Contacts of the helix formed by residues 91 - 100 (chain B) in PDB entry 2AXZ
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 LEU 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B LEU* 5.9 0.9 - - + -
84B LYS* 3.7 35.7 - - + -
85B ILE* 3.5 10.8 - - + +
88B ASN* 2.9 27.5 + - + +
90B ASP* 1.3 82.9 - - + +
92B PHE* 1.3 63.0 + - - +
94B LYS* 4.7 6.2 - - + +
95B ASN* 2.5 41.8 + - - +
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Residues in contact with PHE 92 (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 ILE* 3.9 12.2 - - + +
89B PRO* 3.0 17.7 + - + +
90B ASP 3.3 0.4 - - - -
91B LEU* 1.3 74.6 - - - +
93B ASP* 1.3 85.6 + - - +
95B ASN* 2.9 5.9 + - - +
96B PHE* 2.9 54.2 + + + -
116B TYR* 3.4 48.0 - + + -
119B ILE* 4.1 14.8 - - + -
120B ALA* 3.7 18.8 - - + -
125B ILE* 3.7 41.1 - - + -
126B GLU 5.0 0.7 - - - -
127B VAL* 4.2 7.4 - - + -
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Residues in contact with ASP 93 (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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89B PRO 4.7 2.5 - - - +
90B ASP* 3.8 18.1 - - - +
92B PHE* 1.3 87.6 - - - +
94B LYS* 1.3 68.2 + - + +
96B PHE* 3.8 2.0 - - - +
97B GLN* 2.8 40.9 + - - +
125B ILE* 5.0 7.2 - - - +
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Residues in contact with LYS 94 (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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90B ASP 5.5 0.6 + - - -
91B LEU* 4.3 8.4 + - + +
92B PHE 3.0 2.2 + - - -
93B ASP* 1.3 81.8 - - + +
95B ASN* 1.3 66.7 + - - +
97B GLN* 3.5 19.0 + - - +
98B ARG* 3.6 10.6 + - - +
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Residues in contact with ASN 95 (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 LEU* 4.1 12.5 - - - +
85B ILE* 3.4 16.9 - - + +
91B LEU* 2.5 39.4 + - - +
92B PHE 2.9 5.0 + - - +
94B LYS* 1.3 73.6 - - - +
96B PHE* 1.3 66.3 + - - +
98B ARG* 2.9 42.5 + - - +
99B ILE* 3.0 10.9 + - - +
116B TYR* 3.7 18.8 - - + +
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Residues in contact with PHE 96 (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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92B PHE* 2.9 53.8 + + + +
93B ASP* 3.8 3.8 - - - +
95B ASN* 1.3 68.1 - - - +
97B GLN* 1.3 59.3 + - + +
98B ARG 2.8 14.8 + - - -
99B ILE* 3.0 2.7 + - - +
100B GLU* 2.8 57.5 + - + +
113B TYR* 3.8 28.3 - + - -
116B TYR* 3.6 27.7 - + + -
117B ILE* 4.2 9.0 - - + -
127B VAL* 4.2 22.2 - - + -
129B THR* 4.4 13.9 - - + -
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Residues in contact with GLN 97 (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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93B ASP* 2.8 36.9 + - - +
94B LYS* 3.6 13.5 - - - +
96B PHE* 1.3 82.5 - - + +
98B ARG* 1.3 56.6 + - - +
100B GLU* 4.8 2.0 - - - -
101B PRO* 3.2 20.9 - - - +
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Residues in contact with ARG 98 (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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78B GLU* 2.5 46.0 + - - -
81B LEU* 5.3 3.8 - - - +
94B LYS 3.6 5.6 + - - +
95B ASN* 2.9 36.9 + - - +
96B PHE 2.8 1.8 + - - -
97B GLN* 1.3 79.6 - - - +
99B ILE* 1.3 70.2 + - - +
101B PRO* 3.2 14.0 - - - +
102B LYS* 3.4 23.6 - - + +
109B TYR* 5.6 1.0 + - - -
116B TYR* 4.3 8.1 + - - -
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Residues in contact with ILE 99 (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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78B GLU* 3.6 29.4 - - - +
95B ASN 3.0 8.9 + - - +
96B PHE* 3.0 5.8 + - + +
98B ARG* 1.3 86.1 - - - +
100B GLU* 1.3 68.0 + - - +
102B LYS* 2.7 23.7 + - + +
103B ARG* 3.3 4.1 + - - -
109B TYR* 3.8 27.8 - - + +
112B ILE* 3.9 22.2 - - + -
113B TYR* 4.1 22.4 - - + +
116B TYR* 3.5 29.4 - - + +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 2.8 56.6 + - + +
97B GLN* 4.8 2.2 - - - -
99B ILE* 1.3 72.6 - - - +
101B PRO* 1.3 71.2 - - + +
103B ARG* 3.3 41.9 + - - +
113B TYR* 3.9 17.6 - - + -
129B THR* 3.8 23.2 + - + +
133B THR* 5.6 0.2 - - - +
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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