Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 5IZL
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 LEU 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.6 11.9 - - + -
49A LEU* 4.1 27.8 - - + -
48B THR 3.7 22.9 - - - +
49B LEU* 3.9 22.9 - - + +
94B PRO* 4.0 16.2 - - + -
96B HIS* 3.5 28.4 + - + +
97B ALA 3.1 1.8 - - - -
98B SER* 1.3 83.8 - - - +
100B ILE* 1.3 63.7 + - - +
101B ARG* 3.1 4.9 - - - +
102B THR* 2.9 28.1 + - - +
103B ILE* 3.4 8.3 + - - +
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Residues in contact with ILE 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 HIS 4.1 0.4 + - - -
97B ALA 3.4 17.0 + - - +
98B SER* 3.4 2.0 - - - -
99B LEU* 1.3 77.2 - - - +
101B ARG* 1.3 62.0 + - + +
103B ILE* 3.0 23.2 + - + +
104B ILE* 2.9 41.6 + - + +
126B GLN* 5.0 5.6 - - + -
129B GLU* 3.6 35.9 - - + +
130B CYS* 5.3 1.8 - - - -
133B ILE* 4.3 12.8 - - + -
433B LEU* 3.7 37.5 - - + -
443B ARG* 3.7 5.2 - - - +
444B LEU* 4.6 9.9 - - + -
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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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96A HIS* 6.3 2.9 - - - -
98B SER 4.6 10.1 - - - +
99B LEU* 4.7 1.1 - - - -
100B ILE* 1.3 79.9 - - + +
102B THR* 1.3 62.2 + - - +
104B ILE* 3.6 13.2 + - - +
105B GLY* 3.4 15.4 + - - -
336B HIS* 6.0 1.3 + - - -
338B THR* 5.0 4.1 - - - +
340B GLY 5.1 2.9 - - - +
341B HIS* 5.7 3.9 + - - +
343B THR* 4.0 48.4 + - + +
433B LEU* 4.2 19.3 - - + -
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Residues in contact with THR 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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49B LEU 4.9 4.0 + - - -
50B ASP* 3.6 25.1 + - - +
51B LEU* 3.9 29.3 - - + +
94B PRO* 4.1 12.7 - - + +
99B LEU* 2.9 21.3 + - - +
101B ARG* 1.3 76.3 + - - +
103B ILE* 1.3 59.7 + - - +
105B GLY* 3.1 3.8 + - - -
106B GLY* 3.0 24.3 + - - -
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Residues in contact with ILE 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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13B LEU* 3.8 29.8 - - + -
14B GLY 5.4 0.4 - - - +
93B CYS* 4.4 11.4 - - + -
94B PRO* 3.4 35.9 - - + +
95B GLY* 4.7 4.3 - - - +
96B HIS 4.4 9.2 - - - +
99B LEU 3.7 8.7 - - - +
100B ILE* 3.0 29.5 + - + +
102B THR* 1.3 73.7 - - - +
104B ILE* 1.3 64.2 + - - +
106B GLY* 3.2 1.7 + - - +
107B ALA* 3.1 23.2 + - - +
126B GLN* 5.8 2.5 - - + -
130B CYS* 4.0 18.8 - - - -
133B ILE* 4.2 11.9 - - + -
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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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100B ILE* 2.9 24.4 + - + +
101B ARG* 3.9 7.6 - - - +
102B THR 3.3 0.2 - - - -
103B ILE* 1.3 76.2 - - - +
105B GLY* 1.3 60.9 + - - +
107B ALA* 3.7 4.9 + - - +
108B GLN* 3.1 27.6 + - - +
133B ILE* 3.8 27.3 - - + +
338B THR* 3.7 37.2 - - + +
340B GLY 4.8 0.2 - - - -
429B ILE* 3.7 30.3 - - + -
431B SER* 5.1 4.0 - - - +
433B LEU* 5.8 2.0 - - + -
444B LEU* 4.4 20.4 - - + -
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Residues in contact with GLY 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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51B LEU* 5.1 2.0 - - - -
101B ARG 3.4 8.0 + - - -
102B THR* 3.1 6.7 + - - -
103B ILE 3.1 0.8 - - - -
104B ILE* 1.3 77.4 - - - +
106B GLY* 1.3 65.0 + - - +
108B GLN* 3.0 19.8 + - - +
109B ILE* 3.7 10.4 + - - +
340B GLY 4.0 16.5 + - - -
341B HIS* 4.4 17.8 - - - -
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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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51B LEU* 4.0 15.7 - - - +
91B VAL* 4.7 0.4 - - - -
93B CYS* 4.4 9.2 - - - -
102B THR 3.0 14.4 + - - -
103B ILE 3.2 2.6 + - - -
105B GLY* 1.3 75.3 - - - +
107B ALA* 1.3 59.9 + - - +
108B GLN 3.1 0.2 - - - -
109B ILE* 2.8 37.6 + - - +
110B ILE* 3.1 13.8 - - - +
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Residues in contact with ALA 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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13B LEU* 4.8 11.0 - - + -
93B CYS* 5.1 0.6 - - - -
103B ILE 3.1 15.9 + - - +
104B ILE 4.0 3.6 - - - +
105B GLY 3.2 0.6 - - - -
106B GLY* 1.3 75.5 - - - +
108B GLN* 1.3 59.3 + - - +
109B ILE 3.4 0.4 - - - -
110B ILE* 3.7 27.8 - - + +
113B MET* 6.0 0.2 - - - -
133B ILE* 3.7 27.6 - - + +
134B GLY* 5.6 0.4 - - - +
137B ALA* 3.6 25.4 - - + +
138B CYS* 3.9 6.1 - - - -
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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