Contacts of the strand formed by residues 100 - 106 (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 VAL 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ILE* 6.3 0.2 - - + -
30E PHE 4.0 0.2 - - - +
31E GLU* 3.5 0.7 - - - +
32E PHE* 2.8 50.1 + - + +
45E LEU* 4.9 1.1 - - + -
65E ILE* 3.9 24.0 - - + -
66E VAL 4.1 7.4 - - - +
67E ASP* 5.4 3.4 - - - -
96E LEU* 3.9 39.5 - - + -
97E ASP 4.0 11.9 - - - +
98E PRO* 4.4 4.9 - - + -
99E PRO* 1.3 79.2 - - - +
101E THR* 1.3 72.0 + - - +
102E PHE* 4.8 7.7 - - + -
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Residues in contact with THR 101 (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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29E THR* 3.4 34.3 - - + +
30E PHE 3.4 4.3 - - - +
31E GLU* 3.3 22.1 + - + +
65E ILE* 3.5 8.0 - - - +
66E VAL* 2.8 56.2 + - + -
68E GLN* 5.7 3.1 - - - -
99E PRO 5.3 0.5 - - - -
100E VAL* 1.3 81.1 + - - +
102E PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 102 (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 TRP* 4.0 26.9 - + - -
21E CYS* 4.7 3.4 - - - -
23E LEU* 3.7 10.5 - - + +
28E LYS 3.6 0.7 - - - +
29E THR* 3.4 6.4 + - - -
30E PHE* 2.9 37.1 + + - +
32E PHE* 4.6 8.7 - - + -
45E LEU* 4.1 10.3 - - + -
47E LEU* 3.9 27.4 - - + -
63E VAL* 4.5 7.0 - - + -
64E GLU 3.5 2.0 - - - +
65E ILE* 3.0 38.1 - - + -
78E ILE* 5.0 0.4 - - + -
96E LEU* 3.9 20.0 - - + -
100E VAL* 4.8 7.4 - - + -
101E THR* 1.3 74.5 - - - +
103E ARG* 1.3 62.7 + - - +
113E ILE* 3.9 28.0 - - + -
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Residues in contact with ARG 103 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E LEU* 4.2 4.3 - - - -
28E LYS* 3.4 28.9 - - + +
29E THR* 4.3 10.3 + - - +
63E VAL* 3.3 3.3 - - - +
64E GLU* 2.9 58.3 + - + +
66E VAL* 3.8 24.2 - - + -
75E SER* 6.1 0.2 - - - -
101E THR* 5.4 0.7 - - + -
102E PHE* 1.3 76.6 - - - +
104E LEU* 1.3 71.3 + - - +
105E LYS* 3.1 34.9 + - - +
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Residues in contact with LEU 104 (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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23E LEU* 4.0 11.9 - - + +
24E ASN* 3.8 35.4 - - - +
25E GLU* 5.1 0.2 - - - -
28E LYS* 3.0 33.7 + - + +
61E HIS* 4.5 3.4 - - + -
62E ILE 3.4 11.4 - - - +
63E VAL* 5.2 0.4 - - + -
103E ARG* 1.3 79.8 + - - +
105E LYS* 1.3 62.9 + - - +
106E ALA* 3.3 21.8 + - - +
107E GLY 3.2 23.9 - - - +
108E SER 4.2 3.6 - - - -
109E GLY* 4.2 2.0 - - - +
111E LEU* 4.1 31.4 - - + -
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Residues in contact with LYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D TYR* 4.1 21.5 - - - +
62E ILE* 3.0 35.6 + - + +
64E GLU* 3.1 42.9 + - + +
75E SER* 4.3 5.7 + - - -
77E PRO* 4.5 10.5 - - + -
103E ARG* 3.1 29.2 + - - +
104E LEU* 1.3 72.6 - - - +
106E ALA* 1.3 60.0 + - + +
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ASP* 3.4 28.3 - - - +
60E PHE 3.9 10.3 - - - +
61E HIS* 3.2 2.3 - - - -
62E ILE* 3.2 30.3 + - + +
104E LEU* 3.3 11.5 - - - +
105E LYS* 1.3 81.0 - - + +
107E GLY* 1.3 64.9 + - - +
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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