Contacts of the helix formed by residues 98 - 107 (chain R) in PDB entry 5IYB
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 THR 98 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97R LEU* 1.3 81.5 - - - +
99R LEU* 1.3 65.4 + - - +
100R ASP* 3.6 10.3 + - - +
101R GLU* 3.0 34.7 + - - +
102R ILE* 3.0 26.1 + - - +
120R MET* 5.6 4.5 - - - -
135R GLY 3.5 25.4 - - - +
136R LYS* 4.2 7.2 - - + +
137R TYR* 5.3 3.4 - - - -
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R ILE* 5.4 9.4 - - + -
98R THR* 1.3 73.2 - - - +
100R ASP* 1.3 58.7 + - - +
102R ILE* 3.0 12.6 + - + +
103R LEU* 2.9 41.8 + - + +
116R LYS* 3.6 37.5 - - + +
119R LEU* 4.2 9.4 - - + -
120R MET* 3.5 50.4 - - + +
124R LEU* 3.6 28.5 - - + -
137R TYR* 4.8 7.7 - - + -
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Residues in contact with ASP 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R THR* 3.2 9.3 + - - +
99R LEU* 1.3 80.5 - - - +
101R GLU* 1.3 61.7 + - + +
103R LEU* 3.5 2.4 + - - +
104R ASP* 3.1 23.6 + - - +
109R LEU* 3.5 13.2 - - - +
116R LYS* 2.7 35.7 + - - +
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Residues in contact with GLU 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R HIS* 6.1 1.3 - - - -
96R PRO 4.5 1.6 - - - +
97R LEU* 3.2 21.0 - - + +
98R THR* 3.0 42.3 + - - +
100R ASP* 1.3 78.7 - - + +
102R ILE* 1.3 57.7 + - + +
104R ASP* 3.5 8.9 - - - +
105R GLU* 3.0 31.9 + - - +
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Residues in contact with ILE 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R ILE* 4.1 46.0 - - + -
84R TYR* 4.7 16.2 - - + -
85R MET* 5.3 10.5 - - + -
97R LEU* 3.7 31.9 - - + -
98R THR 3.0 13.8 + - - +
99R LEU* 3.0 13.6 + - + +
101R GLU* 1.3 72.4 - - - +
103R LEU* 1.3 56.3 + - + +
105R GLU* 3.8 6.0 - - - +
106R THR* 2.6 51.4 + - + +
124R LEU* 5.9 3.6 - - + -
137R TYR* 5.8 5.6 - - + -
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Residues in contact with LEU 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77R VAL* 5.3 3.4 - - + -
81R ILE* 5.1 14.4 - - + -
99R LEU* 2.9 39.9 + - + +
100R ASP 3.7 4.0 - - - +
102R ILE* 1.3 76.0 - - + +
104R ASP* 1.3 51.9 + - - +
106R THR* 3.1 4.6 + - - +
107R GLN 2.6 29.8 + - - -
108R HIS* 2.7 38.9 + - + +
109R LEU* 3.8 26.5 - - + -
111R ILE* 4.2 15.0 - - + -
116R LYS* 3.6 29.8 - - + -
119R LEU* 6.2 2.2 - - + -
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Residues in contact with ASP 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R ASP 3.1 15.6 + - - +
101R GLU* 3.5 9.5 - - - +
103R LEU* 1.3 77.8 - - - +
105R GLU* 1.3 61.7 + - - +
107R GLN* 2.8 28.3 + - - +
109R LEU* 5.0 8.4 - - + +
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R TYR* 3.1 13.4 + - + +
88R ARG* 2.4 40.9 + - - -
95R HIS* 5.6 1.6 + - - -
97R LEU* 5.0 10.7 - - - +
101R GLU* 3.0 21.4 + - - +
102R ILE* 4.0 6.3 - - - +
104R ASP* 1.3 77.2 - - - +
106R THR* 1.3 59.9 + - + +
107R GLN* 3.3 6.2 - - - +
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Residues in contact with THR 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R ILE* 5.8 4.0 - - + +
84R TYR* 4.2 28.9 - - + -
102R ILE* 2.6 36.4 + - + +
103R LEU* 3.1 10.9 + - - +
105R GLU* 1.3 77.3 - - - +
107R GLN* 1.3 69.9 + - - +
108R HIS* 3.3 14.1 + - - +
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Residues in contact with GLN 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R LEU 2.6 12.0 + - - -
104R ASP* 2.8 17.9 + - - +
105R GLU 4.3 5.8 - - - +
106R THR* 1.3 78.0 - - - +
108R HIS* 1.3 55.3 + - - +
109R LEU* 3.6 3.9 + - - -
110R ASP* 4.3 5.0 - - - +
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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