Contacts of the strand formed by residues 108 - 113 (chain E) in PDB entry 3VXR
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 108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLN* 3.5 13.6 + - - +
7E ASN 3.9 10.9 + - - -
8E PRO 2.6 27.5 + - - -
9E ARG 3.7 0.2 - - - -
21E PHE* 3.8 29.9 - - - +
22E ARG 4.9 0.3 + - - -
88E ALA 3.8 0.2 - - - +
89E MET* 4.2 1.1 - - - -
90E TYR* 2.8 44.6 + - - +
107E GLY* 1.3 73.1 + - - -
109E ARG* 1.3 61.6 + - - +
110E LEU 3.6 2.3 + - - -
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Residues in contact with ARG 109 (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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41D GLY* 5.5 4.7 - - - +
9E ARG 3.0 17.9 + - - +
10E HIS* 4.4 12.2 + - + +
11E LYS* 2.9 30.6 + - - +
21E PHE* 5.3 0.4 - - - -
88E ALA 3.8 7.0 - - - +
89E MET* 3.9 31.0 - - + -
107E GLY 4.1 0.2 - - - -
108E SER* 1.3 70.3 - - - +
110E LEU* 1.3 64.9 + - - +
111E THR* 4.0 5.7 + - - -
152E ASP* 3.0 45.1 + - - -
153E HIS* 3.2 44.8 + - + +
154E VAL 5.1 0.4 - - - +
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Residues in contact with LEU 110 (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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11E LYS* 3.4 22.4 - - + +
13E THR* 4.0 23.8 - - + -
19E VAL* 4.1 8.3 - - + -
21E PHE* 3.8 22.7 - - + -
79E ILE* 4.0 19.1 - - + -
82E THR* 4.6 0.4 - - + -
86E ASP* 3.7 22.4 - - + +
87E SER* 3.3 4.2 - - - -
88E ALA 2.9 38.5 + - - +
90E TYR* 3.8 13.2 - - + -
108E SER 3.6 0.8 + - - -
109E ARG* 1.3 74.8 - - - +
111E THR* 1.3 64.9 + - - +
112E VAL* 3.9 18.2 - - + -
153E HIS* 4.5 0.2 - - - -
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Residues in contact with THR 111 (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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11E LYS 3.0 7.7 + - - +
12E ILE* 3.4 11.6 - - + +
13E THR* 2.8 28.8 + - - +
87E SER* 3.7 8.1 - - - +
109E ARG* 4.0 6.1 + - - -
110E LEU* 1.3 74.8 + - - +
112E VAL* 1.3 65.8 + - - +
113E LEU* 3.7 29.3 + - + -
151E PRO* 5.4 4.0 - - + -
152E ASP* 4.8 1.4 + - - +
153E HIS* 2.5 34.2 + - + +
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Residues in contact with VAL 112 (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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13E THR* 3.4 18.2 - - + -
15E ARG* 3.5 34.1 - - + +
82E THR* 3.7 19.1 - - - +
83E GLU 3.4 34.3 - - - +
84E GLN* 3.3 19.1 - - - +
86E ASP* 4.2 1.3 - - + -
87E SER* 2.9 19.3 + - - +
110E LEU* 3.9 19.3 - - + -
111E THR* 1.3 74.8 - - - +
113E LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 113 (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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12E ILE* 3.8 17.3 - - + -
13E THR 2.8 12.5 + - - +
14E LYS* 3.4 2.9 - - - -
15E ARG* 2.7 30.3 + - - +
84E GLN* 4.6 1.3 - - - -
111E THR* 3.7 24.5 - - + -
112E VAL* 1.3 75.5 - - - +
114E GLU* 1.3 61.0 + - - +
115E ASP 3.2 16.7 + - - +
116E LEU* 4.1 4.3 - - + -
119E VAL* 3.8 24.7 - - + -
150E TYR* 3.2 45.3 - - + +
151E PRO* 4.6 6.1 - - + -
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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