Contacts of the helix formed by residues 93 - 100 (chain G) in PDB entry 5B31
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 93 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G GLU* 5.4 3.8 - - - +
68G LEU* 3.8 23.1 - - + +
89G ALA 3.5 14.7 + - - +
90G ILE 3.1 4.0 + - - +
92G GLY* 1.3 79.5 - - - +
94G GLU* 1.3 61.0 + - - +
95G GLU* 3.1 9.6 + - - +
96G LEU* 2.8 35.8 + - + +
97G ASP* 2.8 30.5 + - - +
106H LEU* 5.4 1.2 - - - +
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Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ARG* 4.7 12.1 + - - -
92G GLY 4.2 1.6 + - - -
93G ASP* 1.3 73.6 + - - +
95G GLU* 1.3 64.5 + - + +
97G ASP* 3.6 8.5 + - - +
98G SER* 3.3 23.8 + - - -
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G ASP* 3.2 8.8 + - - +
94G GLU* 1.3 81.7 - - + +
96G LEU* 1.3 64.9 + - - +
98G SER* 3.3 4.5 + - - -
99G LEU* 3.1 20.6 + - - +
103H PRO* 2.6 41.7 - - + +
104H GLY* 4.0 1.0 - - - -
105H GLU* 3.1 24.9 + - - +
106H LEU* 2.8 43.6 + - + +
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Residues in contact with LEU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G LEU* 5.2 3.8 - - + -
64G GLU* 4.4 12.8 - - + -
65G VAL* 4.1 32.3 - - + -
68G LEU* 3.4 32.3 - - + -
89G ALA 4.6 2.0 - - - +
90G ILE* 3.8 26.7 - - + +
93G ASP* 2.8 20.4 + - + +
95G GLU* 1.3 74.7 - - - +
97G ASP* 1.3 56.5 + - - +
98G SER 3.2 0.2 + - - -
99G LEU* 3.2 6.8 + - + -
100G ILE* 2.9 44.5 + - + +
65H PHE* 5.6 0.2 - - + -
106H LEU* 4.0 24.0 - - + -
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Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ILE* 3.3 10.9 + - - +
91G ARG* 2.9 61.0 + - - +
93G ASP 2.8 20.2 + - - +
94G GLU* 3.7 9.4 - - - +
96G LEU* 1.3 76.7 - - - +
98G SER* 1.3 63.1 + - - +
100G ILE 3.9 5.5 + - - -
101G LYS* 4.3 4.5 + - - +
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Residues in contact with SER 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G GLU* 3.3 13.0 + - - -
95G GLU* 3.3 8.3 + - - -
96G LEU 3.2 0.6 - - - -
97G ASP* 1.3 81.3 - - - +
99G LEU* 1.3 66.6 + - - +
100G ILE 3.7 0.2 + - - -
101G LYS* 4.5 8.0 + - - +
103H PRO* 3.3 21.1 - - - +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G LEU* 4.3 17.0 - - + -
95G GLU 3.1 13.8 + - - +
96G LEU* 3.7 7.6 - - + +
98G SER* 1.3 84.2 + - - +
100G ILE* 1.3 72.0 - - + +
101G LYS* 3.6 2.4 + - - +
65H PHE* 4.6 2.5 - - + -
69H ILE* 4.1 23.1 - - + -
72H ARG* 3.0 39.0 + - - +
101H LEU* 3.9 14.1 - - + +
102H LEU* 3.6 25.4 - - + -
103H PRO* 4.1 9.6 - - + -
106H LEU* 3.9 20.4 - - + -
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Residues in contact with ILE 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 3.4 37.9 - - + +
65G VAL* 4.4 1.1 - - + -
90G ILE* 3.5 36.8 - - + -
91G ARG* 2.8 30.9 + - - -
96G LEU* 2.9 26.2 + - + +
97G ASP 4.0 1.1 - - - -
98G SER 3.4 0.4 - - - -
99G LEU* 1.3 85.4 - - + +
101G LYS* 1.3 56.2 + - - +
102G ALA* 3.1 5.2 - - + +
104G ILE* 4.8 7.6 - - + -
65H PHE* 3.4 32.5 - - + -
72H ARG* 4.4 3.4 - - - +
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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