4 - - + -
470D LEU* 3.6 31.6 - - + -
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Residues in contact with TYR 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D LEU 3.9 0.2 - - - +
416D TYR* 3.3 6.4 - - - +
417D TYR* 2.8 62.2 + + + -
419D SER* 3.1 29.8 - - - -
421D GLU* 3.7 20.3 - - + +
422D TYR* 3.2 36.6 + - - +
430D ASN* 3.5 26.9 - - + -
431D LEU* 1.3 80.0 - - - +
433D LYS* 1.3 60.8 + - - +
434D ILE 4.2 0.4 - - - -
442D VAL* 4.0 10.8 - - + -
443D THR 3.2 6.7 - - - -
444D CYS* 3.4 32.1 - - + -
445D LEU* 4.7 0.9 - - - -
447D CYS* 3.6 3.2 - - - -
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Residues in contact with LYS 433 (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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414D TYR* 3.4 56.6 + - + -
415D LEU 3.7 2.7 - - - -
416D TYR* 3.5 28.9 - - + +
432D TYR* 1.3 74.4 - - - +
434D ILE* 1.3 59.2 + - - +
441D LYS 3.8 1.6 - - - +
442D VAL* 3.4 3.1 - - - -
443D THR* 2.5 55.8 + - - +
445D LEU* 3.8 16.6 - - + -
485D SER 5.0 4.8 + - - -
486D VAL 5.2 4.6 + - - -
487D ASN* 5.7 0.6 - - - +
488D ASP* 2.7 28.2 + - - +
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Residues in contact with ILE 434 (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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397D ILE* 3.2 55.9 - - + +
398D THR* 3.9 9.4 - - + -
414D TYR* 3.4 7.3 - - - -
415D LEU* 3.1 53.0 + - + +
417D TYR* 4.2 12.8 - - + -
432D TYR 4.2 0.4 - - - -
433D LYS* 1.3 73.5 - - - +
435D GLN* 1.3 72.8 + - - +
436D LEU* 3.6 2.4 + - + +
439D TYR* 3.9 15.3 - - + +
441D LYS 3.6 2.2 - - - -
442D VAL* 3.9 16.6 - - + +
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Residues in contact with GLN 435 (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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413D ASP 4.5 2.9 - - - +
414D TYR* 3.7 29.7 + - + -
434D ILE* 1.3 71.2 - - - +
436D LEU* 1.3 63.8 + - - +
437D SER* 2.7 29.0 + - - +
438D ASP* 3.0 38.7 - - - +
439D TYR* 3.4 9.7 + - - -
441D LYS* 3.0 39.8 + - - +
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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