Contacts of the helix formed by residues 100 - 110 (chain B) in PDB entry 4R0C
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 GLY 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ALA 3.2 3.4 + - - -
97B GLU 3.9 5.6 + - - -
98B GLN 3.1 6.2 + - - -
99B SER* 1.3 76.6 - - - +
101B LEU* 1.3 63.6 + - - +
102B LEU 3.0 4.6 + - - -
103B SER* 3.1 9.2 + - - -
104B VAL* 3.1 25.4 + - - +
310B TYR* 4.2 6.3 - - - -
316B GLN* 5.6 3.4 - - - -
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Residues in contact with LEU 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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96B ALA* 3.5 7.0 + - + +
99B SER* 3.2 19.4 + - - +
100B GLY* 1.3 75.0 - - - +
102B LEU* 1.3 65.5 + - + +
104B VAL* 4.6 1.3 - - - -
105B SER* 2.8 51.2 + - - +
253B MET* 3.9 22.9 - - + -
256B THR* 4.1 11.0 - - + -
303B ALA* 4.7 4.0 - - - +
306B CYS* 3.9 39.9 - - + +
307B GLY* 4.1 3.6 - - - +
310B TYR* 3.8 19.4 - - + -
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Residues in contact with LEU 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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93B LEU* 4.1 10.3 - - + +
96B ALA* 3.6 32.5 + - + -
97B GLU* 4.0 17.7 - - + +
100B GLY 3.0 1.6 + - - -
101B LEU* 1.3 83.3 - - + +
103B SER* 1.3 61.2 + - - +
105B SER* 4.0 5.5 - - - -
106B LEU* 2.9 36.2 + - + +
131B LEU* 4.6 17.9 - - + +
132B THR* 3.4 35.2 - - + -
135B ALA* 5.2 3.1 - - + -
303B ALA* 5.6 6.7 - - + -
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Residues in contact with SER 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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97B GLU* 5.5 3.7 + - - +
100B GLY* 3.1 9.8 + - - -
102B LEU* 1.3 74.9 - - - +
104B VAL* 1.3 56.7 + - - +
106B LEU* 3.5 4.6 + - - +
107B ALA* 2.8 35.7 + - - +
135B ALA* 3.4 17.6 - - - +
139B VAL* 3.2 31.4 - - - +
140B LEU* 5.3 0.2 - - - +
52C ASP* 3.1 25.6 - - - -
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Residues in contact with VAL 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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100B GLY* 3.1 18.9 + - - +
101B LEU 4.0 2.7 - - - +
103B SER* 1.3 72.7 - - - +
105B SER* 1.3 60.2 + - - +
107B ALA* 2.8 21.7 + - - +
108B SER* 3.0 13.3 + - - -
247B GLN* 4.0 17.9 - - - +
253B MET* 3.4 23.6 - - + -
310B TYR* 3.5 22.9 - - + +
51C THR 3.8 13.9 + - - +
52C ASP* 4.6 5.2 - - + +
53C GLU* 3.9 28.5 - - + +
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Residues in contact with SER 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 LEU* 2.8 42.4 + - - +
102B LEU* 4.0 7.9 - - - -
104B VAL* 1.3 74.8 - - - +
106B LEU* 1.3 63.9 + - - +
108B SER* 3.5 6.5 + - - -
109B LEU* 3.5 17.7 + - - +
253B MET* 3.9 12.1 - - - +
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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 LEU* 2.9 22.8 + - + +
103B SER* 3.8 4.9 - - - +
105B SER* 1.3 78.5 - - - +
107B ALA* 1.3 62.8 + - - +
109B LEU* 3.2 31.4 - - + +
110B VAL* 3.8 4.5 + - - +
125B ALA* 3.6 13.1 - - + +
128B LEU* 4.6 22.4 - - + +
129B SER* 3.9 17.7 - - - -
132B THR* 5.8 5.8 - - + -
135B ALA* 5.6 6.1 - - + -
136B GLY* 5.4 2.0 - - - +
140B LEU* 3.6 46.6 - - + +
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Residues in contact with ALA 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 SER 2.8 16.1 + - - +
104B VAL 2.8 10.6 + - - +
106B LEU* 1.3 74.7 - - - +
108B SER* 1.3 59.8 + - - +
110B VAL* 2.9 33.4 + - - +
111B ARG* 4.0 4.5 - - - +
139B VAL* 5.4 2.0 - - + -
140B LEU* 5.0 0.9 - - - -
143B LEU* 3.7 17.6 - - + +
247B GLN* 5.6 0.2 - - - +
50C LEU 3.9 14.1 - - - +
51C THR* 3.4 23.1 - - - +
52C ASP* 4.8 3.1 - - + -
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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 VAL 3.0 8.2 + - - -
105B SER* 3.9 10.3 - - - -
106B LEU 3.4 0.2 - - - -
107B ALA* 1.3 72.4 - - - +
109B LEU* 1.3 67.6 + - - +
111B ARG* 3.3 28.7 - - - +
247B GLN* 2.3 44.6 + - - +
253B MET* 5.3 1.2 - - - +
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Residues in contact with LEU 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 SER 3.5 8.7 + - - +
106B LEU* 3.2 27.3 + - + +
108B SER* 1.3 80.5 - - - +
110B VAL* 1.3 58.8 + - + +
111B ARG 3.2 9.4 + - - +
121B THR* 3.1 25.2 - - + +
124B PHE* 3.6 38.4 - - + -
125B ALA* 3.6 21.3 - - + -
128B LEU* 4.7 3.6 - - + -
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Residues in contact with VAL 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 4.1 10.8 - - - +
107B ALA 2.9 16.1 + - - +
109B LEU* 1.3 74.7 - - - +
111B ARG* 1.3 75.7 + - - +
118B LEU* 4.0 18.2 - - + -
121B THR* 3.9 13.0 - - + +
122B VAL* 3.7 29.8 - - + +
125B ALA* 4.1 20.6 - - + -
140B LEU* 5.1 4.7 - - + -
143B LEU* 4.1 14.8 - - + +
144B ALA* 5.2 1.6 - - - -
147B VAL* 4.2 23.2 - - + +
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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