Contacts of the helix formed by residues 117 - 132 (chain P) in PDB entry 6CNF
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 117 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 4.7 5.1 - - - -
86B ASP* 2.8 60.4 + - + +
87B VAL* 5.3 1.1 - - + -
404B ASP* 5.1 11.3 + - - -
111P LYS* 3.3 6.4 - - - +
116P LEU* 1.3 81.5 - - - +
118P GLN* 1.3 65.9 + - - +
119P HIS* 4.0 13.0 - - + +
120P VAL* 3.3 20.5 - - + +
121P VAL* 3.3 16.3 - - - +
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Residues in contact with GLN 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P SER* 5.8 1.6 - - - +
111P LYS* 3.4 20.9 - - + +
117P HIS* 1.3 72.5 - - - +
119P HIS* 1.3 74.9 + - + +
121P VAL* 3.0 8.7 - - + +
122P LEU* 2.9 48.6 + - + +
53Y G 2.7 54.3 + - - +
54Y A 2.9 28.5 + - - -
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Residues in contact with HIS 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU 5.7 0.7 - - - +
408B LYS* 3.4 75.5 + - + +
409B LYS* 5.9 1.1 - - + -
117P HIS* 3.5 8.7 - - + +
118P GLN* 1.3 85.9 + - + +
120P VAL* 1.3 66.3 + - + +
122P LEU* 3.1 11.5 + - + +
123P LYS* 3.0 32.6 + - - +
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Residues in contact with VAL 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 4.0 19.7 - - - +
87B VAL* 4.9 12.3 - - + -
89P GLU* 4.1 13.9 - - - +
116P LEU* 3.4 25.4 - - + -
117P HIS* 3.3 37.2 - - + +
119P HIS* 1.3 75.8 - - + +
121P VAL* 1.3 61.0 + - - +
123P LYS* 3.1 38.5 - - + +
124P CYS* 3.6 10.0 - - - +
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Residues in contact with VAL 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P GLU* 5.0 0.7 - - - +
93P VAL* 5.2 4.5 - - + -
107P SER* 4.0 12.3 - - - +
110P ILE* 5.0 9.2 - - + -
111P LYS* 3.6 33.9 - - + -
114P THR* 4.2 19.5 - - + -
116P LEU* 4.2 8.1 - - + -
117P HIS 3.3 13.9 - - - +
118P GLN* 3.0 19.3 - - + +
120P VAL* 1.3 79.8 - - - +
122P LEU* 1.3 60.9 + - + +
123P LYS 3.2 0.4 - - - -
124P CYS* 3.0 16.0 - - - -
125P LEU* 2.9 34.8 + - + +
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P SER* 5.2 4.9 - - - +
118P GLN* 2.9 57.2 + - + +
119P HIS* 3.7 9.2 - - + +
121P VAL* 1.3 77.4 - - + +
123P LYS* 1.3 58.7 + - - +
125P LEU* 3.2 24.4 + - + +
126P LYS* 2.9 34.8 + - + +
148P TYR* 6.0 0.7 - - - +
54Y A 4.2 16.2 - - - +
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Residues in contact with LYS 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 5.2 9.3 - - - +
407B LEU 5.4 2.2 + - - -
408B LYS 4.9 9.6 + - - -
410B PRO* 5.0 15.2 - - - +
414B MET* 5.8 2.8 - - - +
89P GLU* 5.7 4.9 - - + -
119P HIS* 3.0 22.4 + - - +
120P VAL* 3.1 38.6 - - + +
122P LEU* 1.3 77.9 - - - +
124P CYS* 1.3 58.5 + - + +
126P LYS* 3.1 15.9 + - + +
127P SER* 2.9 25.2 + - - -
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Residues in contact with CYS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P SER* 4.8 1.3 - - - +
89P GLU* 3.9 21.5 - - + -
90P GLU* 4.1 10.5 - - + -
93P VAL* 3.8 34.3 - - + -
120P VAL 3.6 13.2 - - - +
121P VAL* 3.0 26.7 - - - -
123P LYS* 1.3 78.8 - - + +
125P LEU* 1.3 61.1 + - - +
127P SER* 2.8 24.5 + - - +
128P LEU* 2.9 22.8 + - - +
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Residues in contact with LEU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P VAL* 5.1 7.0 - - + -
97P ILE* 4.8 16.2 - - + -
107P SER* 4.6 14.1 - - - +
110P ILE* 6.1 5.6 - - + -
121P VAL* 2.9 24.2 + - + +
122P LEU* 3.3 32.1 - - + +
123P LYS 3.2 0.2 - - - -
124P CYS* 1.3 79.3 - - - +
126P LYS* 1.3 57.0 + - + +
128P LEU* 3.9 5.2 - - + +
129P GLU* 2.9 29.5 + - - +
134P VAL* 4.9 6.1 - - + +
148P TYR* 3.5 46.7 - - + +
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Residues in contact with LYS 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P LEU* 2.9 21.2 + - + +
123P LYS* 3.1 14.3 + - + +
125P LEU* 1.3 76.9 - - + +
127P SER* 1.3 57.9 + - - +
129P GLU* 3.1 21.9 + - - +
130P SER* 2.9 28.2 + - - -
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Residues in contact with SER 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P GLU* 2.2 31.2 + - - -
123P LYS 2.9 11.8 + - - -
124P CYS* 2.8 22.6 + - - +
126P LYS* 1.3 74.6 - - - +
128P LEU* 1.3 59.1 + - - +
130P SER* 2.9 12.9 + - - -
131P GLN* 2.9 26.3 + - - +
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Residues in contact with LEU 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P MET* 3.5 15.5 - - + -
90P GLU* 3.3 28.7 - - + +
93P VAL* 4.2 11.2 - - + -
94P TYR* 3.5 51.8 - - + +
97P ILE* 4.2 10.8 - - + -
124P CYS 2.9 16.0 + - - +
125P LEU* 4.3 4.7 - - + +
127P SER* 1.3 77.6 + - - +
129P GLU* 1.3 60.5 + - - +
131P GLN* 3.0 9.5 + - + +
132P ARG 2.8 24.1 + - - -
133P TYR* 3.9 0.9 + - + -
134P VAL* 3.4 26.2 - - + +
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Residues in contact with GLU 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P LEU 2.9 20.1 + - - +
126P LYS* 3.1 31.6 + - - +
127P SER 3.1 0.2 - - - -
128P LEU* 1.3 76.8 - - - +
130P SER* 1.3 58.8 + - - +
132P ARG* 3.1 22.6 + - - +
134P VAL* 3.9 10.2 - - + +
644R LYS* 4.5 17.0 + - - +
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Residues in contact with SER 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LYS 2.9 11.8 + - - -
127P SER* 2.9 15.3 + - - -
129P GLU* 1.3 73.2 - - - +
131P GLN* 1.3 66.1 + - - +
132P ARG* 3.3 20.4 + - - +
644R LYS* 5.7 2.0 - - - +
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Residues in contact with GLN 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P LYS* 4.2 6.3 + - - +
85P THR* 5.4 11.5 - - - +
86P MET* 3.3 26.8 - - + +
90P GLU* 4.7 1.8 - - - +
127P SER 2.9 17.5 + - - +
128P LEU* 3.0 32.1 + - + +
130P SER* 1.3 80.4 - - - +
132P ARG* 1.3 66.9 + - - +
133P TYR* 3.0 46.5 + - + +
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Residues in contact with ARG 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P LEU 2.8 8.7 + - - -
129P GLU 3.1 17.9 + - - +
130P SER* 3.5 14.6 + - - +
131P GLN* 1.3 77.4 + - - +
133P TYR* 1.3 59.5 + - - +
134P VAL 3.3 8.3 - - - -
151P TYR* 2.4 44.6 - - + +
640R SER* 3.9 11.9 + - - -
641R LYS* 5.2 0.4 - - - +
643R LEU* 4.6 8.3 - - - +
644R LYS* 3.3 63.1 - - - +
647R ALA* 4.8 8.7 - - - +
509S HIS* 5.7 4.9 + - - -
513S MET* 5.1 18.0 - - + +
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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