Contacts of the strand formed by residues 489 - 495 (chain C) 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 LYS 489 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU* 5.5 2.7 - - - +
483C HIS* 3.3 20.8 - - - +
484C SER* 3.0 29.4 + - - +
486C VAL* 5.4 2.9 - - + -
487C ASN* 3.1 19.5 - - + +
488C ASP* 1.3 78.3 - - - +
490C GLY* 1.3 59.5 + - - +
491C LEU* 3.3 30.9 + - + -
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Residues in contact with GLY 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LEU* 6.3 0.4 - - - -
482C LEU 3.8 1.1 - - - -
483C HIS* 3.6 20.4 - - - -
488C ASP 3.7 2.8 + - - -
489C LYS* 1.3 71.5 - - - +
491C LEU* 1.3 63.9 + - - +
492C ARG 3.7 1.3 - - - -
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA 3.7 12.8 - - - +
82C GLU* 4.6 18.2 - - - +
467C TYR* 3.9 22.4 - - + -
482C LEU* 2.8 43.2 + - + +
483C HIS 4.0 0.9 - - - -
484C SER* 3.9 7.4 - - - -
489C LYS* 3.3 41.9 + - + +
490C GLY* 1.3 75.2 - - - +
492C ARG* 1.3 71.6 + - + +
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Residues in contact with ARG 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C TYR* 5.1 8.1 + - - -
79C PHE* 5.9 1.8 - - - +
80C ASN 3.8 3.0 + - - -
81C ALA* 3.1 29.3 + - - +
82C GLU 4.3 4.8 + - - -
83C TYR* 3.8 8.6 + - - +
84C GLY* 3.3 34.5 - - - +
481C THR* 3.5 4.9 - - - -
482C LEU* 2.9 42.7 + - + +
490C GLY 3.7 1.2 - - - -
491C LEU* 1.3 85.9 + - + +
493C VAL* 1.3 78.9 + - - +
494C LEU* 3.8 13.9 + - + +
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C LEU* 4.2 18.4 - - + -
480C TYR 3.9 9.4 - - - +
481C THR* 4.6 10.1 - - + +
492C ARG* 1.3 84.6 - - - +
494C LEU* 1.3 63.8 + - - +
495C GLU* 4.2 6.5 - - - +
496C ASP* 4.1 20.6 - - + +
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR* 3.6 51.9 - - + +
60C LEU* 4.2 6.3 - - + -
68C TYR* 4.0 17.3 - - - +
469C GLN* 3.7 26.5 - - + +
480C TYR* 2.8 18.8 + - + +
481C THR 4.2 8.5 - - - +
482C LEU* 4.1 26.2 - - + -
492C ARG* 4.3 17.7 - - + +
493C VAL* 1.3 77.5 - - - +
495C GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 3.8 51.0 + - - +
57C LEU 4.0 8.9 - - - +
58C TYR* 4.1 14.8 - - + -
70C TYR* 5.4 1.4 + - - -
479C LEU* 3.6 4.8 - - - +
480C TYR* 2.8 47.7 + - + -
493C VAL* 3.7 2.2 - - - +
494C LEU* 1.3 83.6 - - - +
496C ASP* 1.3 63.3 + - - +
497C ASN* 3.0 29.2 + - - +
498C SER 4.6 0.5 + - - -
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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