Contacts of the strand formed by residues 59 - 64 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E MET* 3.4 33.2 - - + -
43E CYS* 3.7 10.1 - - - -
49E LEU* 3.8 8.3 - - + -
57E ASN 4.1 0.7 - - - +
58E TYR* 1.3 79.5 - - - +
60E ALA* 1.3 75.3 + - - +
61E TRP* 3.7 20.9 - - + +
76E TRP* 3.2 6.4 + - - +
77E ALA* 2.7 36.1 + - + -
97E PHE* 3.5 47.6 - - + -
114E CYS* 4.5 1.1 - - + -
115E LYS 3.0 12.3 - - - +
116E GLN* 3.9 0.2 - - - +
117E SER* 4.5 1.7 + - - +
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E LEU* 1.3 84.2 - - - +
61E TRP* 1.3 71.0 + - - +
62E TYR* 3.3 27.6 - - + +
72E LEU* 3.8 7.4 - - + -
74E ILE 3.2 13.5 - - - +
75E TYR* 4.4 3.8 - - + -
114E CYS* 3.5 3.1 - - - -
115E LYS* 2.5 38.2 + - + +
105F ALA* 4.8 4.0 - - + -
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Residues in contact with TRP 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLN* 3.7 15.7 - - - -
41E MET* 4.3 12.3 - - + -
42E SER 4.4 1.1 - - - -
43E CYS* 3.4 37.2 - - + -
59E LEU* 3.7 14.6 - - + +
60E ALA* 1.3 82.1 - - - +
62E TYR* 1.3 58.6 + - - +
72E LEU* 3.7 0.5 - - - -
73E LEU* 2.7 38.5 + - + -
74E ILE* 2.8 39.5 + - + +
77E ALA* 4.5 4.1 + - - +
90E GLY* 4.7 6.1 - - - -
91E SER 5.4 0.4 - - - +
97E PHE* 4.1 8.4 - - + +
98E THR 4.2 1.9 - - - +
99E LEU* 3.4 64.3 - - + +
112E TYR* 4.6 1.6 - - + -
113E TYR 2.9 31.2 - - - -
114E CYS* 3.7 6.1 - - + -
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Residues in contact with TYR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ALA* 3.3 26.0 - - + -
61E TRP* 1.3 79.8 - - - +
63E GLN* 1.3 59.0 + - - +
64E GLN 4.2 0.2 + - - -
70E PRO* 3.8 14.8 - - + -
71E LYS 3.2 6.7 - - - +
72E LEU* 3.9 20.2 - - + -
73E LEU* 5.0 1.1 - - - -
111E VAL 3.8 0.7 - - - +
112E TYR* 3.6 4.7 - - - +
113E TYR* 3.0 42.2 + - + +
115E LYS* 2.9 35.9 - - + -
123E PHE* 4.8 8.3 - + + -
45F LEU* 6.2 0.7 - - + -
105F ALA* 3.4 3.5 - - - -
106F MET* 2.6 35.6 + - + +
109F TRP* 3.3 46.0 - + - -
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Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E TYR* 1.3 73.5 - - - +
64E GLN* 1.3 59.4 + - - +
65E LYS* 4.1 21.4 + - + +
69E SER 4.3 0.3 - - - +
70E PRO* 3.4 1.1 - - - +
71E LYS* 3.1 48.7 + - + +
73E LEU* 3.9 23.7 - - + +
88E PHE* 5.1 3.8 - - - -
107E GLU 4.8 3.3 - - - +
108E ASP* 4.2 8.6 + - - +
110E ALA* 3.3 18.4 - - + +
111E VAL 3.6 3.6 - - - +
112E TYR* 2.9 49.7 + - + -
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Residues in contact with GLN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E TYR 4.2 0.2 + - - -
63E GLN* 1.3 72.7 - - - +
65E LYS* 1.3 65.3 + - - +
66E PRO* 4.1 0.5 - - - +
68E GLN 2.7 30.7 + - - +
69E SER* 3.4 17.3 - - - +
70E PRO* 3.9 19.3 - - + +
110E ALA* 3.6 4.0 - - - +
111E VAL* 3.0 43.2 + - - +
113E TYR* 3.7 16.8 + - + -
39F GLN* 3.1 39.2 + - - +
43F LYS* 4.8 5.3 - - - +
45F LEU* 5.8 0.2 - - - +
95F TYR* 3.6 7.1 + - - -
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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