Contacts of the helix formed by residues 79 - 88 (chain B) in PDB entry 1G13
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR* 3.8 10.0 - - + +
101A TYR* 5.2 1.4 + - - -
117A PRO* 5.1 0.5 - - - +
118A LYS* 3.4 51.8 + - + +
119A SER* 4.5 0.9 - - - -
120A GLU* 3.0 28.0 + - - -
47B SER* 5.5 4.1 + - - +
48B PRO* 3.9 29.3 - - + +
49B LEU 3.6 4.9 - - - +
77B PHE 3.3 0.2 - - - -
78B GLU* 1.3 90.7 + - + +
80B PHE* 1.3 60.5 + - - +
81B CYS* 3.2 3.1 - - + -
82B ASP* 2.9 23.1 + - + +
83B VAL* 3.1 14.8 + - - +
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Residues in contact with PHE 80 (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* 2.7 34.1 + - + +
51B VAL* 3.5 33.7 - - + -
77B PHE* 3.9 30.4 + + + +
78B GLU 3.8 0.4 - - - -
79B HIS* 1.3 74.2 - - - +
81B CYS* 1.3 60.5 + - - +
83B VAL* 3.1 21.5 + - + +
84B LEU* 3.0 57.8 + - + +
109B PHE* 5.9 1.1 - + - -
143B LEU* 5.7 0.2 - - + -
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Residues in contact with CYS 81 (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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46B SER 4.1 0.7 - - - -
47B SER* 3.5 33.4 - - - +
49B LEU* 3.7 21.2 + - - +
79B HIS* 3.2 1.5 - - + -
80B PHE* 1.3 77.9 - - - +
82B ASP* 1.3 58.0 + - - +
84B LEU* 3.3 5.8 + - - +
85B ASP* 3.0 34.6 + - - +
107B CYS* 2.0 56.8 + - + -
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 4.6 1.4 + - - -
117A PRO* 3.2 11.1 - - + +
118A LYS* 2.7 61.2 + - + +
79B HIS* 2.9 13.7 + - + +
81B CYS* 1.3 77.5 - - - +
83B VAL* 1.3 60.1 + - - +
85B ASP* 3.2 13.4 + - - +
86B MSE 2.9 50.9 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.9 18.2 - - + +
117A PRO* 3.7 29.2 - - + -
71B TYR* 4.2 16.2 - - + -
77B PHE* 4.2 12.3 - - + -
79B HIS 3.1 12.0 + - - +
80B PHE* 3.1 29.8 + - + +
82B ASP* 1.3 76.5 - - - +
84B LEU* 1.3 58.1 + - + +
86B MSE 3.4 1.7 + - + +
87B LEU* 3.0 48.2 + - + +
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Residues in contact with LEU 84 (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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80B PHE* 3.0 51.5 + - + +
81B CYS 3.7 5.4 - - - +
82B ASP 3.2 0.2 - - - -
83B VAL* 1.3 75.6 - - + +
85B ASP* 1.3 66.1 + - - +
87B LEU* 4.8 6.7 - - + -
88B ILE* 3.0 39.2 + - + +
105B CYS* 3.6 26.2 - - + +
106B HIS* 3.7 10.1 + - + -
107B CYS* 4.6 5.6 - - - -
109B PHE* 3.8 29.4 - - + -
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Residues in contact with ASP 85 (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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81B CYS* 3.0 22.1 + - - +
82B ASP* 3.2 18.9 + - - +
84B LEU* 1.3 78.7 - - - +
86B MSE 1.3 60.7 + - - +
88B ILE 3.2 18.1 - - - +
89B PRO* 3.5 7.8 - - - +
90B THR* 5.9 3.1 - - - +
106B HIS* 3.1 30.0 - - - +
107B CYS 5.3 1.0 + - - +
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Residues in contact with MSE 86 (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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19A SER* 4.7 7.9 - - - +
36A SER* 3.6 15.9 - - - +
37A VAL 4.3 7.4 - - - +
38A MSE 4.4 14.6 - - - -
115A SER* 4.3 26.2 - - - -
116A LEU 3.5 20.6 - - - +
117A PRO* 3.9 14.1 - - + -
71B TYR* 5.9 1.6 - - - +
82B ASP* 2.9 45.5 + - - +
83B VAL* 3.7 4.9 - - - +
85B ASP* 1.3 78.3 - - - +
87B LEU* 1.3 66.8 + - + +
88B ILE 3.1 1.0 + - - -
89B PRO* 3.5 14.0 - - - +
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Residues in contact with LEU 87 (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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71B TYR* 4.6 27.6 - - + +
83B VAL* 3.0 37.1 + - + +
84B LEU* 4.3 7.2 - - + +
86B MSE 1.3 78.0 - - + +
88B ILE* 1.3 70.1 + - + +
89B PRO* 3.8 3.9 - - - +
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Residues in contact with ILE 88 (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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84B LEU* 3.0 24.5 + - + +
85B ASP* 3.2 8.2 - - - +
86B MSE 3.1 0.4 - - - -
87B LEU* 1.3 90.4 - - + +
89B PRO* 1.3 73.3 - - - +
92B GLU* 4.4 10.8 - - - +
93B PRO 4.3 17.5 - - - +
95B PRO* 4.1 28.5 - - + -
105B CYS* 4.2 23.6 - - + +
106B HIS* 2.8 32.1 + - + +
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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