Contacts of the strand formed by residues 107 - 112 (chain E) in PDB entry 2VUT
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 HIS 107 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75E HIS 3.7 2.0 + - - -
76E LEU* 3.6 20.8 - - + -
77E ALA 3.3 21.1 + - - -
105E ILE* 3.6 2.9 - - - +
106E GLN* 1.3 80.9 - - + +
108E TYR* 1.3 64.2 + - - +
109E ILE* 4.1 8.0 - - + +
144E PRO 3.4 6.3 - - - -
145E SER* 4.3 5.8 - - - -
146E THR* 2.7 28.0 + - - -
203E ILE* 3.6 29.1 - - + +
204E PHE* 3.6 19.1 + + + -
207E GLY* 3.6 26.3 - - - -
208E PRO* 3.5 27.8 - - + +
211E TRP* 4.3 1.6 - - + -
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Residues in contact with TYR 108 (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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71E PHE* 4.1 6.3 - + - -
77E ALA* 3.9 13.9 - - + -
79E ILE* 3.5 33.0 - - + +
92E GLY 4.6 1.6 + - - -
95E LEU* 3.6 21.3 - - - +
96E ALA* 3.7 11.9 + - - +
99E ALA* 3.4 33.4 - - + -
105E ILE* 3.9 12.3 - - + -
107E HIS* 1.3 72.0 - - - +
109E ILE* 1.3 65.1 + - - +
110E TYR* 3.7 15.6 + + + -
134E VAL* 6.0 0.2 - - - +
138E VAL* 4.0 31.7 - - + +
143E LEU* 4.0 13.2 - - + -
144E PRO 2.6 17.5 + - - +
145E SER* 2.9 33.2 - - - -
146E THR 3.1 2.1 + - - +
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Residues in contact with ILE 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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77E ALA 2.8 14.7 + - - +
78E PHE* 3.2 24.2 - - + -
79E ILE* 2.8 34.0 + - - +
107E HIS* 4.1 13.2 - - - +
108E TYR* 1.3 75.5 - - - +
110E TYR* 1.3 55.0 + - - +
146E THR* 3.3 13.7 - - - +
148E VAL* 4.0 20.0 - - + -
200E LEU* 4.1 11.9 - - + -
203E ILE* 3.5 30.1 - - + -
204E PHE* 3.2 39.9 - - + -
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Residues in contact with TYR 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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79E ILE* 3.4 36.1 - - + -
81E THR* 3.6 22.8 + - + -
88E GLU* 4.8 0.3 + - - -
92E GLY* 5.2 0.7 - - - -
108E TYR* 3.7 16.9 + + + -
109E ILE* 1.3 73.2 - - - +
111E SER* 1.3 77.6 + - - +
112E SER* 3.3 7.9 + - - -
131E LYS* 3.3 34.2 - - - +
134E VAL* 3.2 42.9 - - + +
135E GLU* 4.2 4.7 - - - -
138E VAL* 4.7 1.3 - - + -
146E THR 3.0 6.3 + - - -
147E PHE* 3.3 34.5 - + + -
148E VAL* 3.2 22.5 + - - -
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Residues in contact with SER 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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17E GLN* 2.8 34.9 + - - -
78E PHE* 3.9 7.7 - - - -
79E ILE 2.8 16.0 + - - +
80E ASN* 3.4 18.0 + - - +
81E THR 5.5 0.2 + - - -
109E ILE 4.2 0.4 - - - -
110E TYR* 1.3 86.8 - - - +
112E SER* 1.3 60.4 + - - +
113E MET* 5.9 0.3 - - - +
131E LYS* 3.8 12.0 + - - +
148E VAL* 3.3 17.6 + - - +
150E ALA* 4.9 4.5 + - - +
1354E NAD 5.9 0.9 - - - -
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Residues in contact with SER 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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110E TYR* 3.3 17.3 + - - -
111E SER* 1.3 76.4 + - - +
113E MET* 1.3 93.2 + - - +
131E LYS* 3.7 19.8 + - - -
132E PHE* 3.9 0.7 - - - -
135E GLU* 2.8 28.7 + - - +
147E PHE* 4.4 2.0 - - - -
148E VAL 2.8 17.3 + - - +
149E TYR* 3.6 20.3 + - - -
150E ALA 4.4 0.7 + - - -
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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