Contacts of the strand formed by residues 74 - 79 (chain E) in PDB entry 3VZC
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 ALA 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.3 15.3 - - + -
16E ARG 3.8 3.0 + - - -
17E VAL* 3.6 18.4 - - + -
18E LEU 3.0 22.9 + - - -
72E TRP* 3.5 4.3 - - - +
73E ASP* 1.3 83.1 - - - +
75E LEU* 1.3 72.0 + - - +
76E VAL* 5.0 4.3 - - + -
103E LYS* 4.4 2.5 - - - -
104E PRO* 3.2 21.3 - - + +
105E LEU* 5.3 1.1 - - - -
142E LEU* 5.1 3.1 - - + -
362E VAL* 5.4 2.7 - - + -
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Residues in contact with LEU 75 (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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18E LEU* 3.5 32.8 - - + +
20E LEU* 5.6 3.8 - - + -
64E VAL* 4.5 12.8 - - + -
67E GLU* 5.7 0.2 - - + -
69E LEU* 4.4 21.3 - - + -
72E TRP* 4.2 15.7 - - + -
74E ALA* 1.3 81.0 - - - +
76E VAL* 1.3 62.6 + - - +
77E VAL* 3.9 4.5 + - + +
87E VAL* 4.0 20.6 - - + -
91E LEU* 4.5 9.2 - - + -
103E LYS* 4.0 9.6 - - + -
104E PRO 2.9 7.5 + - - -
105E LEU* 3.4 27.8 - - + +
106E CYS* 3.0 24.4 + - - +
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Residues in contact with VAL 76 (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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17E VAL* 3.0 31.4 - - + -
18E LEU 2.7 11.3 + - - +
19E VAL* 3.2 22.7 - - + -
20E LEU* 2.8 33.2 + - - +
42E LEU* 6.4 0.4 - - + -
74E ALA* 5.0 1.1 - - + -
75E LEU* 1.3 74.6 - - - +
77E VAL* 1.3 60.4 + - - +
78E MET 3.7 0.8 + - - +
106E CYS* 3.6 17.5 - - + +
108E LEU* 3.6 30.5 - - + -
142E LEU* 3.7 22.2 - - + -
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Residues in contact with VAL 77 (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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20E LEU* 3.5 7.0 - - + -
75E LEU* 4.6 7.2 - - + +
76E VAL* 1.3 75.1 - - - +
78E MET* 1.3 58.4 + - - +
79E SER 3.8 1.9 + - - +
80E GLY 4.5 4.9 - - - +
83E LEU* 3.4 38.1 - - + -
84E MET* 3.5 38.8 - - + +
87E VAL* 3.8 28.7 - - + -
105E LEU* 5.6 0.4 - - + -
106E CYS 2.9 11.2 + - - +
107E SER* 3.6 3.0 + - - +
108E LEU 3.0 24.9 + - - +
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Residues in contact with MET 78 (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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19E VAL* 4.6 7.6 - - + -
20E LEU 2.9 13.0 + - - +
21E LEU* 3.6 17.5 - - + +
22E ASN 3.4 18.4 + - - +
30E ALA 3.4 22.9 - - - +
33E LEU* 4.2 2.2 - - + -
34E PHE* 3.6 41.3 - - - +
38E VAL* 3.9 6.5 - - + -
76E VAL 3.7 1.0 + - - -
77E VAL* 1.3 71.3 - - - +
79E SER* 1.3 62.6 + - - +
108E LEU* 3.4 24.7 - - + +
110E ALA* 4.0 15.1 - - + +
135E LEU* 3.8 30.3 - - + -
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Residues in contact with SER 79 (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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22E ASN* 3.7 22.8 + - - +
25E GLY* 5.5 2.3 - - - -
27E LYS* 5.9 0.2 + - - -
77E VAL* 3.7 4.6 + - - +
78E MET* 1.3 77.8 - - - +
80E GLY* 1.3 71.0 + - - -
83E LEU* 3.6 30.8 + - - +
107E SER* 5.4 1.9 + - - -
108E LEU 3.5 6.5 + - - +
109E PRO* 3.9 0.9 - - - +
110E ALA* 3.2 21.5 + - - -
111E GLY* 3.7 18.5 + - - +
114E ASN* 3.4 4.3 - - - +
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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