Contacts of the helix formed by residues 74 - 94 (chain R) in PDB entry 6CNC
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 GLU 74 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 6.1 3.4 - - + -
294A TRP* 4.2 17.5 - - - -
72R ALA 3.9 4.9 + - - +
73R LEU* 1.3 96.3 - - - +
75R SER* 1.3 67.2 + - - +
76R ARG* 4.4 5.6 + - + +
77R GLU* 3.6 40.6 + - + +
78R ALA* 3.0 27.7 + - - +
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Residues in contact with SER 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R GLU* 1.3 75.3 + - - +
76R ARG* 1.3 65.2 + - - +
78R ALA* 4.0 3.1 - - - +
79R THR* 3.2 26.7 + - - +
27X T 3.1 46.3 + - - +
28X T 3.3 32.2 - - - +
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Residues in contact with ARG 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R GLU* 3.3 6.3 + - + +
75R SER* 1.3 77.9 - - - +
77R GLU* 1.3 67.5 + - + +
79R THR* 2.4 26.1 + - - -
80R LEU* 2.9 18.2 + - + +
112R LEU* 5.0 17.2 - - + +
27X T 3.2 29.1 + - - +
28X T 4.5 13.3 + - - -
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Residues in contact with GLU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.3 18.8 - - - +
72R ALA 3.8 21.0 + - - +
74R GLU* 3.6 33.0 + - + +
75R SER 3.5 0.2 - - - -
76R ARG* 1.3 77.4 - - + +
78R ALA* 1.3 63.7 + - - +
80R LEU* 3.0 18.0 + - + +
81R ASN* 2.9 29.7 + - - +
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Residues in contact with ALA 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R LEU* 5.9 5.2 - - + -
74R GLU 3.0 22.7 + - - +
75R SER* 4.0 4.0 - - - +
77R GLU* 1.3 76.4 - - - +
79R THR* 1.3 63.9 + - + +
81R ASN* 2.9 15.1 + - - +
82R ASN* 2.9 21.4 + - - +
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Residues in contact with THR 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R SER 3.2 13.3 + - - +
76R ARG* 2.4 32.4 + - - -
78R ALA* 1.3 75.9 - - + +
80R LEU* 1.3 59.5 + - - +
82R ASN* 3.4 9.5 + - - +
83R ALA* 2.9 28.8 + - - +
108R TYR* 4.8 5.7 + - - -
112R LEU* 4.8 9.0 - - - +
26X T 4.4 32.5 - - - +
27X T 3.6 25.4 + - + +
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Residues in contact with LEU 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R ARG* 2.9 24.5 + - + +
77R GLU* 3.0 21.5 + - + +
79R THR* 1.3 77.7 - - - +
81R ASN* 1.3 59.8 + - - +
83R ALA* 3.2 3.0 + - - +
84R ARG* 2.9 30.5 + - - +
105R PHE* 3.4 21.7 - - + -
108R TYR* 4.2 24.5 - - + -
109R LYS* 4.8 25.4 - - + -
112R LEU* 4.5 14.4 - - + -
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Residues in contact with ASN 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ALA 5.6 4.4 + - - -
77R GLU* 2.9 19.2 + - - +
78R ALA* 2.9 14.0 + - - +
80R LEU* 1.3 77.6 - - - +
82R ASN* 1.3 63.1 + - - +
84R ARG* 2.9 45.0 + - - +
85R ARG* 2.9 19.8 + - - +
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Residues in contact with ASN 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R ALA 2.9 11.1 + - - +
79R THR* 3.6 11.9 - - - +
81R ASN* 1.3 76.3 - - - +
83R ALA* 1.3 57.0 + - - +
85R ARG* 2.8 26.9 + - - +
86R LYS* 2.9 44.7 + - - +
26X T 4.5 13.7 + - - -
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Residues in contact with ALA 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R THR 2.9 11.4 + - - +
80R LEU 3.2 9.2 + - - +
82R ASN* 1.3 74.5 - - - +
84R ARG* 1.3 57.7 + - - +
86R LYS* 3.8 4.8 - - - +
87R LEU* 2.8 31.8 + - - +
105R PHE* 4.2 7.4 - - + -
108R TYR* 3.4 44.9 - - + +
126R ILE* 4.2 7.6 - - + +
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Residues in contact with ARG 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R LEU 2.9 10.5 + - - +
81R ASN* 2.9 52.3 + - - +
83R ALA* 1.3 76.0 - - - +
85R ARG* 1.3 56.1 + - - +
87R LEU* 3.2 6.5 - - + +
88R ARG* 2.8 63.8 + - + +
102R ASP* 6.0 1.8 - - - +
105R PHE* 3.3 34.5 - - + -
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Residues in contact with ARG 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R ASN 2.9 10.2 + - - +
82R ASN* 2.8 25.8 + - - +
84R ARG* 1.3 69.4 - - - +
86R LYS* 1.3 74.6 + - + +
87R LEU 2.9 1.5 + - - -
88R ARG* 3.9 7.0 - - - +
89R ALA* 2.9 27.0 + - + +
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Residues in contact with LYS 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LYS* 4.2 26.5 - - - +
82R ASN* 2.9 42.3 + - - +
83R ALA* 4.3 4.5 - - - +
85R ARG* 1.3 85.9 - - + +
87R LEU* 1.3 62.0 + - - +
89R ALA* 3.7 7.1 - - + +
90R VAL* 3.4 23.0 + - - +
122R SER* 6.2 3.6 - - - -
126R ILE* 4.3 19.8 - - + +
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Residues in contact with LEU 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ALA 2.8 20.3 + - - +
84R ARG* 3.2 6.1 - - + +
85R ARG 2.9 1.2 - - - -
86R LYS* 1.3 77.0 - - - +
88R ARG* 1.3 62.7 + - + +
89R ALA 3.1 0.3 + - - -
90R VAL* 3.3 5.1 - - - +
91R SER* 2.3 32.1 + - - +
101R THR* 3.6 20.4 - - - +
102R ASP* 4.7 4.0 - - - +
104R ALA* 4.9 1.8 - - + -
105R PHE* 3.2 46.2 - - + +
126R ILE* 3.7 23.8 - - + +
130R LEU* 3.9 30.3 - - + +
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Residues in contact with ARG 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R ARG* 2.8 45.6 + - + +
85R ARG* 3.9 6.1 - - - +
87R LEU* 1.3 74.2 - - + +
89R ALA* 1.3 66.2 + - - +
91R SER* 2.9 22.4 + - - -
92R TYR* 3.4 17.9 - - + -
101R THR* 5.6 2.2 - - - -
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Residues in contact with ALA 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 3.6 37.7 - - + +
85R ARG* 2.9 20.8 + - + +
86R LYS* 3.7 9.9 - - + +
87R LEU 3.1 0.2 - - - -
88R ARG* 1.3 80.7 - - - +
90R VAL* 1.3 60.6 + - - +
91R SER 2.9 2.9 + - - -
92R TYR* 3.9 8.1 - - - -
93R ALA* 3.9 7.1 + - - +
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Residues in contact with VAL 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 4.2 6.2 - - + +
86R LYS 3.4 12.1 + - - +
87R LEU* 3.3 16.4 + - - +
89R ALA* 1.3 77.0 - - + +
91R SER* 1.3 64.6 + - - +
93R ALA* 3.8 13.1 + - - +
94R LEU* 3.9 11.8 + - + +
126R ILE* 4.6 12.8 - - + +
127R ALA* 6.4 0.2 - - - -
130R LEU* 3.6 26.7 - - + +
146R PHE* 4.5 15.9 - - + +
149R ARG* 4.7 22.9 - - + -
150R LEU* 6.5 0.7 - - + -
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Residues in contact with SER 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R LEU* 2.3 31.8 + - - +
88R ARG* 2.9 17.4 + - - -
89R ALA 2.9 0.2 + - - -
90R VAL* 1.3 81.7 - - - +
92R TYR* 1.3 65.4 + - - -
93R ALA 3.1 0.2 + - - -
94R LEU 3.3 6.9 + - - -
96R ILE* 3.1 30.4 - - - +
101R THR* 3.0 34.1 - - - +
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Residues in contact with TYR 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B ASN 3.2 21.8 - - - -
424B VAL 2.2 25.5 + - - -
425B HIS* 3.4 2.9 - - - -
426B SER* 2.8 22.5 + - - -
427B ASN* 3.0 35.6 + - + +
428B ASN* 4.6 3.6 + - - -
88R ARG* 3.4 23.3 - - + -
89R ALA* 3.9 4.5 - - - -
91R SER* 1.3 77.6 - - - +
93R ALA* 1.3 62.3 + - - +
94R LEU 3.1 0.2 - - - -
95R HIS* 2.6 39.9 + - + +
96R ILE 4.4 6.9 + - - +
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Residues in contact with ALA 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ASN* 4.4 7.9 - - - +
424B VAL* 3.7 31.6 - - + +
89R ALA 3.9 4.8 + - - +
90R VAL* 3.8 11.9 + - - +
91R SER 3.1 0.6 - - - -
92R TYR* 1.3 88.7 - - - +
94R LEU* 1.3 55.9 + - - +
95R HIS* 3.5 11.8 + - - -
149R ARG* 2.3 43.6 + - - +
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Residues in contact with LEU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R VAL* 4.1 15.9 - - + +
91R SER 3.3 3.0 + - - +
92R TYR 3.1 0.6 - - - -
93R ALA* 1.3 75.2 - - - +
95R HIS* 1.3 73.8 + - - +
96R ILE* 3.7 17.7 - - + -
130R LEU* 5.1 0.7 - - + -
140R HIS* 6.1 0.3 - - - -
141R HIS* 3.2 22.4 + - + -
145R ASP* 4.6 24.5 - - - +
146R PHE* 3.4 44.4 - - + +
149R ARG* 3.5 32.8 - - + +
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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
------------------------------------------------------------
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