Contacts of the strand formed by residues 58 - 63 (chain B) in PDB entry 6XOX
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 ILE 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LEU 5.2 0.4 - - - +
54B HIS* 3.5 33.9 - - + -
57B LYS* 1.3 72.1 - - - +
59B TYR* 1.3 55.9 + - - +
60B ALA 3.5 20.6 - - - +
72B SER* 4.2 10.5 - - - -
73B ALA 3.9 6.5 - - - +
74B SER* 4.1 0.7 - - - +
316B SER* 2.3 29.6 + - - -
317B CYS* 4.3 10.3 - - - -
330B GLY* 4.5 0.9 - - - -
331B SER 3.1 18.6 + - - +
332B TRP* 3.6 3.0 - - - -
334B SER* 3.6 27.3 - - - +
335B PHE 3.7 19.1 - - - +
336B LEU* 3.7 16.8 - - + +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LYS 4.2 3.5 + - - -
236A GLN* 4.1 16.5 + - - +
237A CYS* 3.5 26.9 - - - -
57B LYS* 3.6 8.8 + - + -
58B ILE* 1.3 75.3 - - - +
60B ALA* 1.3 61.6 + - - +
73B ALA* 3.0 9.4 + - + +
75B GLN* 3.2 21.8 - - + +
100B VAL 3.8 15.5 - - - +
101B MET* 3.4 46.5 - - + +
188B MET* 5.5 5.0 - - + +
314B ARG* 5.7 0.2 + - - -
316B SER* 3.8 21.6 + - - +
332B TRP* 3.7 35.1 - + - -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 3.5 9.4 - - - +
59B TYR* 1.3 79.6 - - - +
61B MET* 1.3 66.2 + - - +
72B SER* 3.7 0.3 - - - -
73B ALA* 3.2 24.6 + - + -
101B MET 3.9 3.1 - - - +
102B THR* 3.7 33.0 - - - +
103B CYS* 3.8 11.9 - - - +
317B CYS* 3.6 13.0 - - + -
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA* 1.3 81.3 - - - +
62B HIS* 1.3 66.9 + - - +
63B TRP* 4.2 8.5 - - + +
70B LEU* 3.3 24.7 - - + -
71B VAL 3.3 7.9 - - - +
72B SER* 4.6 0.4 - - - -
103B CYS* 3.6 6.2 - - - +
150B ARG* 4.4 11.1 + - - -
317B CYS* 3.6 15.7 - - + +
318B LEU* 3.9 7.3 + - - +
319B GLY* 3.4 35.9 - - - +
328B ALA* 3.4 34.8 - - + +
329B THR 4.6 3.1 - - - -
336B LEU* 3.7 23.1 - - + -
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 1.3 80.8 - - - +
63B TRP* 1.3 80.0 + - + +
65B THR* 6.5 1.1 - - + -
70B LEU* 4.6 1.1 - - - -
71B VAL* 3.0 33.7 + - - +
103B CYS* 3.7 6.0 - - - +
104B ALA* 3.5 15.3 - - + +
105B TYR* 3.0 44.5 + - - +
150B ARG* 3.8 35.9 + - - +
151B PHE 5.7 1.6 - - - -
319B GLY* 6.3 0.7 - - - -
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Residues in contact with TRP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 4.2 5.2 - - + -
62B HIS* 1.3 95.1 + - + +
64B GLY* 1.3 69.1 + - - +
65B THR* 5.4 1.6 - - - +
67B SER* 3.8 14.6 - - - -
68B ARG 3.8 4.7 - - - -
69B LEU 3.4 18.4 - - - -
70B LEU* 3.8 14.1 - - + +
84B SER* 3.3 36.6 - - - -
105B TYR* 3.6 12.1 - - - +
319B GLY* 2.7 42.0 + - - -
320B VAL 3.9 9.0 - - - +
321B THR* 3.5 35.5 - - + +
322B ASP* 5.6 1.1 - - - +
326B ALA* 4.6 4.7 - - + -
328B ALA* 3.4 30.9 - - + +
338B ILE* 4.3 7.9 - - + -
61G PHE* 4.4 7.9 - + - -
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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