Contacts of the strand formed by residues 58 - 64 (chain X) in PDB entry 5K0Y
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 58 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50X GLU* 3.4 43.7 + - + +
52X GLU* 3.8 34.3 + - + +
53X VAL* 4.8 0.2 - - - -
57X ARG* 1.4 76.5 - - - +
59X ALA* 1.4 60.2 + - - +
90X LYS* 3.4 26.4 - - + +
91X HIS* 3.2 21.5 + - - -
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Residues in contact with ALA 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X GLU* 3.5 3.8 - - - +
51X ILE 2.9 41.2 + - - +
52X GLU* 4.3 0.4 - - - +
53X VAL* 4.2 6.5 - - + -
58X LYS* 1.4 75.8 - - - +
60X ILE* 1.4 63.0 + - - +
61X ILE* 3.7 17.5 - - + +
91X HIS 3.3 11.0 - - - +
172X THR* 4.0 13.2 - - + -
176X VAL* 3.8 17.7 - - + -
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Residues in contact with ILE 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PHE* 4.2 6.7 - - + -
23X ILE* 4.0 37.5 - - + -
48X ALA* 4.7 5.2 - - + -
49X LYS 3.6 3.4 - - - +
50X GLU* 3.6 39.3 - - + +
59X ALA* 1.4 70.6 - - - +
61X ILE* 1.3 66.5 + - - +
62X ILE* 4.1 16.6 - - + -
87X PHE* 4.5 1.1 - - + -
90X LYS* 3.9 28.3 - - + -
91X HIS 3.0 7.0 + - - +
92X VAL* 3.5 20.2 - - + -
93X VAL* 3.2 26.7 + - - +
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Residues in contact with ILE 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ALA* 3.6 2.3 - - - -
49X LYS* 2.8 40.8 + - + +
51X ILE* 3.6 35.0 - - + -
59X ALA* 3.7 18.2 - - + +
60X ILE* 1.3 80.1 - - - +
62X ILE* 1.3 68.7 + - - +
63X PHE* 3.8 30.5 - - + -
93X VAL* 4.3 8.1 - - + -
95X ILE* 3.8 33.0 - - + -
176X VAL* 3.9 14.4 - - + -
180X LEU* 5.3 4.5 - - + -
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Residues in contact with ILE 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X ILE* 5.3 5.8 - - + -
27X LEU* 6.2 2.0 - - + -
45X ILE* 3.6 46.7 - - + -
47X ALA 3.9 3.6 - - - -
48X ALA* 5.0 3.1 - - + -
60X ILE* 4.1 13.9 - - + -
61X ILE* 1.3 81.5 - - - +
63X PHE* 1.4 67.3 + - - +
64X VAL* 4.5 1.8 - - + -
72X PHE* 6.1 0.4 - - + -
83X LEU* 5.0 6.1 - - + -
92X VAL* 3.6 26.2 - - + -
93X VAL 3.5 14.2 + - - +
94X PHE* 3.8 29.3 - - + -
95X ILE* 3.0 27.5 + - - +
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Residues in contact with PHE 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X ILE* 3.8 17.2 - - - +
46X THR* 3.7 30.4 + - + +
47X ALA* 3.3 28.3 + - + +
49X LYS* 3.8 40.4 - - + -
61X ILE* 3.8 22.9 - - + -
62X ILE* 1.4 76.8 - - - +
64X VAL* 1.3 66.3 + - - +
95X ILE* 3.5 19.5 - - + -
97X GLN* 4.3 28.7 - - + +
180X LEU* 5.7 7.4 - - + -
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Residues in contact with VAL 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X ILE* 4.5 2.9 - - + -
46X THR* 5.4 1.8 - - - -
62X ILE* 4.5 6.3 - - + -
63X PHE* 1.3 80.3 - - - +
65X PRO* 1.3 67.0 - - + +
66X VAL 3.2 2.1 + - - +
68X GLN* 4.1 6.5 - - + +
69X LEU* 3.8 36.8 - - + +
72X PHE* 3.7 35.2 - - + -
94X PHE* 4.8 5.6 - - + -
95X ILE 3.5 23.9 + - - +
96X ALA* 3.9 17.3 - - + -
97X GLN 3.9 8.1 + - - +
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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