Contacts of the helix formed by residues 111 - 120 (chain B) in PDB entry 4YCV
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A LYS* 6.3 0.9 - - - -
108B ARG* 3.2 33.0 - - - +
110B ILE* 1.3 76.8 - - - +
112B ILE* 1.3 60.1 + - - +
113B PRO* 4.0 6.2 - - - +
114B GLU* 2.9 36.5 + - - +
115B PHE* 2.8 25.0 + - - -
135B ILE* 4.8 0.2 - - - -
157B ASP* 4.0 8.9 + - - -
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Residues in contact with ILE 112 (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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108B ARG* 4.7 1.8 - - - +
110B ILE 4.2 0.6 + - - -
111B SER* 1.3 72.5 - - - +
113B PRO* 1.3 68.0 - - + +
115B PHE* 3.1 8.0 + - - +
116B ILE* 2.8 38.7 + - + +
135B ILE* 3.6 20.4 - - + -
136B THR 3.9 16.8 - - - +
154B LEU* 3.8 20.9 - - + +
155B VAL 3.5 9.2 - - - +
156B GLY* 3.4 31.6 - - - +
157B ASP* 4.6 1.6 + - - +
159B GLU* 4.0 17.7 - - + +
160B LYS 4.4 0.2 - - - +
161B ILE* 3.9 22.4 - - + -
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Residues in contact with PRO 113 (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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111B SER* 3.9 7.9 - - - +
112B ILE* 1.3 94.5 - - + +
114B GLU* 1.3 57.5 + - + +
116B ILE* 3.3 3.4 - - + +
117B GLU* 3.0 29.3 + - - +
156B GLY 4.0 1.8 - - - +
157B ASP* 3.6 40.4 - - + +
159B GLU* 3.2 28.8 - - - +
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Residues in contact with GLU 114 (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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109B THR 5.3 0.9 - - - +
110B ILE* 3.7 20.3 - - + +
111B SER* 2.9 31.0 + - - +
113B PRO* 1.3 74.2 - - + +
115B PHE* 1.3 60.4 + - - +
117B GLU* 3.4 6.6 + - - +
118B LYS* 2.9 31.7 + - - +
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Residues in contact with PHE 115 (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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110B ILE* 3.4 25.2 - - + +
111B SER 2.8 11.5 + - - +
112B ILE* 3.1 13.9 - - - +
114B GLU* 1.3 73.3 - - - +
116B ILE* 1.3 70.7 + - - +
119B TYR* 3.0 30.3 + + - +
133B LEU* 4.1 20.4 - - + -
135B ILE* 3.8 20.6 - - + -
161B ILE* 3.7 19.1 - - + -
196B PRO* 3.9 22.7 - - + -
204B LEU* 3.5 33.2 - - + -
205B SER 4.1 5.4 - - - -
206B ILE* 4.0 31.0 - - + -
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Residues in contact with ILE 116 (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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112B ILE* 2.8 31.5 + - + +
113B PRO 3.3 7.4 - - - +
115B PHE* 1.3 77.8 - - - +
117B GLU* 1.3 63.9 + - - +
119B TYR 3.7 0.5 - - - -
120B LYS* 2.9 37.1 + - + +
159B GLU* 3.6 25.4 - - + +
160B LYS 3.6 25.6 - - - +
161B ILE* 3.6 15.0 - - + -
204B LEU* 3.9 14.8 - - + +
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Residues in contact with GLU 117 (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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113B PRO 3.0 13.5 + - - +
114B GLU* 3.4 7.2 + - - +
116B ILE* 1.3 80.3 - - + +
118B LYS* 1.3 63.6 + - - +
120B LYS* 3.8 25.5 + - + +
121B ASP* 5.2 2.3 - - - +
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Residues in contact with LYS 118 (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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110B ILE* 4.9 4.5 - - + -
114B GLU 2.9 18.1 + - - +
117B GLU* 1.3 78.4 - - - +
119B TYR* 1.3 89.6 + - + +
121B ASP* 5.4 1.0 + - - +
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Residues in contact with TYR 119 (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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110B ILE* 4.5 9.1 - - + +
115B PHE* 3.0 27.8 + + + +
116B ILE 3.7 0.7 - - - -
118B LYS* 1.3 94.4 - - + +
120B LYS* 1.3 64.6 + - - +
121B ASP 3.2 3.7 + - - -
122B LEU* 3.2 29.0 - - + +
128B LEU* 3.7 29.6 - - + -
131B THR* 3.9 15.4 - - + +
133B LEU* 3.9 28.0 - - + +
196B PRO* 3.6 27.4 - - + -
204B LEU* 3.8 24.0 - - + +
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Residues in contact with LYS 120 (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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116B ILE* 2.9 32.3 + - + +
117B GLU* 3.8 25.6 + - + +
118B LYS 3.7 2.0 + - - -
119B TYR* 1.3 72.8 - - - +
121B ASP* 1.3 72.3 + - - +
198B LYS* 2.6 40.0 + - - +
204B LEU* 4.8 7.4 - - - -
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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