Contacts of the helix formed by residues 90 - 97 (chain M) in PDB entry 5GSE
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 ASP 90 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61M GLU* 4.7 6.4 - - - +
65M LEU* 4.0 24.2 - - + +
86M ALA 3.6 15.6 + - - +
87M ILE 3.0 5.5 + - - +
89M ASN* 1.3 78.4 - - - +
91M GLU* 1.3 60.8 + - - +
92M GLU* 3.2 11.6 + - - +
93M LEU* 2.9 39.6 + - + +
94M ASN* 2.8 30.6 + - - +
106N LEU* 5.1 1.1 - - - +
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Residues in contact with GLU 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M ASN 4.1 2.4 + - - -
90M ASP* 1.3 72.6 + - - +
92M GLU* 1.3 64.8 + - + +
94M ASN* 3.7 6.5 - - - +
95M LYS* 2.9 70.6 + - + +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90M ASP* 3.2 8.4 + - - +
91M GLU* 1.3 84.0 - - + +
93M LEU* 1.3 57.4 + - - +
95M LYS* 3.2 18.7 + - - +
96M LEU* 2.9 24.6 + - - +
103N PRO* 2.7 46.1 - - + +
104N GLY* 3.5 2.9 - - - -
105N GLU* 3.0 27.6 + - + -
106N LEU* 3.8 27.1 + - + +
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Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M LEU* 5.4 2.5 - - + -
61M GLU* 4.0 14.8 - - + -
62M ILE* 3.6 33.4 - - + -
65M LEU* 3.9 26.0 - - + -
86M ALA 5.2 0.2 - - - -
87M ILE* 4.2 24.7 - - + +
90M ASP* 2.9 24.2 + - + +
92M GLU* 1.3 73.3 - - - +
94M ASN* 1.3 53.5 + - - +
96M LEU* 3.1 12.9 + - + +
97M LEU* 2.6 41.6 + - + +
106N LEU* 3.5 31.4 - - + -
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Residues in contact with ASN 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ILE 3.4 11.8 + - - +
88M ARG* 3.3 45.6 + - - +
90M ASP 2.8 25.2 + - - +
91M GLU* 3.8 6.4 - - - +
93M LEU* 1.3 72.7 - - - +
95M LYS* 1.3 57.1 + - + +
98M GLY* 3.1 24.6 + - - -
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Residues in contact with LYS 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K ARG* 5.7 9.4 - - - -
91M GLU* 2.9 56.0 + - + +
92M GLU* 3.4 17.2 + - - +
94M ASN* 1.3 75.4 - - - +
96M LEU* 1.3 66.1 + - - +
98M GLY* 3.2 12.1 + - - -
103N PRO* 4.3 21.0 - - + +
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M LEU* 4.3 21.3 - - + -
92M GLU 2.9 13.4 + - - +
93M LEU* 3.5 13.7 - - + +
95M LYS* 1.3 76.9 - - - +
97M LEU* 1.3 63.9 + - + +
98M GLY 3.6 1.6 + - - -
100M VAL* 5.0 0.9 - - - +
65N PHE* 4.5 16.4 - - + -
69N ILE* 4.7 5.8 - - + -
72N ARG* 2.9 46.5 + - - +
101N LEU* 4.2 15.9 - - + +
102N LEU* 4.0 21.8 - - + -
103N PRO* 4.1 11.8 - - + +
106N LEU* 4.2 18.2 - - + -
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Residues in contact with LEU 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M ILE* 4.2 8.3 - - + -
87M ILE* 4.1 30.3 - - + -
88M ARG* 2.6 32.5 + - - +
93M LEU* 2.6 20.6 + - + +
94M ASN 3.5 3.8 - - - -
96M LEU* 1.3 83.5 - - + +
98M GLY* 1.3 58.5 + - - +
99M ARG 3.5 1.3 - - - -
100M VAL* 3.3 29.6 - - + +
102M ILE* 5.4 1.8 - - + -
65N PHE* 4.1 24.0 - - + -
68N ASP* 4.6 0.9 - - - +
69N ILE* 4.2 9.2 - - + -
72N ARG* 4.8 0.7 - - - +
98P TYR* 3.5 33.9 - - + +
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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