Contacts of the helix formed by residues 100 - 110 (chain B) in PDB entry 3EWS
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 LYS 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 ARG 4.5 4.2 + - - -
99B LEU* 1.3 86.7 - - - +
101B PRO* 1.3 78.5 - - + -
102B GLN* 3.2 5.8 - - + +
103B LEU* 2.9 25.2 + - + +
104B LEU 3.2 6.8 + - - -
127B LEU* 5.0 3.4 - - - +
154B SER* 3.5 52.2 + - - +
189B TYR* 3.2 26.5 - - - +
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Residues in contact with PRO 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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99B LEU 3.4 4.4 - - - +
100B LYS* 1.3 83.5 - - + +
102B GLN* 1.3 80.5 + - - +
104B LEU* 3.5 6.6 + - + +
105B GLN* 3.1 25.1 + - - +
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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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100B LYS* 4.7 3.7 - - + +
101B PRO* 1.3 99.8 - - + +
103B LEU* 1.3 63.3 + - - +
105B GLN* 3.3 11.4 + - - +
106B GLY* 3.2 17.7 + - - -
185B MET 4.9 1.4 - - - +
188B PHE* 3.2 40.7 + - + +
189B TYR* 3.9 30.8 - - + +
190B PRO* 4.5 11.9 - - - +
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Residues in contact with LEU 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 LEU* 3.9 12.6 - - + -
100B LYS* 2.9 28.7 + - + +
102B GLN* 1.3 80.1 - - - +
104B LEU* 1.3 63.5 + - - +
106B GLY* 3.2 3.6 + - - -
107B VAL* 3.1 18.2 + - - +
150B LEU* 3.5 36.1 - - + +
153B LEU* 4.0 28.3 - - + -
154B SER* 3.1 34.5 - - - +
185B MET* 4.2 9.8 - - + +
189B TYR* 4.1 11.1 - - + -
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Residues in contact with LEU 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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94B PHE* 3.9 37.2 - - + +
95B GLU* 3.9 33.0 - - + +
99B LEU* 4.3 29.4 - - + +
100B LYS 3.2 7.9 + - - +
101B PRO* 3.9 9.0 - - + +
103B LEU* 1.3 79.0 - - - +
105B GLN* 1.3 63.1 + - - +
107B VAL* 3.1 9.7 + - + +
108B TYR* 2.9 38.1 + - + +
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Residues in contact with GLN 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 PRO 3.1 15.5 + - - +
102B GLN* 3.5 12.6 - - - +
103B LEU 3.2 0.2 - - - -
104B LEU* 1.3 78.2 - - - +
106B GLY* 1.3 55.9 + - - +
108B TYR* 3.4 8.8 + - + +
109B ALA* 3.0 25.1 + - - +
188B PHE* 3.1 46.5 - - + +
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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 GLN 3.2 4.0 + - - -
103B LEU 3.2 4.0 + - - -
104B LEU 3.2 0.6 - - - -
105B GLN* 1.3 75.9 - - - +
107B VAL* 1.3 64.7 + - - +
109B ALA* 3.2 4.1 + - - +
110B MET* 3.2 29.6 + - - +
184B GLN 4.5 3.6 - - - +
185B MET* 3.6 22.9 - - - -
188B PHE* 3.4 19.7 - - - -
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Residues in contact with VAL 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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94B PHE* 3.5 46.0 - - + -
99B LEU* 5.2 2.9 - - + -
103B LEU 3.1 13.7 + - - +
104B LEU* 3.1 12.5 + - + +
106B GLY* 1.3 75.1 - - - +
108B TYR* 1.3 66.4 + - + +
109B ALA 3.4 0.3 + - - -
110B MET* 3.4 12.6 - - - +
112B PHE* 3.1 26.7 + - + +
150B LEU* 3.7 29.8 - - + -
185B MET* 3.8 15.9 - - + -
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Residues in contact with TYR 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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94B PHE* 3.9 27.9 + + + +
95B GLU* 4.1 26.2 + - + +
104B LEU* 2.9 30.8 + - + +
105B GLN* 3.6 10.3 - - - +
107B VAL* 1.3 81.4 - - + +
109B ALA* 1.3 60.9 + - - +
110B MET 3.4 0.2 - - - -
111B GLY* 3.5 11.1 + - - -
112B PHE 4.0 16.3 + - - +
113B ASN* 4.4 7.5 + - - -
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Residues in contact with ALA 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 GLN 3.0 13.8 + - - +
106B GLY* 3.4 9.6 - - - +
107B VAL 3.2 0.6 - - - -
108B TYR* 1.3 75.2 - - - +
110B MET* 1.3 56.6 + - - +
111B GLY 3.1 9.4 + - - -
184B GLN* 5.4 0.4 - - + -
187B LYS* 4.8 14.1 - - + +
188B PHE* 3.8 22.9 - - + -
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Residues in contact with MET 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 3.2 15.9 + - - +
107B VAL* 3.4 11.7 - - - +
109B ALA* 1.3 74.8 - - - +
111B GLY* 1.3 57.1 + - - +
112B PHE* 3.0 41.1 - - + -
181B VAL* 4.2 19.3 - - + -
184B GLN* 3.2 47.6 - - + +
185B MET* 3.4 48.7 - - + +
602B ADP 5.8 0.9 - - - +
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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