Contacts of the helix formed by residues 86 - 103 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C MET 2.9 11.3 + - - +
85C LEU* 1.3 85.6 + - + +
87C PRO* 1.3 54.3 - - - -
88C ASP 3.2 2.9 - - - -
89C TYR* 2.7 28.6 + - + +
90C PHE 2.7 12.8 + - - -
373C LEU* 4.1 6.4 - - + +
375C TYR* 2.7 38.9 + + - +
450C SER* 3.0 43.6 + - - -
451C GLU* 5.3 0.2 - - - -
453C VAL* 3.7 24.3 - - + +
454C HIS* 3.6 17.4 + - + -
457C LEU* 3.7 28.0 - - + -
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Residues in contact with PRO 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY* 3.8 19.7 - - - +
67C LEU* 3.9 22.2 - - + +
84C GLY 3.5 11.4 - - - +
85C LEU 3.4 9.0 - - - +
86C HIS* 1.3 88.1 - - - +
88C ASP* 1.3 57.6 + - - +
90C PHE* 3.5 12.5 - - + +
91C THR* 2.9 38.4 + - + +
375C TYR* 4.4 4.5 - - - +
329D ARG* 4.2 21.3 - - - +
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Residues in contact with ASP 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS 3.0 1.4 + - - -
87C PRO* 1.3 78.5 - - - +
89C TYR* 1.3 58.2 + - - +
91C THR* 3.1 22.3 + - - +
92C SER* 4.2 1.4 + - - -
369C ALA* 3.9 17.2 - - + +
373C LEU* 4.0 18.8 - - + +
375C TYR* 5.3 2.6 + - + -
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C MET* 3.6 32.5 - - + +
86C HIS* 2.7 16.0 + - + +
88C ASP* 1.3 71.3 - - - +
90C PHE* 1.3 55.0 + - - +
92C SER* 2.8 27.7 + - - -
93C PHE* 2.9 18.9 + - + +
366C LYS* 3.3 43.8 + - + +
369C ALA* 4.6 5.4 - - + -
370C ALA* 4.1 21.3 - - + -
373C LEU* 4.2 10.5 - - + +
457C LEU* 3.5 43.7 - - + -
460C LEU* 3.6 15.9 - - + +
461C GLU* 3.4 24.9 - - + +
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.6 20.0 - - + -
70C LEU* 3.9 23.3 - - + -
76C VAL* 6.0 2.2 - - + -
80C ALA* 3.4 28.9 - - + -
83C MET* 3.6 18.1 + - + +
84C GLY* 3.5 22.4 - - - -
86C HIS 2.7 8.7 + - - -
87C PRO* 3.5 18.2 - - + +
89C TYR* 1.3 73.0 - - - +
91C THR* 1.3 60.5 + - + +
93C PHE* 3.5 10.7 - + - +
94C TRP* 2.7 64.8 + + + +
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Residues in contact with THR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 6.4 0.7 - - + -
87C PRO* 2.9 23.6 + - + +
88C ASP* 3.1 23.3 + - - +
90C PHE* 1.3 82.1 - - + +
92C SER* 1.3 69.8 + - - +
94C TRP* 3.3 4.1 + - - +
95C ARG* 3.1 46.6 + - - +
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ASP 4.4 0.2 + - - -
89C TYR* 2.8 13.8 + - - -
91C THR* 1.3 77.8 + - - +
93C PHE* 1.3 65.8 + - - +
95C ARG* 3.6 13.8 + - - +
96C LEU* 3.6 15.8 + - - +
362C LEU* 4.8 5.8 - - - +
365C GLU* 3.7 23.3 + - - +
366C LYS* 3.6 35.2 - - - +
369C ALA* 3.8 13.5 - - - +
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Residues in contact with PHE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 3.7 21.1 - - + -
80C ALA* 4.3 11.7 - - + -
83C MET* 3.7 43.3 - - + -
89C TYR* 2.9 30.2 + + + +
90C PHE* 3.5 16.4 - + - +
92C SER* 1.3 78.7 - - - +
94C TRP* 1.3 84.1 + + - +
96C LEU* 3.4 3.6 + - - +
97C HIS* 3.1 44.0 + + - +
203C HIS* 4.4 9.6 - + - -
207C LEU* 4.0 18.2 - - + -
366C LYS* 4.0 11.9 - - - +
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Residues in contact with TRP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.3 20.0 - - + -
80C ALA* 4.1 22.2 - - + -
90C PHE* 2.7 48.9 + + + +
91C THR* 3.7 4.7 - - - +
93C PHE* 1.3 86.5 - + - +
95C ARG* 1.3 68.5 + - + +
97C HIS* 2.9 19.0 + + + +
98C TYR* 2.9 51.8 + + + +
102C HIS* 6.2 2.0 - + - -
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C THR* 3.1 51.8 + - - +
92C SER* 3.7 13.8 + - - +
93C PHE 3.4 0.6 - - - -
94C TRP* 1.3 81.2 - - + +
96C LEU* 1.3 57.6 + - - +
98C TYR* 3.7 5.2 + - - +
99C LEU* 3.0 27.7 + - - +
362C LEU* 3.3 35.8 - - + +
365C GLU* 4.8 11.1 + - - -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C SER 3.6 8.5 + - - +
93C PHE 3.4 7.1 + - - +
94C TRP 3.1 0.6 - - - -
95C ARG* 1.3 76.1 - - - +
97C HIS* 1.3 56.4 + - - +
99C LEU* 3.0 19.6 + - + +
100C LEU* 2.7 69.3 + - + +
199C VAL* 4.6 3.1 - - + -
203C HIS* 4.0 9.4 - - + +
359C GLY* 4.6 3.4 - - - +
362C LEU* 4.4 19.4 - - + +
363C LEU* 4.0 26.2 - - + -
366C LYS* 3.5 35.0 - - - +
464C MET* 4.5 2.5 - - + -
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 5.3 6.6 + - - -
79C LEU* 5.6 2.9 - - + -
93C PHE* 3.1 34.7 + + + +
94C TRP* 2.9 30.6 + + + +
96C LEU* 1.3 74.6 - - - +
98C TYR* 1.3 56.4 + - - +
100C LEU* 5.0 0.4 - - - -
101C LEU* 3.1 60.2 + - + +
102C HIS* 3.4 17.5 + + - -
128C LEU* 5.9 2.2 - - + -
132C HIS* 5.0 5.8 - + - -
135C GLU* 5.2 6.1 + - - -
203C HIS* 3.7 17.3 + - - -
207C LEU* 4.4 14.6 - - + -
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Residues in contact with TYR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP* 2.9 41.8 + + + +
95C ARG* 3.9 5.4 - - - +
97C HIS* 1.3 75.5 - - - +
99C LEU* 1.3 63.2 + - - +
102C HIS* 3.0 48.1 + + + -
103C THR* 2.9 24.5 + - - -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG 3.0 17.1 + - - +
96C LEU* 3.0 17.2 + - + +
98C TYR* 1.3 79.5 - - - +
100C LEU* 1.3 68.2 + - - +
101C LEU 3.1 0.3 + - - -
103C THR* 3.4 39.8 + - + +
104C ASP 5.3 2.5 - - - +
112C ARG* 4.9 0.2 - - - -
356C TYR* 3.4 25.2 + - + +
358C GLU* 3.7 33.0 - - + +
359C GLY* 3.6 30.5 - - - +
362C LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 2.7 49.3 + - + +
97C HIS 4.4 0.2 - - - +
99C LEU* 1.3 74.1 - - + +
101C LEU* 1.3 63.6 + - + +
112C ARG* 2.6 40.1 + - - +
196C GLN* 4.7 4.5 - - + +
199C VAL* 3.9 26.7 - - + +
200C LEU* 4.1 20.4 - - + +
203C HIS* 3.5 36.1 - - + -
356C TYR* 3.6 23.6 - - + +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C HIS* 3.1 51.8 + - + +
100C LEU* 1.3 82.6 - - + +
102C HIS* 1.3 85.5 + - + +
109C SER* 3.6 9.7 + - - -
112C ARG* 3.8 9.4 - - + +
113C HIS* 3.6 28.2 + - + +
116C ALA* 4.4 5.8 - - + -
132C HIS* 3.7 28.9 - - + +
200C LEU* 3.8 23.8 - - + -
203C HIS* 4.5 14.6 - - + -
204C CYS* 5.3 0.9 - - - -
207C LEU* 5.8 0.2 - - + -
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Residues in contact with HIS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP* 6.2 2.2 - + - -
97C HIS* 3.4 31.4 + + - -
98C TYR* 3.0 44.3 + + + +
101C LEU* 1.3 103.7 + - + +
103C THR* 1.3 64.5 + - - +
109C SER* 5.3 0.7 - - - -
112C ARG* 4.2 2.2 - - - +
113C HIS* 4.4 3.7 + + - -
135C GLU* 3.5 27.5 + - - -
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Residues in contact with THR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TYR* 2.9 26.7 + - - -
99C LEU* 3.4 33.0 + - + +
102C HIS* 1.3 76.3 + - - +
104C ASP* 1.3 80.7 + - + +
105C GLY* 4.4 0.2 - - - -
112C ARG* 3.1 24.5 + - - +
196C GLN* 5.6 0.2 + - - -
358C GLU* 5.2 6.5 - - - +
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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