Contacts of the helix formed by residues 100 - 110 (chain B) in PDB entry 2IZZ
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 THR 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 GLY 3.9 11.0 - - - +
99B VAL* 1.3 75.4 - - - +
101B ILE* 1.3 63.7 + - - +
102B SER* 3.7 11.9 + - - -
103B SER* 2.9 39.5 + - - -
104B ILE* 3.2 11.8 + - - +
119B ARG* 3.8 5.4 - - - +
164B GLU* 3.3 14.4 - - - +
269B GLN* 3.5 16.6 + - + +
273B ASP* 4.0 5.7 + - - +
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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
----------------------------------------------------------
99B VAL 3.8 0.8 + - - -
100B THR* 1.3 70.5 - - - +
102B SER* 1.3 54.1 + - - +
104B ILE* 3.2 9.7 + - - +
105B GLU* 2.8 65.0 + - + +
117B VAL* 4.2 9.2 - - + -
119B ARG* 3.6 23.1 - - + +
136B ALA* 3.7 29.2 - - + +
137B THR 3.9 17.3 - - - +
138B GLY* 3.8 8.7 - - - +
139B THR* 4.7 0.9 - - - +
164B GLU* 2.8 36.1 + - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 3.1 11.5 - - - -
101B ILE* 1.3 80.9 - - - +
103B SER* 1.3 57.1 + - - +
105B GLU* 3.4 6.8 + - - +
106B LYS* 2.9 32.7 + - - +
164B GLU* 4.8 1.4 + - - -
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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
----------------------------------------------------------
79B LEU* 5.1 0.7 - - - -
99B VAL* 3.5 18.0 - - - +
100B THR* 2.9 27.1 + - - -
102B SER* 1.3 80.5 - - - +
104B ILE* 1.3 60.7 + - - +
106B LYS* 3.6 8.3 + - - +
107B LYS* 3.3 27.0 + - - +
269B GLN* 3.8 3.8 + - - -
273B ASP* 3.9 21.5 - - - -
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Residues in contact with ILE 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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68B LEU* 5.0 1.3 - - + -
75B ILE* 4.4 2.9 - - + -
79B LEU* 3.8 28.5 - - + -
92B VAL* 4.8 5.6 - - + -
94B SER* 3.4 34.5 - - - +
99B VAL* 3.8 21.5 - - + +
100B THR 3.4 18.2 - - - +
101B ILE* 3.2 7.5 + - + +
103B SER* 1.3 80.1 + - - +
105B GLU* 1.3 65.6 + - - +
107B LYS* 3.3 2.8 + - - +
108B LEU* 3.0 42.0 + - + +
117B VAL* 4.0 24.5 - - + -
119B ARG* 5.6 1.3 - - + -
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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 ILE* 2.8 41.8 + - + +
102B SER* 3.9 6.6 - - - +
104B ILE* 1.3 73.2 - - - +
106B LYS* 1.3 55.2 + - - +
109B SER* 2.7 41.1 + - - +
115B PRO* 4.4 14.1 - - + +
117B VAL* 4.0 19.9 + - + +
138B GLY* 3.3 3.6 - - - -
139B THR* 2.7 49.1 + - - -
140B HIS* 4.2 11.0 + - + +
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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 SER* 2.9 19.0 + - - +
103B SER* 3.8 7.6 - - - +
104B ILE 3.3 0.2 - - - -
105B GLU* 1.3 77.3 - - - +
107B LYS* 1.3 63.5 + - + +
109B SER* 3.6 4.8 + - - -
110B ALA* 3.5 15.8 + - - +
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Residues in contact with LYS 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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76B PRO* 3.9 30.5 - - + +
79B LEU* 4.0 25.4 - - + -
80B ASP* 3.2 36.4 + - - +
103B SER 3.3 14.9 + - - +
104B ILE 3.7 7.0 - - - +
106B LYS* 1.3 80.8 - - + +
108B LEU* 1.3 61.8 - - - +
110B ALA* 3.4 20.2 + - - +
111B PHE* 3.5 14.0 - - - -
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Residues in contact with LEU 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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79B LEU* 3.8 28.9 - - + +
82B ILE* 4.5 1.8 - - + -
83B GLY* 3.7 28.7 - - - +
86B ILE* 3.9 16.2 - - + -
92B VAL* 4.2 19.3 - - + -
104B ILE* 3.0 32.9 + - + +
107B LYS* 1.3 81.1 - - - +
109B SER* 1.3 58.2 + - - +
111B PHE* 3.0 22.6 + - - +
112B ARG* 3.2 13.9 + - - +
115B PRO* 3.8 28.5 - - + -
117B VAL* 4.2 6.7 - - + -
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Residues in contact with SER 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 GLU* 2.7 27.8 + - - +
106B LYS* 4.0 5.4 - - - -
107B LYS 3.3 0.2 - - - -
108B LEU* 1.3 76.4 - - - +
110B ALA* 1.3 61.2 + - - +
111B PHE 3.3 0.7 + - - -
112B ARG 3.4 19.7 + - - +
113B PRO* 4.2 7.6 - - - +
114B ALA 4.6 1.9 + - - -
115B PRO* 3.5 17.5 - - - +
140B HIS* 4.9 4.5 + - - -
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Residues in contact with ALA 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 LYS 3.5 9.4 + - - +
107B LYS* 3.4 15.5 + - - +
108B LEU 3.1 0.6 - - - -
109B SER* 1.3 77.2 - - - +
111B PHE* 1.3 68.0 + - + +
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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