Contacts of the helix formed by residues 94 - 106 (chain B) in PDB entry 6E8Y
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 PRO 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B VAL 4.9 0.4 - - - +
93B VAL* 1.3 92.8 - - + +
95B HIS* 1.3 67.7 + - - +
96B GLN* 3.6 20.4 - - - +
97B PHE* 2.8 41.6 + - + +
98B ILE* 3.5 7.1 + - - +
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Residues in contact with HIS 95 (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 VAL 3.6 2.0 + - - -
94B PRO* 1.3 71.0 - - - +
96B GLN* 1.3 71.8 + - - +
97B PHE 3.0 1.6 + - - -
98B ILE* 3.2 22.5 + - + +
99B GLY 4.7 0.3 + - - -
119B ILE* 3.9 18.8 - - + +
120B LYS 5.3 3.6 - - - +
121B GLY* 5.0 1.8 - - - -
122B VAL 2.9 40.5 - - - -
132B ILE* 3.3 25.7 - - + +
298B GLN* 3.9 19.9 + - - -
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Residues in contact with GLN 96 (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 PRO* 3.0 16.6 + - - +
95B HIS* 1.3 89.2 + - - +
97B PHE* 1.3 83.0 + - + +
99B GLY 5.0 1.8 + - - -
100B LYS* 5.4 1.7 + - - +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.8 2.7 - - + -
94B PRO* 2.8 38.4 + - + +
96B GLN* 1.3 98.6 - - + +
98B ILE* 1.3 67.0 + - - +
99B GLY 3.2 3.1 - - - -
100B LYS* 3.2 13.3 + - + +
101B ILE* 3.0 37.7 + - + +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.8 26.5 - - + -
93B VAL* 3.9 14.6 - - + +
94B PRO 3.5 2.9 + - - +
95B HIS* 3.2 26.0 + - + +
97B PHE* 1.3 78.7 - - - +
99B GLY* 1.3 62.4 + - - +
101B ILE* 3.4 7.2 + - + -
102B CYS* 2.9 34.9 + - - -
119B ILE* 3.8 27.1 - - + -
132B ILE* 4.2 16.4 - - + -
135B VAL* 5.6 7.9 - - + -
136B ILE* 3.6 25.4 - - + -
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Residues in contact with GLY 99 (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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95B HIS 4.7 0.8 + - - -
96B GLN 5.0 1.6 + - - -
97B PHE 3.2 1.0 - - - -
98B ILE* 1.3 85.9 - - - +
100B LYS* 1.3 61.6 + - - +
102B CYS* 3.4 1.9 + - - -
103B ASP* 3.1 18.5 + - - -
135B VAL* 5.3 3.8 - - - -
139B ARG* 2.9 37.3 + - - -
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Residues in contact with LYS 100 (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 GLN 5.4 2.1 + - - +
97B PHE* 3.2 17.4 + - + +
99B GLY* 1.3 75.3 - - - +
101B ILE* 1.3 65.4 + - + +
103B ASP* 3.2 11.4 + - + +
104B GLN* 2.9 55.1 + - + +
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Residues in contact with ILE 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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9B VAL* 3.9 22.7 - - + -
39B TRP* 3.7 23.1 - - + -
79B VAL* 4.1 11.4 - - + -
91B PHE* 5.4 0.2 - - + -
93B VAL* 3.6 40.6 - - + -
97B PHE* 3.0 26.2 + - + +
98B ILE* 3.7 10.1 - - + +
100B LYS* 1.3 81.0 - - + +
102B CYS* 1.3 62.5 + - - +
104B GLN* 3.2 9.3 + - - +
105B LEU* 3.0 33.3 + - + +
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Residues in contact with CYS 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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91B PHE* 4.9 2.5 - - - -
98B ILE* 2.9 39.1 + - - +
99B GLY* 3.8 4.7 - - - +
101B ILE* 1.3 77.3 - - - +
103B ASP* 1.3 59.9 + - - +
105B LEU* 4.5 1.6 - - - -
106B LYS* 2.8 31.2 + - - +
135B VAL* 5.1 2.0 - - + -
136B ILE* 4.0 20.6 - - - -
139B ARG* 4.1 19.2 - - + +
140B LEU* 3.4 37.0 - - + +
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Residues in contact with ASP 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 GLY 3.1 18.1 + - - +
100B LYS* 3.2 13.4 + - + +
102B CYS* 1.3 77.0 - - - +
104B GLN* 1.3 67.5 + - - +
106B LYS* 4.2 13.6 + - - +
139B ARG* 3.2 30.2 + - - -
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Residues in contact with GLN 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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79B VAL* 4.2 19.5 - - + -
80B VAL* 3.6 10.7 - - + +
100B LYS* 2.9 52.7 + - + +
101B ILE* 3.6 7.6 - - - +
102B CYS 3.2 0.4 - - - -
103B ASP* 1.3 83.8 + - - +
105B LEU* 1.3 61.5 + - - +
106B LYS 4.4 0.3 - - - +
108B HIS* 3.3 19.4 + - - -
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Residues in contact with LEU 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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9B VAL* 4.6 3.1 - - + -
79B VAL* 3.6 42.4 - - + +
80B VAL* 4.0 8.7 - - + -
83B ALA* 3.7 15.5 - - + -
89B LEU* 4.6 10.3 - - + -
91B PHE* 4.2 21.1 - - + -
101B ILE* 3.0 33.9 + - + +
102B CYS* 3.1 0.6 + - - -
104B GLN* 1.3 76.8 - - - +
106B LYS* 1.3 67.9 + - - +
107B GLY 3.1 0.7 + - - -
108B HIS* 2.9 23.4 + - + +
109B LEU* 4.1 15.8 - - + +
140B LEU* 3.7 19.5 - - + -
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Residues in contact with LYS 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 CYS 2.8 16.6 + - - +
103B ASP* 4.2 12.4 - - - +
104B GLN 3.4 1.5 - - - +
105B LEU* 1.3 76.5 - - - +
107B GLY* 1.3 63.0 + - - +
108B HIS* 3.5 13.9 + - - -
138B GLU 4.0 4.9 + - - -
139B ARG* 2.8 41.5 + - + +
140B LEU* 3.5 10.5 - - - +
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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