Contacts of the helix formed by residues 98 - 107 (chain A) in PDB entry 6O81
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 LYS 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A SER 3.8 8.7 - - - +
61A LYS 3.5 27.6 + - - -
62A ASP* 3.4 28.3 + - - +
64A PRO* 3.9 22.9 - - + -
96A CYS 3.6 1.8 + - - -
97A TRP* 1.3 100.4 - - + +
99A ALA* 1.3 63.6 + - - +
100A ALA* 3.3 3.6 - - - -
101A GLN* 3.2 26.3 + - + +
102A ILE* 3.3 14.9 + - - +
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Residues in contact with ALA 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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95A CYS* 3.4 43.4 - - - +
96A CYS 3.8 11.3 + - - +
97A TRP 3.2 2.4 - - - -
98A LYS* 1.3 74.4 - - - +
100A ALA* 1.3 61.5 + - - +
102A ILE* 3.5 5.0 + - - +
103A LYS* 2.9 28.8 + - - +
124A THR* 3.7 22.4 + - + +
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Residues in contact with ALA 100 (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 LYS 3.3 1.0 - - - -
99A ALA* 1.3 79.2 - - - +
101A GLN* 1.3 57.6 + - - +
103A LYS* 3.6 9.7 - - + +
104A GLU* 2.9 31.1 + - - +
124A THR* 5.5 0.8 - - - +
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Residues in contact with GLN 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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62A ASP 3.5 17.2 + - - +
63A GLN* 3.6 25.9 - - - +
64A PRO* 3.8 11.5 - - + +
67A LEU* 3.8 13.6 - - + +
98A LYS* 3.2 20.7 + - + +
100A ALA* 1.3 77.0 - - - +
102A ILE* 1.3 59.7 + - - +
104A GLU* 3.3 21.8 + - - +
105A HIS* 2.9 28.6 + - - +
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Residues in contact with ILE 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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49A ALA* 3.7 27.1 - - + +
64A PRO* 3.7 28.0 - - + -
66A VAL* 3.9 7.2 - - + -
67A LEU* 3.8 20.9 - - + -
76A ILE* 4.6 7.0 - - + -
93A VAL* 5.4 0.2 - - + -
95A CYS* 3.7 24.9 - - + -
97A TRP 4.0 9.0 - - - +
98A LYS 3.3 15.8 + - - +
99A ALA* 3.8 5.6 - - - +
101A GLN* 1.3 75.3 - - - +
103A LYS* 1.3 56.8 + - - +
105A HIS* 3.3 1.8 + - + +
106A LEU* 2.9 46.7 + - + +
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Residues in contact with LYS 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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95A CYS* 5.5 0.2 - - - -
99A ALA 2.9 18.2 + - - +
100A ALA* 3.6 9.4 - - - +
102A ILE* 1.3 78.2 - - - +
104A GLU* 1.3 57.8 + - - +
106A LEU* 3.3 8.1 + - - +
107A LEU* 2.9 56.9 + - + +
122A ILE* 3.5 44.8 + - + +
124A THR* 5.1 8.5 + - + +
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Residues in contact with GLU 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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67A LEU* 5.6 0.2 - - - +
100A ALA 2.9 17.8 + - - +
101A GLN* 3.3 31.2 + - - +
103A LYS* 1.3 75.0 - - - +
105A HIS* 1.3 64.5 + - - +
107A LEU* 4.2 10.6 + - - +
108A LYS* 3.4 36.1 + - - +
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Residues in contact with HIS 105 (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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67A LEU* 3.8 34.2 - - + +
74A ALA* 3.5 26.2 - - + +
76A ILE* 4.5 12.4 - - + +
77A ASP* 3.6 25.2 + - - -
101A GLN 2.9 19.4 + - - +
102A ILE* 3.6 4.3 - - + +
103A LYS 3.2 0.2 - - - -
104A GLU* 1.3 82.9 - - - +
106A LEU* 1.3 62.6 + - - +
108A LYS* 3.4 23.4 + - - +
109A SER* 4.1 5.8 + - - -
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Residues in contact with LEU 106 (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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76A ILE* 4.5 23.1 - - + -
77A ASP* 5.5 0.4 - - - +
80A LEU* 5.2 7.6 - - + -
93A VAL* 4.5 23.1 - - + -
95A CYS* 6.0 0.9 - - - -
102A ILE* 2.9 40.7 + - + +
103A LYS* 4.1 5.8 - - - +
105A HIS* 1.3 77.5 - - + +
107A LEU* 1.3 62.6 + - - +
108A LYS 3.3 2.0 - - - -
109A SER* 2.9 29.2 + - - +
111A TRP* 6.5 0.7 - - + -
112A CYS* 3.2 28.5 - - - -
120A VAL* 4.5 9.9 - - + -
122A ILE* 3.8 26.9 - - + -
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Residues in contact with LEU 107 (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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103A LYS* 2.9 51.7 + - + +
104A GLU* 4.8 7.2 - - - +
105A HIS 3.5 0.6 - - - -
106A LEU* 1.3 77.0 - - - +
108A LYS* 1.3 57.9 + - - +
109A SER 3.2 4.7 + - - +
112A CYS* 3.6 34.1 - - + +
122A ILE* 3.9 13.9 - - + -
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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