Contacts of the helix formed by residues 100 - 110 (chain B) in PDB entry 4HZF
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 TYR 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.4 21.5 - - - +
38B GLU* 3.2 23.5 + - - +
39B THR 3.3 22.0 - - - -
40B LEU* 3.6 19.3 - - + -
72B GLY 2.6 24.1 + - - -
75B GLY* 3.3 39.2 + - - -
76B LEU* 3.5 30.3 - - + -
83B ARG* 3.3 9.0 + - - -
99B SER* 1.3 71.8 - - - +
101B LYS* 1.3 58.8 + - + +
103B PHE* 3.1 3.8 + - - +
104B ARG* 2.8 55.2 + - - +
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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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79B GLU* 3.3 23.6 + - - -
99B SER* 3.2 10.2 + - - +
100B TYR* 1.3 79.6 - - + +
102B LYS* 1.3 61.7 + - - +
104B ARG* 3.3 26.5 + - - +
105B GLN* 3.2 27.2 + - - +
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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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18B HIS* 3.4 59.6 + - + +
98B ILE* 3.7 16.8 - - + -
99B SER* 3.0 17.5 + - - +
101B LYS* 1.3 74.5 - - - +
103B PHE* 1.3 66.0 + - - +
105B GLN* 3.2 23.2 + - - +
106B LEU* 3.1 22.2 + - + +
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Residues in contact with PHE 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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15B PHE* 3.7 23.1 - + - -
40B LEU* 3.5 27.1 - - + -
70B PHE* 4.2 3.1 - + - -
76B LEU* 3.7 17.3 - - + -
98B ILE* 3.9 13.0 - - + +
99B SER 3.0 14.2 + - - +
100B TYR* 3.1 11.2 + - - +
102B LYS* 1.3 78.1 - - - +
104B ARG* 1.3 61.9 + - - +
106B LEU* 3.0 7.5 + - + +
107B ILE* 3.0 45.0 + - + +
113B ILE* 3.7 47.1 - - + -
114B LEU* 4.8 3.6 - - + -
117B LEU* 3.8 24.0 - - + -
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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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115A MET* 3.8 28.0 - - + -
75B GLY 5.1 0.2 + - - -
76B LEU* 2.9 40.5 + - + -
77B PHE 5.5 0.2 - - - -
78B GLU 5.5 1.4 - - - +
79B GLU* 4.5 20.9 + - - +
100B TYR* 2.8 37.2 + - - +
101B LYS* 3.8 39.7 - - - +
102B LYS 3.3 0.2 - - - -
103B PHE* 1.3 75.2 - - - +
105B GLN* 1.3 60.9 + - + +
107B ILE* 3.4 19.2 + - + +
108B GLN* 3.5 17.5 + - - +
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Residues in contact with GLN 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* 3.2 13.5 + - - +
102B LYS* 3.2 29.2 + - - +
103B PHE 3.1 0.8 - - - -
104B ARG* 1.3 74.1 - - - +
106B LEU* 1.3 67.4 + - + +
108B GLN* 3.2 17.2 + - - +
109B VAL* 3.5 14.0 + - - +
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Residues in contact with LEU 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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14B TRP* 3.4 36.8 - - + +
15B PHE* 3.9 26.0 - - + -
18B HIS* 3.9 38.4 - - + +
98B ILE* 3.8 26.2 - - + -
102B LYS* 3.1 13.8 + - + +
103B PHE* 3.0 9.7 + - + +
105B GLN* 1.3 79.5 - - + +
107B ILE* 1.3 57.8 + - - +
109B VAL* 3.1 6.7 + - + -
110B ASN 2.9 26.5 + - - +
113B ILE* 4.5 6.5 - - + -
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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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111A PRO* 4.0 22.6 - - + +
115A MET* 3.8 27.4 - - + -
76B LEU* 4.7 1.3 - - + -
103B PHE* 3.0 44.8 + - + +
104B ARG* 3.6 16.6 - - + +
105B GLN 3.2 0.4 - - - -
106B LEU* 1.3 76.5 - - - +
108B GLN* 1.3 67.3 + - - +
110B ASN 4.0 6.3 - - - -
111B PRO* 3.1 28.4 - - + +
113B ILE* 4.0 4.7 - - + +
114B LEU* 3.8 36.8 - - + -
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Residues in contact with GLN 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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110A ASN* 5.1 1.4 + - - -
111A PRO* 4.0 32.2 - - - +
112A ASP* 3.4 23.1 + - - +
115A MET* 5.5 3.4 - - - +
104B ARG 3.5 14.4 + - - +
105B GLN* 3.2 10.2 + - - +
106B LEU 3.2 0.8 - - - -
107B ILE* 1.3 80.3 - - - +
109B VAL* 1.3 62.8 + - + +
111B PRO* 4.5 3.6 - - - +
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Residues in contact with VAL 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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14B TRP* 3.6 28.7 - - + +
105B GLN 3.8 12.1 - - - +
106B LEU* 3.1 11.8 + - + +
108B GLN* 1.3 79.3 - - + +
110B ASN* 1.3 61.2 + - + +
111B PRO* 4.1 2.4 - - - +
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Residues in contact with ASN 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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108A GLN* 5.5 3.8 + - - +
11B THR* 3.6 25.8 + - - +
14B TRP* 3.8 19.6 - - + -
106B LEU 2.9 10.2 + - - +
107B ILE 3.3 2.5 - - - -
109B VAL* 1.3 79.2 - - + +
111B PRO* 1.3 65.9 - - - +
112B ASP* 3.0 28.3 + - - +
113B ILE* 3.2 22.3 + - - +
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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