Contacts of the helix formed by residues 110 - 114 (chain A) in PDB entry 3QV2
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE 3.7 22.7 - - - +
64A ILE* 3.5 31.4 - - + +
67A ILE* 3.6 31.0 - - + -
75A TRP* 4.1 12.3 - - + -
105A HIS* 3.8 18.4 - - + +
106A LEU* 3.1 21.1 + - + +
108A ARG 3.7 0.2 - - - -
109A ASP* 1.3 80.4 - - + +
111A LEU* 1.3 69.7 + - - +
112A PRO* 3.3 2.0 - - - -
113A TYR* 3.0 16.5 + - - +
114A LEU* 3.3 29.6 + - + +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 4.0 11.6 - - + -
106A LEU 3.0 12.8 + - - +
107A TYR* 3.8 16.8 - - + +
110A ILE* 1.3 75.7 - - - +
112A PRO* 1.3 65.6 - - + +
113A TYR 3.0 5.4 + - - -
114A LEU* 3.4 18.4 + - - +
117A LYS* 3.6 18.9 - - + +
118A PRO* 4.7 3.8 - - + -
121A ILE* 3.8 30.1 - - + -
141A ILE* 4.5 5.4 - - + -
142A LEU* 3.8 14.4 - - + -
145A ASN* 3.6 38.1 - - + +
147A TYR* 4.0 15.0 - - + +
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Residues in contact with PRO 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR 3.1 24.7 - - - +
108A ARG* 3.6 16.8 - - - +
110A ILE 3.3 4.7 - - - +
111A LEU* 1.3 90.9 - - + +
113A TYR* 1.3 74.0 + - + +
114A LEU 5.0 1.8 - - - +
117A LYS* 5.8 0.7 - - - -
141A ILE* 4.2 4.0 - - + -
144A LYS* 5.8 4.5 - - - +
145A ASN* 3.4 33.9 - - - +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.0 22.3 - - + +
68A GLU* 4.5 0.9 - - - +
108A ARG 3.8 18.1 + - - -
109A ASP* 3.4 24.5 - - - -
110A ILE 3.0 6.8 + - - +
112A PRO* 1.3 93.2 - - + +
114A LEU* 1.3 68.7 + - - +
115A ILE* 3.5 6.2 + - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.8 23.3 - - + -
67A ILE* 4.4 8.5 - - + -
68A GLU* 3.5 25.6 - - + +
75A TRP* 4.0 22.2 - - + +
110A ILE* 3.3 17.6 + - + +
111A LEU* 3.4 14.2 + - - +
112A PRO 5.0 1.2 - - - +
113A TYR* 1.3 79.9 + - - +
115A ILE* 1.3 64.1 + - - +
116A ASN 3.9 16.6 - - - +
117A LYS* 4.2 12.9 + - - +
118A PRO* 3.8 28.0 - - + -
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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