Contacts of the strand formed by residues 59 - 64 (chain B) in PDB entry 2ZUQ
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 LEU 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B MET* 3.6 26.2 - - + -
43B CYS* 3.6 11.0 - - - -
49B LEU* 3.9 5.6 - - + -
57B ASN 2.8 13.5 + - - +
58B TYR* 1.3 76.6 - - - +
60B ALA* 1.3 75.8 - - - +
61B TRP* 3.5 30.7 - - + +
75B TYR 3.7 0.2 - - - -
76B TRP 3.4 26.7 + - - +
77B ALA* 3.5 5.7 + - + -
97B PHE* 3.4 43.7 - - + -
114B CYS* 4.3 0.9 - - + -
115B LYS 3.3 11.0 - - - +
117B SER* 5.7 0.2 - - - -
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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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59B LEU* 1.3 82.6 - - - +
61B TRP* 1.3 58.3 + - - +
62B TYR* 3.5 27.8 - - + +
72B LEU* 4.4 3.8 - - + -
74B ILE 3.3 13.7 - - - +
75B TYR* 4.4 8.3 - - + -
114B CYS* 3.1 4.7 - - - -
115B LYS* 2.6 50.6 + - + +
117B SER* 5.7 0.2 + - - -
105C ALA* 5.5 3.1 - - + -
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Residues in contact with TRP 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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26B GLN* 4.0 11.0 - - - -
41B MET* 4.2 14.1 - - + -
42B SER 4.2 4.3 - - - -
43B CYS* 3.3 38.1 - - + -
59B LEU* 3.5 21.8 - - + +
60B ALA* 1.3 72.3 - - - +
62B TYR* 1.3 62.8 + - - +
72B LEU* 4.3 0.2 - - - +
73B LEU* 2.9 33.0 + - + +
74B ILE* 3.0 37.7 + - + +
77B ALA 4.7 6.0 + - - -
90B GLY* 5.0 0.4 - - - -
91B SER 5.0 0.4 + - - -
97B PHE* 4.2 4.7 - - + +
98B THR 3.9 14.8 + - - -
99B LEU* 3.5 58.8 - - + +
112B TYR* 4.5 5.2 - - + -
113B TYR 3.2 21.8 - - - -
114B CYS* 3.9 10.3 - - + -
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Residues in contact with TYR 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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60B ALA* 3.5 14.8 - - + +
61B TRP* 1.3 76.4 - - - +
63B GLN* 1.3 59.0 + - - +
70B PRO* 4.2 13.5 - - + -
71B LYS 3.3 15.9 - - - +
72B LEU* 3.9 11.4 - - + -
73B LEU* 4.4 2.0 - - - -
111B VAL 3.9 0.3 - - - +
112B TYR* 3.4 1.9 - - - -
113B TYR* 2.6 53.0 + - + +
115B LYS* 3.1 53.9 - - + +
123B PHE* 4.4 9.0 - + + -
105C ALA* 3.4 5.4 - - - -
106C MET* 2.9 48.5 + - + +
109C TRP* 3.6 26.9 - + - -
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Residues in contact with GLN 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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62B TYR* 1.3 73.7 - - - +
64B GLN* 1.3 55.3 + - - +
65B LYS* 3.3 37.6 + - - +
70B PRO* 3.3 1.8 - - - +
71B LYS* 2.5 69.4 + - + +
73B LEU* 3.5 24.4 - - + +
88B PHE* 5.4 5.7 - - - -
108B ASP* 5.5 3.2 - - - +
110B ALA* 3.4 25.1 - - - +
111B VAL 3.6 4.3 - - - -
112B TYR* 3.3 32.3 + - + -
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Residues in contact with GLN 64 (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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63B GLN* 1.3 76.3 - - - +
65B LYS* 1.3 66.3 + - - +
67B GLY 6.1 0.4 - - - -
68B GLN 3.0 28.9 + - - +
69B SER 4.7 0.2 - - - -
70B PRO* 3.4 35.2 - - + +
71B LYS* 5.6 0.2 - - - -
110B ALA* 4.0 2.7 - - - -
111B VAL* 2.8 37.6 + - - +
113B TYR* 3.4 24.6 + - + -
39C GLN* 2.8 38.7 + - - +
95C TYR* 4.1 1.6 + - - -
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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