Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 3F9C
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 ASN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ILE* 3.2 3.4 + - - +
99A PRO* 1.3 100.4 + - - +
101A LYS* 1.3 65.1 + - - +
102A GLU* 4.1 3.2 - - - +
103A TYR* 3.3 29.7 + - + +
104A PHE* 3.8 10.8 - - - -
157A ARG* 4.7 1.2 - - - +
188A TYR* 4.0 16.8 + - - -
201A LYS* 3.7 20.1 + - - +
203A TRP* 3.8 28.7 - - + -
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Residues in contact with LYS 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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100A ASN* 1.3 71.1 - - - +
102A GLU* 1.3 89.4 + - - +
103A TYR 3.2 1.0 + - - -
104A PHE* 3.2 24.8 + - - +
105A TRP* 3.4 51.6 + - + +
122A ARG* 3.5 45.7 - - - +
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Residues in contact with GLU 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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100A ASN* 3.3 3.2 - - - +
101A LYS* 1.3 111.4 + - - +
103A TYR* 1.4 54.7 + - - +
105A TRP* 3.5 22.0 + - + +
106A GLY 2.9 21.8 + - - -
186A ALA* 3.7 3.6 - - - +
201A LYS* 5.5 0.7 - - - +
203A TRP* 3.5 56.3 + - + +
205A TYR* 3.3 31.3 - - - +
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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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98A ILE* 3.6 15.9 - - + -
99A PRO* 4.0 12.1 - - + -
100A ASN* 3.3 45.2 + - + +
101A LYS 3.2 1.6 - - - -
102A GLU* 1.4 73.9 - - - +
104A PHE* 1.3 54.5 - - - +
106A GLY* 3.2 1.4 + - - -
107A LEU* 2.6 41.4 + - - +
156A PHE* 3.5 42.5 - + + -
157A ARG* 2.8 17.0 + - - -
178A GLU* 2.6 23.7 + - - -
185A SER* 4.5 0.5 - - - -
186A ALA* 3.2 31.6 - - + -
188A TYR* 3.6 13.2 - - - -
203A TRP* 3.7 14.6 - + - -
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Residues in contact with PHE 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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98A ILE* 3.4 46.9 - - + -
100A ASN 3.8 9.6 - - - -
101A LYS* 3.2 16.1 + - - +
103A TYR* 1.3 72.8 - - - +
105A TRP* 1.3 61.3 + - + +
107A LEU* 3.8 12.8 - - + +
108A SER* 2.9 31.2 + - - -
118A GLY* 3.5 21.8 - - - +
121A LEU* 3.5 36.0 - - + +
122A ARG* 3.8 23.8 - - + -
125A PHE* 3.8 13.9 - + + -
126A GLY* 3.9 26.0 - - - -
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Residues in contact with TRP 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 LYS* 3.4 54.7 + - + +
102A GLU* 3.7 25.6 - - + +
103A TYR 3.4 0.4 - - - -
104A PHE* 1.3 77.2 - - + +
106A GLY* 1.3 63.4 + - - +
108A SER* 3.6 5.4 + - - -
109A LYS* 3.0 35.6 + - + +
115A TRP* 5.5 4.0 - - - -
118A GLY* 4.6 15.3 - - - -
119A ASN* 4.6 16.0 + - - +
122A ARG* 5.6 3.6 - - - +
205A TYR* 3.6 22.2 - + + -
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Residues in contact with GLY 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 GLU 2.9 16.0 + - - -
103A TYR 3.2 3.8 + - - -
105A TRP* 1.3 77.6 - - - +
107A LEU* 1.3 55.7 + - - +
109A LYS* 3.2 8.0 + - - +
110A PHE* 3.0 23.0 + - - +
185A SER* 3.5 34.2 + - - +
186A ALA* 4.4 0.2 - - - -
205A TYR* 4.1 10.2 - - - -
206A LEU* 5.4 0.7 - - - +
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Residues in contact with LEU 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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98A ILE* 4.2 6.5 - - + -
103A TYR 2.6 24.4 + - - +
104A PHE* 3.8 17.5 - - + +
106A GLY* 1.3 71.5 - - - +
108A SER* 1.3 58.5 + - - +
110A PHE* 3.1 11.4 + - + +
111A LEU* 3.0 34.6 + - + +
121A LEU* 4.2 13.5 - - + -
154A GLY 3.5 23.6 - - - +
156A PHE* 3.9 24.2 - - + -
159A LEU* 4.5 7.9 - - + -
185A SER* 3.6 5.3 - - - +
357A PHE* 3.7 33.2 - - + -
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Residues in contact with SER 108 (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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104A PHE 2.9 18.8 + - - -
105A TRP* 3.8 5.1 + - - -
107A LEU* 1.3 73.2 - - - +
109A LYS* 1.3 65.5 + - - +
111A LEU* 3.2 9.7 + - - +
113A THR* 3.1 40.0 + - - -
114A HIS 2.5 33.5 + - - -
117A MET* 4.3 2.9 - - - -
118A GLY* 3.6 15.7 - - - -
121A LEU* 4.4 5.5 - - - +
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Residues in contact with LYS 109 (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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105A TRP* 3.0 27.6 + - + +
106A GLY* 3.4 7.9 - - - +
108A SER* 1.3 75.2 + - - +
110A PHE* 1.3 60.6 + - - +
112A GLY* 3.4 11.1 + - - -
113A THR 4.5 8.1 - - - +
185A SER 6.0 0.2 - - - +
205A TYR* 4.2 45.3 - - + +
206A LEU* 4.7 12.7 - - + +
208A THR* 5.0 8.7 - - - +
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Residues in contact with PHE 110 (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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106A GLY 3.0 4.8 + - - +
107A LEU* 3.1 13.6 + - + +
109A LYS* 1.3 74.0 - - - +
111A LEU* 1.3 76.6 + - + +
112A GLY* 2.9 9.7 + - - -
153A LEU* 3.6 33.4 - - + -
154A GLY* 3.7 28.3 - - - -
185A SER* 3.5 16.8 - - - +
206A LEU* 3.6 26.2 - - + +
352A GLN* 6.1 0.4 - - - -
473A DFP 4.3 22.7 - - + -
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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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107A LEU* 3.0 22.7 + - + +
108A SER* 3.2 5.3 + - - +
110A PHE* 1.3 91.8 - - + +
112A GLY* 1.3 61.0 + - - +
113A THR* 3.2 15.6 + - + +
117A MET* 4.2 27.1 - - + -
121A LEU* 4.5 13.9 - - + -
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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