Contacts of the helix formed by residues 86 - 103 (chain E) in PDB entry 6N0M
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 HIS 86 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E MET 3.0 13.0 + - - +
84E GLY 3.1 0.4 - - - -
85E LEU* 1.3 85.1 + - + +
87E PRO* 1.3 55.3 - - - +
88E ASP 3.3 2.9 - - - -
89E TYR* 3.0 16.8 + - + -
90E PHE 2.6 31.9 + - - -
373E LEU* 3.6 13.8 - - + +
375E TYR* 3.3 38.6 + + - +
450E SER* 2.8 38.2 + - - -
453E VAL* 3.8 23.8 - - + -
454E HIS* 3.8 23.5 + + + -
457E LEU* 4.4 5.8 - - + -
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Residues in contact with PRO 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG* 4.5 20.6 - - + +
66E GLY* 3.7 27.1 - - - +
67E LEU* 3.7 23.1 - - + +
84E GLY 3.6 3.8 - - - +
85E LEU 3.4 9.2 - - - +
86E HIS* 1.3 88.5 - - - +
88E ASP* 1.3 62.7 + - - +
90E PHE* 3.1 1.3 + - + +
91E THR* 3.0 37.7 + - + +
375E TYR* 3.7 8.7 - - + +
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Residues in contact with ASP 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E HIS 3.3 0.6 - - - -
87E PRO* 1.3 82.3 - - - +
89E TYR* 1.3 59.3 + - - +
91E THR* 3.5 14.7 + - - -
92E SER* 4.2 2.3 + - - -
369E ALA* 4.0 18.5 - - + +
373E LEU* 4.5 13.5 - - + -
375E TYR* 4.1 20.1 + - - -
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Residues in contact with TYR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E MET* 3.6 32.1 - - + +
86E HIS* 3.0 20.7 + - + +
88E ASP* 1.3 76.6 - - - +
90E PHE* 1.3 59.6 + - - +
92E SER* 3.1 4.5 + - - -
93E PHE* 2.9 37.7 + - + +
207E LEU* 5.9 0.2 - - - +
366E LYS* 3.6 24.2 - - + +
369E ALA* 4.9 3.4 - - + -
370E ALA* 3.9 32.1 - - + -
373E LEU* 4.4 9.0 - - + +
457E LEU* 3.4 36.6 - - + -
460E LEU* 3.6 12.3 - - - +
461E GLU* 2.4 34.9 + - + +
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Residues in contact with PHE 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 4.2 18.8 - - + -
70E LEU* 3.7 28.7 - - + -
76E VAL* 5.9 0.4 - - + -
80E ALA* 3.4 28.9 - - + -
83E MET* 3.6 26.5 - - + +
84E GLY* 3.6 9.6 - - - -
86E HIS 2.6 17.4 + - - +
87E PRO* 3.1 14.3 + - + +
89E TYR* 1.3 72.5 - - - +
91E THR* 1.3 61.0 + - + +
93E PHE* 3.6 8.9 - + - +
94E TRP* 2.8 67.2 + + + +
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Residues in contact with THR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 6.3 2.2 - - + -
87E PRO* 3.0 18.7 + - + +
88E ASP* 3.5 14.8 + - - -
90E PHE* 1.3 84.6 - - + +
92E SER* 1.3 60.7 + - - +
94E TRP* 3.5 4.9 + - - +
95E ARG* 3.0 51.0 + - - +
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Residues in contact with SER 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ASP 4.4 2.1 + - - -
89E TYR* 3.1 7.7 + - - -
91E THR* 1.3 79.1 + - - +
93E PHE* 1.3 66.9 + - - +
95E ARG* 3.4 21.2 + - - +
96E LEU* 3.4 10.2 + - - +
362E LEU* 4.9 2.6 - - - +
365E GLU* 3.6 27.5 + - - +
366E LYS* 3.8 31.0 + - - +
369E ALA* 3.8 14.4 - - - +
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Residues in contact with PHE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ASP* 6.1 0.2 - - - -
79E LEU* 3.8 22.2 - - + -
80E ALA* 4.5 10.5 - - + -
83E MET* 3.5 45.8 - - + -
89E TYR* 2.9 36.8 + + + +
90E PHE* 3.6 9.4 - + - +
92E SER* 1.3 74.8 - - - +
94E TRP* 1.3 80.1 + + - +
96E LEU* 3.4 3.1 + - - +
97E HIS* 2.9 53.7 + + + +
203E HIS* 4.4 11.8 - + - -
207E LEU* 4.2 13.0 - - + -
366E LYS* 3.9 10.7 - - + +
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Residues in contact with TRP 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E VAL* 4.6 17.9 - - + -
77E ASP* 5.3 1.8 - - - -
80E ALA* 4.2 20.4 - - + -
90E PHE* 2.8 52.1 + + + +
91E THR* 3.8 5.2 - - - +
93E PHE* 1.3 84.1 - + - +
95E ARG* 1.3 59.0 + - + +
97E HIS* 4.3 24.2 - + - -
98E TYR* 2.9 56.3 + + + +
102E HIS* 6.3 2.0 - + - -
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Residues in contact with ARG 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E THR* 3.0 49.3 + - - +
92E SER* 3.4 14.7 + - - +
93E PHE 3.3 0.4 - - - -
94E TRP* 1.3 79.4 - - + +
96E LEU* 1.3 57.3 + - - +
98E TYR* 3.8 5.2 - - - +
99E LEU* 3.2 25.6 + - - +
362E LEU* 3.5 33.5 - - + +
365E GLU* 4.3 12.8 + - - -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E SER 3.4 8.7 + - - +
93E PHE 3.4 5.9 + - - +
94E TRP 3.2 0.2 - - - -
95E ARG* 1.3 77.0 - - - +
97E HIS* 1.3 66.0 + - - +
99E LEU* 3.0 20.0 + - + +
100E LEU* 2.9 46.5 + - + +
199E VAL* 4.4 10.1 - - + -
203E HIS* 3.7 22.7 - - + +
359E GLY* 4.7 6.7 - - - +
362E LEU* 4.0 21.5 - - + +
363E LEU* 4.2 14.1 - - + -
366E LYS* 3.3 32.8 - - - +
464E MET* 5.1 0.9 - - + -
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Residues in contact with HIS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ASP* 5.2 11.6 + - - -
93E PHE* 2.9 43.4 + + + +
94E TRP* 3.9 30.4 - + - +
96E LEU* 1.3 77.4 - - - +
98E TYR* 1.3 64.0 + - - +
100E LEU* 3.5 0.4 + - - -
101E LEU* 3.3 45.9 + - + +
102E HIS* 3.5 28.9 + + - -
132E HIS* 5.1 4.0 - - - -
135E GLU* 5.4 2.5 + - - -
203E HIS* 4.1 19.2 + - - +
207E LEU* 4.9 6.3 - - + -
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Residues in contact with TYR 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E TRP* 2.9 45.5 + + + +
95E ARG* 3.8 5.6 - - - +
97E HIS* 1.3 78.8 + - - +
99E LEU* 1.3 63.1 + - - +
102E HIS* 3.0 52.6 + + + -
103E THR* 3.1 36.8 + - + -
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ARG 3.2 12.9 + - - +
96E LEU* 3.0 16.7 + - + +
98E TYR* 1.3 80.1 - - - +
100E LEU* 1.3 64.7 + - - +
103E THR* 3.3 40.2 - - + +
104E ASP 4.6 6.2 - - - +
196E GLN* 5.5 2.0 + - - +
356E TYR* 3.5 19.7 + - + +
358E GLU* 3.2 31.6 - - + +
359E GLY* 3.4 33.2 - - - -
362E LEU* 3.5 17.9 - - + -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 2.9 41.0 + - + +
97E HIS 4.2 0.7 - - - +
99E LEU* 1.3 76.2 - - + +
101E LEU* 1.3 65.5 + - + +
112E ARG* 2.6 40.5 + - - +
196E GLN* 4.8 5.3 + - + +
199E VAL* 3.8 23.8 - - + -
200E LEU* 4.1 23.6 - - + -
203E HIS* 3.5 41.3 - - + -
356E TYR* 3.5 22.9 - - + +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E HIS* 3.3 37.8 + - + +
100E LEU* 1.3 83.2 - - + +
102E HIS* 1.3 77.0 + - + +
103E THR 3.9 0.7 - - - -
109E SER* 3.5 12.0 + - - -
112E ARG* 4.0 13.0 - - + +
113E HIS* 3.5 42.3 + - + +
116E ALA* 4.5 1.8 - - + -
132E HIS* 3.5 28.7 - - + +
200E LEU* 3.5 27.1 - - + -
203E HIS* 4.7 12.6 - - + -
204E CYS* 5.5 1.1 - - - -
207E LEU* 6.0 0.7 - - + -
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Residues in contact with HIS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E TRP* 6.4 2.2 - + - -
97E HIS* 3.5 36.0 + + - -
98E TYR* 3.0 41.3 + + + +
101E LEU* 1.3 100.8 + - + +
103E THR* 1.3 60.8 + - - +
109E SER* 5.4 0.2 - - - -
112E ARG* 4.6 2.5 - - - +
113E HIS* 5.1 0.7 - + - -
135E GLU* 3.4 26.6 + - - -
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Residues in contact with THR 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TYR* 3.1 37.9 + - + -
99E LEU* 3.3 33.5 + - + +
101E LEU 3.9 0.4 - - - -
102E HIS* 1.3 73.8 - - - +
104E ASP* 1.3 80.6 + - - +
105E GLY* 4.7 0.2 - - - -
112E ARG* 3.2 21.9 + - - +
196E GLN* 5.6 0.5 + - - -
358E GLU* 4.7 8.3 - - - +
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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
------------------------------------------------------------
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