Contacts of the helix formed by residues 113 - 118 (chain X) in PDB entry 3FEW
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 ASP 113 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108X PRO* 4.1 11.8 - - + +
109X GLU* 4.6 5.0 + - - +
110X ASN* 3.1 45.0 + - - +
112X ASN* 1.3 78.9 - - - +
114X GLU* 1.3 68.4 + - - +
115X VAL* 4.5 8.0 - - + +
116X ALA* 3.0 8.7 + - + +
117X ARG* 2.9 20.9 + - - +
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Residues in contact with GLU 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X ASP* 1.3 71.7 - - - +
115X VAL* 1.3 60.5 + - + +
117X ARG* 3.3 26.1 + - - +
118X LYS* 3.0 30.6 + - - +
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Residues in contact with VAL 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X VAL 5.2 0.2 - - - +
91X TYR* 3.5 46.7 - - + +
93X VAL* 4.5 22.4 - - + +
106X TYR 5.8 0.7 - - - +
108X PRO* 4.3 18.4 - - + -
113X ASP* 4.8 5.6 - - + -
114X GLU* 1.3 78.1 - - + +
116X ALA* 1.3 62.3 + - - +
118X LYS* 3.7 28.5 - - - +
119X TRP* 3.6 11.8 + - - -
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Residues in contact with ALA 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X TYR* 4.3 6.2 + - + -
108X PRO* 3.9 18.5 - - + +
110X ASN 3.6 16.6 - - - +
111X PRO* 3.5 20.4 - - + +
113X ASP 3.0 9.6 + - - +
115X VAL* 1.3 80.2 - - - +
117X ARG* 1.3 65.3 + - - +
119X TRP* 3.0 19.4 + - - +
120X ASP* 3.9 6.6 + - - +
294X SER 5.8 3.8 - - - +
295X PHE* 5.9 0.3 - - - -
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Residues in contact with ARG 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X PRO 3.9 2.2 - - - +
112X ASN* 3.2 48.8 + - + -
113X ASP 2.9 11.6 + - - +
114X GLU* 3.7 31.3 - - - +
116X ALA* 1.3 73.1 - - - +
118X LYS* 1.3 64.3 + - - +
120X ASP* 2.9 34.1 + - - +
123X ASN* 3.0 25.9 + - - +
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Residues in contact with LYS 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X TYR* 3.2 31.2 + - + +
90X VAL 4.7 1.8 + - - -
92X GLY 4.5 6.1 + - - -
93X VAL 5.4 0.4 - - - +
114X GLU 3.0 16.9 + - - +
115X VAL* 3.7 30.3 - - - +
117X ARG* 1.3 74.5 - - - +
119X TRP* 1.3 97.7 + - + +
123X ASN* 3.8 24.1 - - - +
124X LEU* 4.6 0.7 - - - +
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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