Contacts of the strand formed by residues 116 - 120 (chain F) in PDB entry 4B3E
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 THR 116 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F HIS 3.8 0.2 - - - +
47F VAL* 3.4 3.2 - - - -
48F HIS* 2.7 36.2 + - - +
50F PHE 2.6 25.4 + - - -
51F GLY* 3.3 11.1 - - - -
52F ASP 3.9 4.3 + - - -
60F ALA* 3.7 16.0 - - + +
115F ARG* 1.3 77.2 + - - +
117F LEU* 1.3 69.5 + - - +
118F VAL* 3.7 9.9 - - + -
146F CYS* 3.7 20.2 - - + -
147F GLY 3.2 13.4 + - - +
148F VAL* 4.3 4.7 - - - +
149F ILE* 4.4 2.0 - - - -
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F CYS* 3.7 17.5 - - - -
8F LEU* 3.3 11.7 - - + +
18F ILE* 3.7 30.3 - - + -
20F PHE* 4.0 11.7 - - + -
45F PHE* 3.6 44.9 - - + -
46F HIS 3.6 16.8 - - - +
47F VAL* 4.1 16.8 - - + -
84F LEU* 4.5 5.4 - - + -
115F ARG 4.1 1.2 + - - -
116F THR* 1.3 72.3 - - - +
118F VAL* 1.3 61.2 + - - +
146F CYS* 3.1 26.3 - - - +
147F GLY 2.9 9.6 + - - -
149F ILE* 4.1 10.3 - - + +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 5.0 0.2 - - - -
44F GLY 3.8 0.3 - - - +
45F PHE* 3.4 9.5 + - - -
46F HIS 2.9 30.3 + - - -
48F HIS* 3.4 34.1 - - + +
60F ALA* 4.6 4.7 - - + -
116F THR* 3.7 17.7 - - + +
117F LEU* 1.3 82.0 - - - +
119F VAL* 1.3 66.0 + - - +
120F HIS* 3.6 24.5 - - + +
143F ARG* 3.9 30.1 - - + -
145F ALA 3.6 6.1 - - - +
146F CYS* 4.0 5.8 - - + -
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Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 4.5 12.9 - - + +
14F VAL* 3.9 28.0 - - + -
35F ILE* 4.3 10.8 - - + -
38F LEU* 4.3 11.7 - - + -
43F HIS* 3.9 18.2 - - + -
44F GLY 3.4 10.1 - - - +
45F PHE* 4.3 9.2 - - + -
87F VAL* 4.1 15.9 - - + -
118F VAL* 1.3 75.5 - - - +
120F HIS* 1.3 63.3 + - - +
143F ARG 3.8 1.2 - - - -
144F LEU* 2.9 24.5 + - + +
145F ALA* 3.1 19.1 + - + +
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Residues in contact with HIS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F HIS* 2.8 35.3 + - - +
44F GLY 2.8 21.0 + - - +
46F HIS* 3.2 37.7 + + - -
48F HIS* 3.6 16.8 + + - -
63F HIS* 5.2 1.8 - - - -
118F VAL* 3.6 12.0 - - + +
119F VAL* 1.3 75.8 - - - +
121F GLU* 1.3 54.4 + - - +
122F LYS 3.4 0.2 - - - -
137F THR* 6.0 3.8 - - + -
140F ALA* 3.3 24.7 + - + +
141F GLY 2.9 26.3 + - - -
142F SER 3.0 9.3 + - - -
143F ARG* 3.8 24.2 - - + -
144F LEU* 3.7 6.8 - - - +
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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