Contacts of the strand formed by residues 75 - 81 (chain E) in PDB entry 2VTX
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 SER 75 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64E GLU* 3.3 31.7 + - - +
65E ILE 3.3 8.3 - - - -
66E VAL* 3.9 15.3 - - - -
74E LYS* 1.3 77.8 - - - +
76E VAL* 1.3 61.6 + - - +
77E PRO* 3.5 10.0 - - - +
105E LYS* 4.3 6.1 + - - -
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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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18D ILE* 4.2 29.6 - - + -
19D TRP* 3.5 24.5 - - - +
20D GLY* 3.8 23.8 - - - +
113D ILE 4.5 1.1 - - - +
114D SER* 3.7 22.4 - - - -
64E GLU* 2.9 2.8 - - - -
65E ILE 2.8 37.6 + - - +
74E LYS* 4.7 12.3 - - + +
75E SER* 1.3 77.5 - - - +
77E PRO* 1.3 67.3 - - + +
78E ILE* 3.5 4.3 + - + +
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Residues in contact with PRO 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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21D CYS 5.8 0.9 - - - +
49D THR* 4.4 0.5 + - - -
51D CYS* 4.1 8.3 - - - -
112D TYR* 3.7 56.5 - - + +
113D ILE 4.9 0.8 - - - +
114D SER* 3.8 8.3 + - - -
62E ILE* 4.0 15.7 - - + -
63E VAL 3.4 7.4 - - - +
64E GLU* 3.5 15.9 - - + +
75E SER 3.5 10.5 - - - +
76E VAL* 1.3 93.6 - - + +
78E ILE* 1.4 60.5 - - - +
79E ALA 3.8 0.2 - - - -
105E LYS* 4.5 8.3 - - + -
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Residues in contact with ILE 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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18D ILE* 5.0 4.3 - - + -
49D THR* 3.0 34.4 + - - +
51D CYS* 4.1 4.3 - - - -
88D MET* 3.8 5.0 - - - +
114D SER* 4.4 13.9 - - - +
47E LEU* 3.7 30.3 - - + -
50E VAL* 5.4 2.9 - - + -
63E VAL* 2.7 35.2 + - + +
64E GLU* 4.7 1.1 - - - -
65E ILE* 4.1 26.5 - - + -
76E VAL* 3.6 12.6 - - + +
77E PRO* 1.4 78.5 - - - +
79E ALA* 1.3 63.1 + - + +
91E MET* 4.4 13.3 - - - +
94E ILE* 4.4 15.0 - - + -
102E PHE* 4.9 0.7 - - + -
113E ILE* 6.3 0.4 - - + -
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Residues in contact with ALA 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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51D CYS* 3.9 3.8 - - - -
88D MET* 3.8 15.5 - - + -
50E VAL* 4.5 19.5 - - + -
61E HIS 3.8 0.3 - - - +
62E ILE* 3.2 6.9 - - - +
63E VAL* 3.0 46.5 + - + +
77E PRO 3.8 0.2 - - - -
78E ILE* 1.3 85.2 - - + +
80E THR* 1.3 62.7 + - - +
81E LEU* 4.8 4.3 - - + -
89E ALA* 5.5 0.2 - - + -
91E MET* 4.7 3.8 - - + -
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Residues in contact with THR 80 (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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51D CYS* 3.4 15.5 - - - +
52D LEU* 2.8 29.1 + - + +
53D GLY 5.5 0.7 - - - -
87D PRO* 3.8 28.2 - - + +
88D MET* 3.2 25.8 - - - +
60E PHE* 3.9 26.7 - - + -
61E HIS 3.2 9.9 - - - +
62E ILE* 3.9 13.3 - - + +
79E ALA* 1.3 74.1 + - - +
81E LEU* 1.3 69.0 + - - +
86E LEU* 4.2 0.2 - - - +
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Residues in contact with LEU 81 (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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87D PRO* 4.9 2.9 - - - -
88D MET* 4.1 1.6 - - - -
50E VAL* 3.3 41.5 - - + +
51E CYS* 4.3 0.2 - - - -
52E LEU* 3.9 30.1 - - + -
59E GLU 3.6 0.2 - - - +
60E PHE* 3.5 4.7 - - - -
61E HIS* 2.8 33.5 + - - +
79E ALA* 4.8 2.5 - - + -
80E THR* 1.3 85.0 - - - +
82E LYS* 1.3 65.7 + - - +
86E LEU* 3.3 23.8 - - + +
88E MET* 3.5 29.2 - - - +
89E ALA* 3.9 9.0 - - + +
111E LEU* 4.5 3.4 - - + -
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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