Contacts of the helix formed by residues 99 - 107 (chain A) in PDB entry 4WNO
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 4.0 1.1 + - - +
98A GLY* 1.3 75.2 - - - -
100A LEU* 1.3 63.6 + - - +
101A ALA* 3.8 9.9 - - - +
102A ASP* 2.6 38.8 + - - +
103A TYR* 3.1 18.9 + - - +
141A PRO 4.0 1.1 - - - +
142A GLN* 3.7 27.0 - - - +
144A ILE 3.4 10.5 - - - +
145A LEU* 3.7 13.9 - - + -
146A LEU* 3.8 4.6 - - - +
401A 3RF 4.8 12.4 + - - +
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Residues in contact with LEU 100 (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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99A ASP* 1.3 71.1 - - - +
101A ALA* 1.3 60.8 + - - +
103A TYR* 4.3 7.2 - - + -
104A LEU* 2.9 30.8 + - + +
110A LEU* 4.0 15.3 - - + -
118A PHE* 3.8 35.9 - - + -
122A ILE* 5.1 5.4 - - + -
141A PRO* 3.3 15.9 + - + +
144A ILE* 2.8 39.5 + - + +
146A LEU* 3.7 8.4 - - + +
210A ILE* 3.9 28.3 - - + -
214A CYS* 3.9 13.0 - - - -
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Residues in contact with ALA 101 (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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99A ASP* 3.3 8.0 - - - +
100A LEU* 1.3 77.1 - - - +
102A ASP* 1.3 64.5 + - - +
104A LEU* 3.6 5.1 - - - +
105A HIS* 2.8 35.2 + - + +
141A PRO* 3.3 16.8 + - + +
142A GLN* 3.8 42.0 - - + +
213A GLN* 6.2 0.9 - - - +
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Residues in contact with ASP 102 (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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98A GLY* 6.2 0.2 - - - -
99A ASP* 2.6 38.5 + - - +
101A ALA* 1.3 78.6 - - - +
103A TYR* 1.3 57.7 + - - +
105A HIS* 3.2 5.5 + - - +
106A ALA* 2.8 31.4 + - - +
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Residues in contact with TYR 103 (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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97A GLY 5.6 1.3 - - - +
99A ASP 3.1 16.8 + - - +
100A LEU* 3.9 6.1 - - + +
102A ASP* 1.3 75.1 - - - +
104A LEU* 1.3 67.0 + - - +
106A ALA* 3.2 4.9 + - + -
107A MET* 3.0 61.0 + - + +
110A LEU* 3.7 21.7 - - + +
114A THR* 4.5 6.9 + - + +
118A PHE* 3.8 29.8 - + - -
146A LEU* 3.6 24.5 - - + -
156A PRO* 4.0 12.5 + - + +
159A ILE* 3.7 24.3 - - + +
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Residues in contact with LEU 104 (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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100A LEU 2.9 23.7 + - - +
101A ALA* 3.6 6.7 - - - +
103A TYR* 1.3 75.2 - - - +
105A HIS* 1.3 82.9 + - + +
107A MET 3.7 0.2 + - - -
108A ARG 3.5 1.6 + - - -
109A THR* 2.8 31.5 + - - -
110A LEU* 3.9 28.7 - - + -
141A PRO* 4.0 20.0 - - + -
213A GLN* 3.4 45.8 - - + +
214A CYS* 4.2 17.5 - - - +
217A GLY* 4.0 8.5 - - - -
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Residues in contact with HIS 105 (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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101A ALA* 2.8 28.0 + - + +
102A ASP* 3.2 5.1 + - - +
103A TYR 3.1 0.4 - - - -
104A LEU* 1.3 89.0 - - + +
106A ALA* 1.3 65.9 + - - +
107A MET 3.2 1.8 - - - -
108A ARG* 3.0 22.5 + - - -
109A THR 5.0 0.4 - - - +
213A GLN* 3.7 23.5 + - - -
217A GLY* 3.3 19.4 + - - -
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Residues in contact with ALA 106 (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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102A ASP 2.8 20.3 + - - +
103A TYR* 3.2 7.6 + - + +
105A HIS* 1.3 73.1 - - - +
107A MET* 1.3 75.0 + - + +
108A ARG* 3.2 5.6 + - - +
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Residues in contact with MET 107 (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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103A TYR* 3.0 47.9 + - + +
104A LEU 4.1 0.9 - - - +
105A HIS 3.2 0.4 - - - -
106A ALA* 1.3 91.8 - - + +
108A ARG* 1.3 69.2 + - - +
109A THR 3.2 16.7 - - - +
110A LEU* 3.7 19.1 - - + -
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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