Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 2I6A
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 ASP 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLY* 3.1 4.4 + - - -
92B ILE* 1.3 76.8 - - - +
94B LYS* 1.3 66.0 + - - +
95B PHE* 3.7 6.9 + - - +
96B GLY 3.1 5.4 + - - -
97B GLU* 3.0 22.7 + - - +
119B PRO* 3.5 14.4 - - - +
120B THR* 2.9 44.9 + - - -
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Residues in contact with LYS 94 (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 ASP* 1.3 75.3 - - - +
95B PHE* 1.3 75.3 + - + +
97B GLU* 3.3 9.6 + - - +
98B ILE* 3.0 41.0 + - + +
340B GLU* 3.2 34.7 + - - -
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Residues in contact with PHE 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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17B LEU* 3.7 34.9 - - + +
19B ILE* 4.5 5.8 - - + -
60B TYR* 4.1 21.3 - + - -
93B ASP* 3.4 6.0 + - - +
94B LYS* 1.3 89.7 - - + +
96B GLY* 1.3 60.3 + - - +
98B ILE* 3.3 19.7 + - + +
99B LEU* 2.9 34.7 + - - +
120B THR* 4.0 21.8 - - + -
122B THR* 4.1 22.7 - - + -
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Residues in contact with GLY 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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90B ILE* 4.3 9.4 - - - -
91B GLY 3.9 9.4 - - - -
93B ASP* 3.1 15.0 + - - -
95B PHE* 1.3 76.3 - - - +
97B GLU* 1.3 62.6 + - - +
99B LEU* 3.0 5.9 + - - +
100B LYS* 2.9 32.5 + - - +
120B THR* 3.3 19.4 + - - -
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Residues in contact with GLU 97 (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 ASP 3.0 12.2 + - - +
94B LYS* 3.3 12.5 + - - +
96B GLY* 1.3 74.4 - - - +
98B ILE* 1.3 56.0 + - - +
100B LYS* 3.3 32.4 + - - +
101B ARG* 2.9 29.6 + - - +
100D LYS* 5.8 2.1 + - - -
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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
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17B LEU* 4.0 24.0 - - + -
60B TYR* 5.6 6.1 - - + -
62B ALA 5.4 1.8 - - - +
94B LYS* 3.0 35.6 + - + +
95B PHE* 3.3 29.6 - - + +
97B GLU* 1.3 73.4 - - - +
99B LEU* 1.3 67.3 + - + +
101B ARG* 3.1 24.5 + - - +
102B LYS* 3.0 38.5 + - + +
340B GLU* 5.1 7.6 - - - +
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Residues in contact with LEU 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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15B PRO* 3.4 38.8 - - + +
16B LEU 3.5 20.2 - - - +
17B LEU* 4.0 13.5 - - + +
62B ALA* 3.6 26.7 - - + -
67B GLN* 4.3 8.4 - - - +
71B LYS* 4.9 1.2 + - - -
90B ILE* 4.1 7.0 - - + -
95B PHE 2.9 14.9 + - - +
96B GLY* 3.5 6.7 - - - +
98B ILE* 1.3 76.4 - - - +
100B LYS* 1.3 63.8 + - - +
102B LYS* 3.6 4.5 + - - +
103B ALA* 3.1 22.0 + - - +
112B TYR* 3.6 10.7 + - + +
120B THR* 3.5 22.2 - - + -
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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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90B ILE* 3.4 31.0 - - + -
96B GLY 2.9 22.8 + - - +
97B GLU* 3.3 34.9 + - - +
99B LEU* 1.3 73.9 - - - +
101B ARG* 1.3 66.3 + - - +
103B ALA* 3.3 3.0 + - - +
104B ALA* 3.1 23.2 + - - +
112B TYR* 3.7 23.6 - - + -
114B GLU* 3.1 25.3 + - - +
97D GLU* 5.9 0.8 + - - -
100D LYS* 5.8 4.0 - - - +
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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 GLU* 2.9 17.6 + - - +
98B ILE* 3.1 31.2 + - - +
100B LYS* 1.3 77.0 - - - +
102B LYS* 1.3 84.9 + - - +
104B ALA* 3.0 9.0 + - - +
105B GLU* 3.0 56.6 + - + +
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Residues in contact with LYS 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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62B ALA* 4.0 27.1 - - + +
71B LYS* 3.6 8.6 - - - +
98B ILE* 3.0 32.3 + - + +
99B LEU 3.9 4.0 - - - +
101B ARG* 1.3 100.0 - - - +
103B ALA* 1.3 58.7 + - - +
105B GLU* 3.4 22.4 + - - +
106B ALA* 3.4 20.3 + - - +
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Residues in contact with ALA 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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67B GLN* 4.8 0.7 - - + +
71B LYS* 4.0 13.7 - - - +
99B LEU 3.1 9.5 + - - +
100B LYS* 3.6 6.5 - - - +
101B ARG 3.1 0.4 - - - -
102B LYS* 1.3 76.0 - - - +
104B ALA* 1.3 64.1 + - - +
105B GLU 3.2 0.4 - - - -
106B ALA* 3.0 11.5 + - - +
107B HIS 3.1 8.5 + - - -
108B VAL* 3.1 20.0 + - + +
110B ALA* 3.8 18.4 - - + -
112B TYR* 3.4 25.8 - - - +
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Residues in contact with ALA 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 LYS 3.1 11.6 + - - +
101B ARG* 3.0 10.6 + - - +
103B ALA* 1.3 76.2 - - - +
105B GLU* 1.3 58.4 + - + +
106B ALA 3.1 0.2 - - - -
107B HIS* 3.1 25.1 + - - +
108B VAL 4.6 6.1 - - - -
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Residues in contact with GLU 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* 3.0 49.7 + - + +
102B LYS* 3.4 32.9 + - - +
104B ALA* 1.3 75.0 - - + +
106B ALA* 1.3 58.5 + - - +
107B HIS* 3.3 15.8 + - - -
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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