Contacts of the helix formed by residues 84 - 91 (chain B) in PDB entry 2AX1
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 SER 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B LEU 3.8 1.4 + - - -
83B LEU* 1.3 77.1 - - - +
85B VAL* 1.3 66.0 + - - +
86B GLU* 3.7 16.9 + - - +
87B GLU* 3.2 34.7 + - - +
88B ALA* 3.0 21.3 + - - +
173B MET* 4.0 1.1 - - - -
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Residues in contact with VAL 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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84B SER* 1.3 73.3 - - - +
86B GLU* 1.3 72.1 + - - +
88B ALA* 3.4 2.0 + - - +
89B CYS* 2.8 50.6 + - - -
111B LEU* 5.3 0.2 - - + -
116B VAL* 4.5 15.9 - - + -
119B ILE* 4.0 24.2 - - + -
120B HIS* 3.8 31.6 - - + +
169B VAL* 5.0 0.2 - - + -
173B MET* 3.7 25.7 - - + -
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Residues in contact with GLU 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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84B SER* 3.1 18.5 + - - +
85B VAL* 1.3 90.2 + - - +
87B GLU* 1.3 64.3 + - + +
89B CYS* 3.3 3.3 + - - +
90B LYS* 3.1 30.7 + - + +
111B LEU* 3.8 34.4 - - + +
116B VAL* 5.3 6.8 - - - +
120B HIS* 5.8 1.4 - - - -
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Residues in contact with GLU 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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82B LEU 4.5 1.9 - - - +
83B LEU* 3.7 25.3 - - + +
84B SER* 3.2 34.7 + - - +
86B GLU* 1.3 76.5 - - + +
88B ALA* 1.3 62.3 + - - +
90B LYS* 3.4 15.5 + - - +
91B LEU* 3.4 17.9 + - + +
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Residues in contact with ALA 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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83B LEU* 4.2 6.9 - - + +
84B SER 3.0 8.8 + - - +
85B VAL 3.7 1.1 - - - +
87B GLU* 1.3 77.0 - - - +
89B CYS* 1.3 63.2 + - - +
91B LEU* 3.0 18.6 + - - +
92B THR* 3.5 4.4 + - - -
169B VAL* 3.6 21.1 - - + +
172B LYS* 3.4 24.1 - - + +
173B MET* 3.5 33.7 - - + +
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Residues in contact with CYS 89 (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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85B VAL* 2.8 41.2 + - - +
86B GLU 3.3 5.4 + - - +
88B ALA* 1.3 76.5 - - - +
90B LYS* 1.3 62.5 + - + +
92B THR* 3.1 20.8 + - - -
108B VAL* 3.2 46.2 - - - +
109B ARG* 3.9 8.7 - - - +
111B LEU* 3.6 17.5 - - + -
116B VAL* 5.1 2.5 - - - -
119B ILE* 3.8 13.2 - - - -
169B VAL* 4.4 2.5 - - - -
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Residues in contact with LYS 90 (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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86B GLU* 3.1 17.9 + - - +
87B GLU* 3.7 9.6 - - - +
88B ALA 3.3 0.2 - - - -
89B CYS* 1.3 75.9 - - + +
91B LEU* 1.3 58.6 + - + +
92B THR 3.1 0.7 - - - -
109B ARG* 2.8 61.7 + - - +
110B ASN* 5.3 0.4 - - - +
111B LEU* 4.3 22.7 - - - +
561B TYR* 3.9 8.8 - - - +
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Residues in contact with LEU 91 (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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83B LEU* 3.5 32.5 - - + -
87B GLU* 3.4 9.8 + - + +
88B ALA 3.0 10.8 + - - +
90B LYS* 1.3 76.6 - - + +
92B THR* 1.3 58.7 + - - +
93B PRO* 3.5 3.1 - - - +
172B LYS* 3.7 14.4 - - + -
176B TYR* 3.7 35.2 - - + +
559B ASP 3.5 5.5 - - - +
560B ILE* 3.7 4.8 - - + -
561B TYR 2.9 42.0 + - - +
562B HIS* 3.8 19.3 - - + -
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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