Contacts of the helix formed by residues 100 - 112 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ILE* 3.3 3.2 + - - +
99B PRO* 1.3 95.3 - - - +
101B LYS* 1.3 66.6 + - - +
102B GLU* 3.2 7.0 + - - +
103B TYR* 3.1 42.7 + - + +
104B PHE* 3.8 11.1 - - - -
157B ARG* 5.0 0.4 - - - +
188B TYR* 3.7 15.6 + - - -
201B LYS* 3.8 19.1 + - - -
203B TRP* 3.6 30.2 - - + -
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Residues in contact with LYS 101 (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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100B ASN* 1.3 72.4 - - - +
102B GLU* 1.3 90.7 + - - +
104B PHE* 3.1 30.2 + - - +
105B TRP* 3.3 45.8 + - + +
122B ARG* 3.5 46.1 - - - +
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Residues in contact with GLU 102 (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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100B ASN* 3.2 7.2 - - - +
101B LYS* 1.3 111.5 + - - +
103B TYR* 1.3 60.9 + - - +
104B PHE 3.3 0.2 - - - -
105B TRP* 3.4 23.8 + - + +
106B GLY 2.9 22.5 + - - -
186B ALA* 3.6 4.0 - - - +
203B TRP* 3.1 59.5 + - + +
205B TYR* 3.4 28.0 - - - +
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Residues in contact with TYR 103 (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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98B ILE* 3.5 23.1 - - + -
99B PRO* 4.2 11.9 - - + -
100B ASN* 3.1 46.2 + - + +
101B LYS 3.2 0.4 - - - -
102B GLU* 1.3 76.1 - - - +
104B PHE* 1.3 59.5 + - - +
106B GLY* 3.3 1.2 + - - -
107B LEU* 2.8 35.4 + - - +
156B PHE* 3.5 38.6 - + + -
157B ARG* 2.8 19.8 + - - -
178B GLU* 2.8 21.5 + - - -
185B SER* 4.6 0.3 - - - -
186B ALA* 3.2 34.8 - - + -
188B TYR* 3.4 13.9 - - - -
203B TRP* 3.7 10.1 - + - -
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Residues in contact with PHE 104 (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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98B ILE* 3.5 51.8 - - + -
100B ASN 3.8 12.3 - - - -
101B LYS* 3.1 9.2 + - - +
103B TYR* 1.3 75.7 - - - +
105B TRP* 1.3 64.9 + - + +
107B LEU* 3.5 13.9 + - + +
108B SER* 3.1 18.4 + - - -
118B GLY* 3.5 29.3 - - - +
121B LEU* 3.7 30.5 - - + +
122B ARG* 3.7 23.6 - - + -
125B PHE* 3.8 9.6 - + + -
126B GLY* 3.7 33.9 - - - -
357B PHE* 5.2 0.7 - + - -
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Residues in contact with TRP 105 (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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101B LYS* 3.3 51.6 + - + +
102B GLU* 3.5 27.4 - - + +
103B TYR 3.3 0.2 - - - -
104B PHE* 1.3 76.4 - - + +
106B GLY* 1.3 61.0 + - - +
108B SER* 3.3 5.1 + - - -
109B LYS* 3.0 38.4 + - - +
115B TRP* 5.2 19.8 - + + -
118B GLY* 4.7 13.7 - - - -
119B ASN* 4.1 21.0 + - - +
122B ARG* 5.1 4.5 - - - +
205B TYR* 3.5 24.0 - + + -
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Residues in contact with GLY 106 (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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102B GLU 2.9 15.0 + - - -
103B TYR 3.7 2.7 - - - -
105B TRP* 1.3 76.5 - - - +
107B LEU* 1.3 55.0 + - - +
109B LYS* 3.2 8.3 + - - +
110B PHE* 3.0 27.0 + - - +
185B SER* 3.2 32.6 - - - +
205B TYR* 3.9 10.2 - - - -
206B LEU* 5.1 1.4 - - - +
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Residues in contact with LEU 107 (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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98B ILE* 4.6 1.3 - - + -
103B TYR 2.8 22.4 + - - +
104B PHE* 3.7 22.2 - - + +
105B TRP 3.3 0.2 - - - -
106B GLY* 1.3 73.2 - - - +
108B SER* 1.3 57.5 + - - +
110B PHE* 3.0 12.3 + - + +
111B LEU* 2.9 37.7 + - + +
121B LEU* 4.2 11.2 - - + -
154B GLY 3.6 22.2 - - - +
156B PHE* 4.0 24.5 - - + -
159B LEU* 4.8 3.4 - - + -
185B SER* 3.6 6.7 - - - +
357B PHE* 4.1 31.0 - - + -
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Residues in contact with SER 108 (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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104B PHE 3.1 11.8 + - - -
105B TRP* 3.7 4.3 - - - -
107B LEU* 1.3 79.0 - - - +
109B LYS* 1.3 56.2 + - - +
111B LEU* 3.4 4.2 + - - -
112B GLY 2.9 22.5 + - - -
113B THR* 2.9 26.8 + - - -
114B HIS 2.5 29.8 + - - -
117B MET* 3.6 4.4 - - - +
118B GLY* 3.6 20.0 - - - -
121B LEU* 4.0 5.7 - - - +
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Residues in contact with LYS 109 (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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105B TRP* 3.0 21.4 + - - +
106B GLY* 3.2 8.3 + - - +
108B SER* 1.3 76.3 - - - +
110B PHE* 1.3 60.7 + - - +
112B GLY* 3.4 11.0 + - - -
113B THR 4.2 7.9 - - - +
114B HIS 5.9 0.9 - - - +
115B TRP* 3.1 45.9 - - + -
185B SER 5.8 0.2 - - - +
205B TYR* 4.1 45.1 - - + +
206B LEU* 4.7 10.7 - - + +
208B THR* 4.9 8.7 - - - +
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Residues in contact with PHE 110 (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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106B GLY 3.0 12.6 + - - +
107B LEU* 3.4 15.0 - - + +
109B LYS* 1.3 74.1 - - - +
111B LEU* 1.3 80.3 + - + +
112B GLY* 3.3 0.6 - - - -
153B LEU* 3.9 33.4 - - + -
154B GLY* 3.7 28.0 - - - -
185B SER* 3.7 10.8 - - - +
206B LEU* 3.8 26.9 - - + +
473B DFP 4.2 21.3 - - + -
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Residues in contact with LEU 111 (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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107B LEU* 2.9 23.1 + - + +
108B SER* 3.4 7.2 + - - +
110B PHE* 1.3 96.2 - - + +
112B GLY* 1.3 59.5 + - - +
113B THR* 3.4 11.4 - - + +
117B MET* 4.7 10.8 - - + -
121B LEU* 4.3 26.0 - - + -
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Residues in contact with GLY 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 SER 2.9 4.8 + - - -
109B LYS* 3.4 9.8 + - - -
110B PHE 3.3 3.6 - - - -
111B LEU* 1.3 79.5 - - - +
113B THR* 1.3 65.6 + - - +
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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