Contacts of the helix formed by residues 100 - 112 (chain B) in PDB entry 3DF0
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 GLU 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B SER* 4.7 19.1 + - - +
98B GLU 3.2 0.6 - - - +
99B GLU* 1.3 77.2 - - + +
101B ARG* 1.3 55.9 + - - +
103B PHE* 2.8 8.6 + - - +
104B ARG* 2.6 48.4 + - - +
163B PHE* 4.0 14.6 - - + -
164B GLU* 5.0 3.6 - - - +
167B LYS* 2.5 48.5 + - - +
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Residues in contact with ARG 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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97B SER 4.7 9.5 + - - +
98B GLU* 3.4 11.9 + - - +
100B GLU* 1.3 76.9 - - - +
102B GLN* 1.3 62.0 + - + +
104B ARG* 3.8 6.5 + - - +
105B LYS* 3.2 45.4 + - + +
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Residues in contact with GLN 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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98B GLU* 3.3 38.6 + - - +
99B GLU* 3.4 10.4 + - - +
100B GLU 3.2 0.4 - - - -
101B ARG* 1.3 80.4 - - + +
103B PHE* 1.3 58.7 + - - +
105B LYS* 4.4 22.6 - - + +
106B LEU* 4.6 9.7 - - - +
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Residues in contact with PHE 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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99B GLU 2.8 16.4 + - - +
100B GLU* 2.8 11.1 + - - +
102B GLN* 1.3 79.0 - - - +
104B ARG* 1.3 65.2 + - - +
105B LYS 3.1 1.1 - - - -
106B LEU* 3.2 12.8 + - - +
107B PHE* 3.2 12.8 + - + +
163B PHE* 4.3 17.0 - + + -
166B PHE* 4.8 14.8 - + - -
167B LYS* 4.6 21.8 - - + -
170B TRP* 3.8 32.5 - + + -
171B ASN* 5.4 4.0 - - - -
215C ALA 5.6 4.5 - - - -
216C LEU* 4.6 14.4 - - + -
219C ASP* 5.0 5.6 - - - -
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Residues in contact with ARG 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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49A PRO* 6.1 4.0 - - - +
100B GLU* 2.6 28.9 + - - +
101B ARG* 4.3 5.4 - - - +
103B PHE* 1.3 68.0 - - - +
105B LYS* 1.3 53.6 + - - +
106B LEU 2.8 16.1 + - - -
107B PHE* 3.2 12.8 + - + +
108B VAL* 3.2 19.5 + - + +
163B PHE* 3.2 64.6 - - + +
164B GLU* 5.3 4.8 + - - +
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Residues in contact with LYS 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 ARG* 3.2 33.9 + - + +
102B GLN* 4.4 17.9 - - + -
103B PHE 3.1 0.2 - - - -
104B ARG* 1.3 79.5 - - + +
106B LEU* 1.3 82.5 + - + +
108B VAL* 4.4 10.1 - - - +
109B GLN 5.1 0.5 + - - -
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Residues in contact with LEU 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 GLN 4.6 10.1 - - - +
103B PHE 3.2 6.6 + - - +
104B ARG 2.9 0.2 - - - -
105B LYS* 1.3 109.3 - - + +
107B PHE* 1.3 64.3 + - - +
108B VAL 3.0 1.7 + - - +
109B GLN* 3.5 37.5 + - + +
110B LEU* 3.8 15.6 - - - +
212C ALA 5.3 4.1 - - - +
215C ALA* 6.4 3.1 - - + -
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Residues in contact with PHE 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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103B PHE* 3.2 15.2 + - + +
104B ARG* 3.7 8.7 - - + +
106B LEU* 1.3 77.4 - - - +
108B VAL* 1.3 66.9 + - + +
110B LEU* 3.2 23.9 - - + +
111B ALA* 3.2 11.5 + - + +
115B MET* 3.4 46.9 - - + -
117B VAL* 3.5 28.5 - - + -
161B LEU 4.2 0.2 - - - -
162B GLY 3.8 4.0 - - - -
163B PHE* 3.8 50.7 - + + -
166B PHE* 3.6 38.1 - + + -
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Residues in contact with VAL 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 ARG* 3.2 24.7 - - + +
105B LYS* 4.4 9.2 - - - +
107B PHE* 1.3 77.2 - - + +
109B GLN* 1.3 59.1 + - - +
110B LEU 2.8 12.7 + - - -
111B ALA* 3.0 18.1 + - - +
112B GLY 3.6 11.7 - - - +
115B MET* 3.6 32.5 - - + -
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Residues in contact with GLN 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 LYS 5.5 0.2 - - - +
106B LEU* 3.5 35.0 + - + +
107B PHE 3.4 0.8 - - - -
108B VAL* 1.3 77.6 - - - +
110B LEU* 1.3 59.2 + - + +
112B GLY* 4.9 1.6 + - - -
211C HIS* 5.5 3.7 + - - -
212C ALA* 3.7 35.5 + - - +
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Residues in contact with LEU 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 LEU 3.8 12.6 - - - +
107B PHE* 3.2 33.4 - - + +
108B VAL 2.9 0.2 - - - -
109B GLN* 1.3 77.9 - - + +
111B ALA* 1.3 60.9 + - - +
112B GLY 3.0 9.6 + - - +
117B VAL* 5.5 5.6 - - + +
121B GLU* 4.3 16.3 - - - +
125B ILE* 4.2 26.2 - - + +
166B PHE* 5.0 13.2 - - + -
212C ALA* 3.7 27.8 - - + +
213C ILE* 4.0 19.3 - - + -
216C LEU* 4.3 15.0 - - + -
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Residues in contact with ALA 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 PHE* 3.2 28.8 + - + +
108B VAL* 3.0 12.7 + - - +
110B LEU* 1.3 78.1 - - - +
112B GLY* 1.3 56.1 + - - +
114B ASP* 3.4 2.4 - - - +
115B MET* 3.4 29.2 - - - +
116B GLU 2.7 30.5 + - - +
117B VAL* 4.7 5.6 - - - +
121B GLU* 4.3 1.3 - - - -
601B CA 2.7 10.8 - - - -
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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 VAL* 3.6 16.9 + - - +
109B GLN 4.9 1.3 - - - -
110B LEU* 3.0 8.1 + - - +
111B ALA* 1.3 83.6 - - - +
113B ASP* 1.3 63.1 + - - +
115B MET* 4.5 2.0 + - - +
121B GLU* 3.9 13.9 - - - -
601B CA 4.1 1.3 - - - -
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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