Contacts of the helix formed by residues 100 - 113 (chain B) in PDB entry 2Z1Z
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 ALA 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* 4.5 0.6 + - - +
99B GLY* 1.3 71.9 - - - -
101B LYS* 1.3 72.1 + - + +
102B PRO* 4.1 11.2 - - + -
103B LEU* 2.9 28.9 + - + +
104B ARG* 3.0 13.3 + - - +
316B GLN* 2.8 26.1 + - + +
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Residues in contact with LYS 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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95B GLY 4.2 5.1 + - - -
96B ALA* 3.1 33.5 - - - +
99B GLY 3.5 2.0 + - - -
100B ALA* 1.3 78.0 - - + +
102B PRO* 1.4 63.8 - - + +
103B LEU 3.1 1.9 + - - -
104B ARG* 3.3 28.8 + - - +
105B ALA* 2.7 37.1 + - - +
119B ASP* 4.9 3.1 - - - +
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Residues in contact with PRO 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 ALA* 3.7 9.9 - - + -
101B LYS* 1.4 101.5 - - + +
103B LEU* 1.3 56.4 + - - +
105B ALA* 3.8 7.2 - - + +
106B ALA* 3.0 28.4 + - - +
320B LEU* 3.5 19.3 - - + +
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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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100B ALA* 2.9 15.7 + - + +
102B PRO* 1.3 79.1 - - - +
104B ARG* 1.3 62.3 + - - +
106B ALA* 3.3 0.3 + - - +
107B ILE* 2.9 54.5 + - + +
124B VAL* 3.8 24.5 - - + -
279B LEU* 4.2 6.7 - - + -
316B GLN* 3.7 50.3 - - + +
319B ALA* 3.9 20.0 - - + -
320B LEU* 3.8 21.1 - - + +
323B LEU* 4.4 5.4 - - + -
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Residues in contact with ARG 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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96B ALA* 6.0 1.0 - - - +
98B GLN* 3.0 47.2 + - - +
99B GLY 3.1 16.1 + - - +
100B ALA 3.0 7.2 + - - +
101B LYS* 3.6 35.8 + - - +
103B LEU* 1.3 74.3 - - - +
105B ALA* 1.3 57.5 + - - +
107B ILE* 4.0 0.7 - - - +
108B ALA* 2.9 31.7 + - - +
119B ASP* 2.9 47.6 + - - +
120B ASP* 3.9 5.5 - - - +
122B VAL* 3.2 26.6 - - + +
124B VAL* 4.0 16.6 - - + -
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Residues in contact with ALA 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 LYS 2.7 20.7 + - - +
102B PRO* 3.8 9.4 - - + +
104B ARG* 1.3 74.8 - - - +
106B ALA* 1.3 57.2 + - - +
109B LYS* 2.3 47.3 + - + +
119B ASP* 3.6 27.1 - - - +
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Residues in contact with ALA 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 PRO 3.0 19.4 + - - +
103B LEU 3.3 4.0 + - - +
105B ALA* 1.3 74.3 - - - +
107B ILE* 1.3 61.4 + - - +
109B LYS* 4.4 5.6 - - - -
110B THR* 2.6 39.5 + - - +
320B LEU* 4.1 12.6 - - + -
323B LEU* 3.7 24.2 - - + +
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Residues in contact with ILE 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 LEU* 2.9 34.1 + - + +
104B ARG 4.0 2.9 - - - +
106B ALA* 1.3 74.3 - - - +
108B ALA* 1.3 69.4 + - - +
111B PHE* 3.2 22.3 + - + -
112B TYR* 3.5 11.6 - - + -
122B VAL* 3.9 11.0 - - + -
124B VAL* 3.9 21.8 - - + -
268B PHE* 4.5 5.2 - - + -
279B LEU* 5.0 1.3 - - + -
281B TRP* 3.6 59.9 - - + +
323B LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 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 ARG 2.9 22.4 + - - +
105B ALA 3.6 4.5 - - - +
107B ILE* 1.3 73.1 - - - +
109B LYS* 1.4 64.2 + - - +
112B TYR* 3.0 46.9 + - - +
113B GLY* 4.9 0.2 - - - -
117B ILE* 3.9 21.7 - - + +
118B GLY 4.0 5.4 - - - +
119B ASP 3.9 14.8 - - - +
122B VAL* 4.1 7.0 - - + +
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Residues in contact with LYS 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 ALA* 2.3 45.6 + - + +
106B ALA* 3.8 7.0 - - - +
108B ALA* 1.4 78.9 - - - +
110B THR* 1.3 66.4 + - - +
113B GLY* 3.2 25.5 + - - +
117B ILE 5.3 1.8 + - - -
118B GLY* 5.5 0.6 - - - -
119B ASP* 2.4 31.9 + - - +
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Residues in contact with THR 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 ALA* 2.6 28.5 + - - +
109B LYS* 1.3 78.5 - - - +
111B PHE* 1.4 76.8 + - + +
113B GLY 4.9 0.2 + - - -
323B LEU* 4.0 31.5 + - + +
328B LEU* 4.4 20.4 - - + -
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Residues in contact with PHE 111 (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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107B ILE* 3.2 18.7 + - + -
110B THR* 1.4 89.3 - - + +
112B TYR* 1.3 84.1 + - + +
113B GLY 3.9 0.9 - - - -
115B LEU* 4.2 7.6 - - - +
242B MET* 3.7 39.5 - - + -
251B SER* 4.7 4.0 - - - -
268B PHE* 4.7 2.2 - + - -
271B TYR* 4.3 16.6 - + - -
281B TRP* 3.7 35.9 - + - -
323B LEU* 3.7 37.2 - - + -
328B LEU* 5.4 1.8 - - + -
331B MET* 4.8 5.4 - - + -
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Residues in contact with TYR 112 (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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107B ILE* 3.5 18.8 - - + -
108B ALA* 3.0 17.8 + - - +
111B PHE* 1.3 99.6 - - + +
113B GLY* 1.3 57.8 + - - +
114B GLY 3.4 0.5 + - - -
115B LEU* 3.0 33.5 + - + +
116B GLY 4.2 1.0 + - - -
117B ILE* 3.7 30.7 + - + +
238B SER* 4.3 0.7 + - - -
251B SER* 3.6 21.5 - - - -
253B PHE* 4.1 13.9 - + - -
264B GLU* 2.6 37.2 + - - +
266B ALA* 4.4 0.2 - - - +
281B TRP* 3.0 30.3 + - - -
283B VAL* 3.5 26.6 - - + +
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Residues in contact with GLY 113 (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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108B ALA 3.2 3.1 + - - -
109B LYS* 3.2 24.2 + - - -
110B THR 4.7 0.2 - - - -
111B PHE 3.9 1.2 - - - -
112B TYR* 1.3 74.7 - - - +
114B GLY* 1.3 61.7 + - - -
115B LEU* 4.2 5.2 - - - +
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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