Contacts of the helix formed by residues 96 - 104 (chain A) in PDB entry 2L80
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 HIS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA 3.3 28.3 + - - -
6A ASN* 4.3 9.9 + - - -
94A ASP* 2.7 27.5 + - - +
95A PRO* 1.3 103.3 - - + +
97A LEU* 1.3 58.4 + - - +
98A ALA 3.2 2.9 - - - +
99A LYS* 3.2 17.1 + - + +
100A HIS* 2.8 41.4 + + + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.9 8.5 - - + -
79A ASP 5.4 0.9 - - - +
80A GLY* 4.2 10.3 - - - -
81A ALA* 3.8 29.8 - - + +
83A VAL* 3.5 24.7 - - + -
93A LEU* 3.9 22.0 - - + -
94A ASP* 2.9 45.1 + - + +
95A PRO 3.6 0.8 - - - -
96A HIS* 1.3 76.0 - - - +
98A ALA* 1.3 55.6 + - - +
100A HIS* 3.1 3.0 + - + +
101A LEU* 2.7 49.6 + - + +
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Residues in contact with ALA 98 (chain A).
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 3.2 0.6 - - - -
97A LEU* 1.3 78.9 - - - +
99A LYS* 1.3 58.3 + - - +
101A LEU* 4.1 0.3 - - - +
102A ALA* 2.8 34.2 + - - +
108A MET* 3.8 30.0 - - + +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN* 6.0 0.7 - - - +
96A HIS* 3.2 20.9 + - + +
98A ALA* 1.3 79.3 - - - +
100A HIS* 1.3 63.1 + - + +
102A ALA* 3.8 4.7 - - + +
103A HIS* 2.9 48.7 + - + +
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 37.7 + - + +
10A GLN* 3.4 31.2 + - + +
37A LEU* 3.7 24.8 - - + +
94A ASP* 2.5 34.6 + - - +
96A HIS* 2.8 34.4 + + + +
97A LEU* 3.7 3.1 - - - +
99A LYS* 1.3 78.5 - - + +
101A LEU* 1.3 64.8 + - + +
103A HIS* 3.3 6.3 + - - +
104A PHE* 3.0 31.0 + - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.2 30.7 - - + -
76A ILE* 4.3 8.7 - - + -
80A GLY* 5.6 0.9 - - - -
81A ALA* 4.7 13.2 - - + +
97A LEU* 2.7 39.8 + - + +
100A HIS* 1.3 74.8 - - + +
102A ALA* 1.3 54.6 + - - +
104A PHE* 2.8 18.1 + - + +
106A ILE* 2.7 69.2 + - + +
108A MET* 3.5 31.6 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA 2.8 22.4 + - - +
99A LYS* 3.8 6.3 - - + +
101A LEU* 1.3 77.1 - - - +
103A HIS* 1.3 57.8 + - - +
105A GLY* 3.1 16.5 + - - +
106A ILE 3.5 8.9 + - - +
108A MET* 6.1 1.6 - - + -
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN* 4.7 24.0 + - + +
12A ASP* 6.1 6.3 - - + -
99A LYS* 2.9 35.6 + - + +
100A HIS* 3.6 7.4 - - - +
101A LEU 3.2 0.2 - - - -
102A ALA* 1.3 76.2 - - - +
104A PHE* 1.3 62.5 + - - +
105A GLY 3.4 0.2 - - - -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN* 4.1 16.2 - - - -
15A VAL* 4.2 12.6 - - + -
17A ILE* 3.9 37.4 - - + +
35A LEU* 3.6 28.0 - - + -
36A ASN 3.4 22.0 - - - -
37A LEU* 4.0 25.4 - - + -
38A THR 5.0 1.8 - - - -
39A ASP 5.2 0.7 - - - -
40A GLY* 3.9 15.0 - - - -
71A VAL* 5.8 1.1 - - + -
100A HIS* 3.0 24.3 + - + -
101A LEU* 2.8 16.7 + - + +
103A HIS* 1.3 83.3 - - - +
105A GLY* 1.3 56.4 + - - +
106A ILE* 3.2 16.7 - - + +
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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