Contacts of the helix formed by residues 139 - 142 (chain B) in PDB entry 1VHQ
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 ILE 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLY 3.6 27.1 - - - +
98B PHE* 5.0 2.5 - - + -
100B ALA* 4.1 9.0 - - + -
101B ALA* 4.3 15.4 - - + +
107B PHE* 4.0 27.1 - - + -
138B CSO 1.3 83.8 - - - +
140B ALA* 1.3 65.5 + - - +
141B PRO* 3.3 2.2 - - - -
142B ALA* 3.1 20.3 + - + +
143B MSE 5.6 0.7 - - - +
156B ILE* 4.6 3.4 - - + -
162B THR* 3.6 30.5 - - + +
196B MSE 4.4 17.9 - - + -
231B ACT 6.1 0.9 - - + -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 3.8 28.5 - - + +
95B PRO 4.2 2.0 - - - +
96B GLY* 4.9 0.2 - - - -
100B ALA* 4.2 9.6 - - + +
136B PHE* 3.5 23.1 - - + -
137B MSE 3.0 16.1 + - - +
139B ILE* 1.3 80.1 - - - +
141B PRO* 1.3 65.3 - - + +
142B ALA 3.0 1.6 + - - -
143B MSE 3.1 28.9 + - + +
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.7 12.6 - - + +
137B MSE 3.5 8.3 - - - +
138B CSO 3.2 16.6 - - - +
139B ILE 3.3 1.6 - - - -
140B ALA* 1.3 91.2 - - + +
142B ALA* 1.3 54.7 + - - +
143B MSE 3.1 0.2 - - - -
144B LEU* 2.9 39.7 + - + +
145B PRO* 3.6 3.8 - - - +
154B LEU* 3.8 10.9 - - + +
155B THR 3.6 21.1 - - - +
156B ILE* 4.2 6.1 - - + -
166B LEU* 4.3 2.0 - - + -
191B THR* 3.5 29.4 - - + -
192B THR 5.1 0.4 - - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 3.8 43.7 - - + -
114B CYS* 4.9 0.3 - - - -
139B ILE* 3.1 20.0 + - + +
140B ALA 3.0 0.8 + - - -
141B PRO* 1.3 77.4 - - - +
143B MSE 1.3 61.1 + - + +
145B PRO* 3.5 9.3 - - - +
156B ILE* 4.7 1.8 - - + +
166B LEU* 3.6 21.5 - - + +
169B MSE 3.6 19.4 - - - +
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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