Contacts of the helix formed by residues 89 - 101 (chain O) in PDB entry 6CNB
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 89 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60O ARG* 4.4 7.9 - - - +
86O MET* 3.2 29.1 - - + +
87O ASP 2.8 12.9 + - - +
88O VAL* 1.3 93.5 - - - +
90O SER* 1.3 61.9 + - - +
91O VAL 4.1 0.4 - - - +
92O LYS* 3.6 2.4 + - - +
93O THR* 2.8 35.6 + - - -
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Residues in contact with SER 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ARG* 3.4 43.3 - - - +
83O ILE* 5.9 1.0 - - - +
85O GLY* 2.8 28.2 + - - -
86O MET 3.9 0.8 + - - -
89O ASP* 1.3 75.4 - - - +
91O VAL* 1.3 72.3 + - - +
93O THR* 2.9 2.7 + - - -
94O THR* 2.3 50.6 + - - +
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Residues in contact with VAL 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O VAL* 6.2 0.9 - - + -
76O VAL* 3.9 30.7 - - + +
79O LEU* 3.7 34.1 - - + -
80O VAL* 3.7 29.4 - - + -
83O ILE* 5.7 3.6 - - + -
85O GLY* 5.4 1.1 - - - +
87O ASP* 5.3 0.7 - - - +
88O VAL* 4.5 10.8 - - - +
89O ASP 3.5 0.8 - - - +
90O SER* 1.3 86.3 + - - +
92O LYS* 1.3 57.5 + - + +
94O THR* 3.5 5.8 + - - -
95O LEU* 2.5 48.3 + - + +
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Residues in contact with LYS 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O VAL* 4.8 19.7 - - + +
88O VAL* 3.2 44.9 - - + +
89O ASP 3.6 6.4 + - - +
90O SER 3.2 0.2 - - - -
91O VAL* 1.3 81.3 - - - +
93O THR* 1.3 68.5 + - - +
95O LEU* 4.7 3.4 - - + -
96O VAL* 3.1 31.0 + - + +
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Residues in contact with THR 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ARG* 5.4 6.0 + - - +
89O ASP 2.8 27.7 + - - -
90O SER* 2.9 5.5 + - - -
92O LYS* 1.3 72.5 - - - +
94O THR* 1.3 64.8 + - + +
96O VAL* 3.3 6.0 - - - +
97O SER* 2.5 39.3 + - - +
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Residues in contact with THR 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ARG* 3.7 39.0 - - + -
61O ALA* 3.7 25.3 - - + +
64O VAL* 4.4 15.7 - - - +
90O SER* 2.3 44.6 + - - +
91O VAL* 3.5 5.2 + - - -
93O THR* 1.3 71.8 - - + +
95O LEU* 1.3 57.4 + - - +
97O SER* 3.3 8.0 - - - -
98O LEU* 2.9 35.1 + - - +
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Residues in contact with LEU 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O VAL* 5.5 9.9 - - + -
68O LEU* 6.2 1.1 - - + -
76O VAL* 4.6 3.8 - - + -
79O LEU* 5.7 5.2 - - + -
91O VAL* 2.5 40.6 + - + +
92O LYS* 3.9 2.9 - - + +
94O THR* 1.3 77.9 + - - +
96O VAL* 1.3 66.1 + - + +
98O LEU* 3.0 14.6 + - + +
99O THR* 2.9 23.5 + - - +
104O VAL* 4.3 20.0 - - + -
120O TYR* 3.4 61.0 - - + +
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Residues in contact with VAL 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O LYS* 3.1 29.1 + - + +
93O THR* 3.3 7.9 - - - +
95O LEU* 1.3 80.9 - - + +
97O SER* 1.3 66.8 + - - +
99O THR* 2.9 12.4 + - - +
100O GLN* 2.9 29.0 + - + +
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Residues in contact with SER 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O ALA* 6.4 1.3 - - - -
93O THR* 2.5 34.3 + - - +
94O THR* 3.3 9.1 - - - -
96O VAL* 1.3 80.5 - - - +
98O LEU* 1.3 64.1 + - - +
100O GLN* 3.3 12.7 + - - +
101O LEU* 3.3 11.6 + - - +
70Q PHE* 3.4 40.7 - - - -
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Residues in contact with LEU 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O VAL* 4.5 2.2 - - + -
57O LEU* 3.8 28.9 - - + -
61O ALA* 4.4 5.8 - - + +
64O VAL* 4.1 17.7 - - + -
65O ILE* 3.7 39.3 - - + -
94O THR* 2.9 20.5 + - - +
95O LEU* 3.2 13.0 - - + +
97O SER* 1.3 75.5 - - - +
99O THR* 1.3 52.4 + - - +
101O LEU* 2.9 7.1 + - - +
102O ARG 2.6 30.5 + - - -
103O CYS* 2.9 19.6 + - + -
104O VAL* 3.7 22.7 - - + -
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Residues in contact with THR 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O LEU* 2.9 17.3 + - - +
96O VAL* 2.9 15.4 + - - +
98O LEU* 1.3 74.8 - - - +
100O GLN* 1.3 65.1 + - - +
102O ARG* 2.8 23.0 + - - +
104O VAL* 3.3 19.9 - - + +
106O TYR* 5.5 6.9 - - + +
120O TYR* 5.4 3.3 - - - -
208O TYR* 3.3 33.0 + - + +
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Residues in contact with GLN 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O VAL* 2.9 20.5 + - + +
97O SER* 3.5 11.2 - - - +
98O LEU 3.2 0.2 - - - -
99O THR* 1.3 81.5 - - - +
101O LEU* 1.3 59.1 + - - +
102O ARG* 3.5 2.3 + - - +
166O LEU* 4.1 14.5 + - + +
167O GLY* 3.3 23.6 - - - -
168O SER 4.3 2.3 + - - -
70Q PHE* 4.4 17.3 - - + -
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Residues in contact with LEU 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O HIS* 5.3 4.9 - - + +
57O LEU* 4.3 27.1 - - + -
97O SER 3.3 7.4 + - - +
98O LEU* 2.9 9.4 + - + +
100O GLN* 1.3 75.9 - - - +
102O ARG* 1.3 77.0 + - - +
103O CYS* 3.5 23.7 - - - -
126O GLY 5.1 2.4 - - - +
129O ILE* 5.1 4.6 - - + +
130O LEU* 3.8 25.9 - - + +
164O ILE* 3.5 28.5 - - + +
165O SER* 4.3 10.1 - - - +
166O LEU 4.5 3.1 + - - +
167O GLY* 5.0 1.8 - - - -
61Q PHE* 6.1 1.3 - - + -
65Q VAL* 5.8 3.4 - - + -
70Q PHE* 5.9 2.9 - - + -
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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