Contacts of the strand formed by residues 112 - 117 (chain D) in PDB entry 1VLH
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 GLU 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D LYS 2.9 10.8 + - - +
83D VAL* 3.3 6.2 - - - +
84D LEU 2.9 23.4 + - - +
105D LYS* 3.7 17.4 + - - +
110D ASP 4.8 2.7 - - - +
111D LEU* 1.3 78.4 - - - +
113D THR* 1.3 64.0 + - - +
114D VAL* 3.9 0.9 - - - -
22E ARG* 2.6 61.1 + - - +
25E SER* 6.0 1.8 - - - -
26E ILE* 3.8 33.7 - - + -
116E LEU* 3.9 19.0 - - + +
117E ILE 5.0 0.2 + - - -
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Residues in contact with THR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.3 29.3 - - + +
86D ARG* 3.9 20.2 - - + -
101D ALA* 4.0 28.3 + - + -
104D ASN* 4.9 0.5 + - - +
105D LYS* 6.0 0.6 - - - +
111D LEU* 4.0 9.7 - - - +
112D GLU* 1.3 75.4 + - - +
114D VAL* 1.3 64.4 + - - +
115D PHE* 3.5 33.2 - - + -
115E PHE 3.7 8.5 - - - +
116E LEU* 4.1 10.9 - - - +
117E ILE* 4.4 4.7 + - - +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 4.5 17.9 - - + -
83D VAL* 4.3 12.1 - - + -
84D LEU 2.8 10.6 + - - +
85D VAL* 3.2 8.2 - - + +
86D ARG 3.0 24.3 + - - +
112D GLU 4.8 0.9 - - - +
113D THR* 1.3 74.6 - - - +
115D PHE* 1.3 65.3 + - - +
116D LEU* 4.7 4.0 - - + -
26E ILE* 3.7 23.1 - - + -
114E VAL* 3.2 35.4 - - + -
115E PHE 3.4 3.1 - - - -
116E LEU* 3.6 25.6 - - + -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ARG* 3.2 24.5 - - + -
87D GLY 4.5 0.2 - - - -
88D LEU* 3.6 37.9 - - + -
97D GLU* 3.4 52.9 - - + -
101D ALA* 4.4 0.7 - - + -
113D THR* 3.5 24.2 - - + -
114D VAL* 1.3 76.5 - - - +
116D LEU* 1.3 61.9 + - - +
88E LEU* 4.8 1.6 - - + -
114E VAL* 3.5 7.8 - - - -
115E PHE* 3.0 46.1 + - + -
117E ILE* 3.2 40.2 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 4.1 21.1 - - + +
22D ARG* 4.0 16.6 - - + +
23D ALA* 3.9 32.1 - - + +
26D ILE* 4.2 6.7 - - + -
27D PHE* 6.2 1.1 - - + -
85D VAL* 4.3 11.9 - - + -
86D ARG 3.0 8.1 + - - +
87D GLY* 3.3 3.7 - - - -
88D LEU* 2.8 27.5 + - - +
114D VAL* 4.1 5.4 + - + -
115D PHE* 1.3 76.5 - - - +
117D ILE* 1.3 64.6 + - - +
112E GLU* 3.7 20.0 - - - +
113E THR 3.8 7.0 - - - +
114E VAL* 3.5 31.9 - - + -
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 4.5 2.0 - - - -
22D ARG* 2.6 36.3 + - - +
88D LEU* 3.7 24.5 - - + +
116D LEU* 1.3 73.2 - - - +
118D ALA* 1.3 74.4 + - - +
123D SER* 5.9 0.7 - - - +
98E LEU* 3.3 38.1 - - + -
101E ALA* 3.7 19.1 - - + -
102E LEU* 4.0 23.6 - - + +
113E THR 4.5 4.7 + - - +
115E PHE* 3.3 34.1 - - + -
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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