Contacts of the helix formed by residues 69 - 82 (chain K) 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 69 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927B LYS* 3.7 29.4 + - - +
929B GLU* 4.1 1.6 - - - +
930B ASP* 4.7 3.8 - - - +
69C ARG* 3.2 21.6 + - - +
68K GLU* 1.3 87.4 + - - +
70K HIS* 1.3 104.6 + - - +
71K THR* 3.0 11.0 + - + +
72K LEU 3.4 9.1 + - - -
73K GLY 3.8 4.9 + - - -
93K ILE* 3.2 17.9 - - - +
101K LEU* 4.2 9.8 - - - +
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Residues in contact with HIS 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ARG* 5.2 8.9 + - - -
930B ASP* 4.2 19.2 + - - -
1008B ILE* 3.4 47.2 - - + +
69C ARG* 4.2 12.3 - - - +
69K ASP* 1.3 103.9 + - - +
71K THR* 1.3 64.9 + - - +
72K LEU 3.0 1.8 + - - -
73K GLY 4.0 0.4 - - - +
74K ASN* 3.1 25.9 + - + +
91K TYR* 3.3 35.3 + + - +
92K SER* 5.9 0.9 - - - -
93K ILE* 3.4 25.0 - - + +
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Residues in contact with THR 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B GLU* 3.9 13.2 - - - +
66C ALA* 3.7 25.3 - - - +
69C ARG* 3.3 41.7 - - + +
70C ILE* 4.5 15.3 - - - +
74C GLU* 5.4 6.0 - - + +
321C LEU* 4.1 8.5 - - - +
324C LYS* 3.5 13.1 + - - -
68K GLU* 3.5 14.6 + - - -
69K ASP* 4.0 10.8 + - + +
70K HIS* 1.3 77.0 - - - +
72K LEU* 1.3 63.7 + - - +
74K ASN* 5.3 0.3 - - - +
75K ALA* 4.1 2.4 + - - +
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LEU* 5.4 8.1 - - + +
324C LYS* 4.6 17.0 - - + +
325C ALA* 5.3 5.6 - - + -
328C LEU* 4.3 24.2 - - + -
65K ILE* 4.5 14.6 - - + -
68K GLU* 3.2 37.2 - - + +
69K ASP 3.4 1.0 + - - -
70K HIS 3.1 0.6 - - - -
71K THR* 1.3 81.0 + - - +
73K GLY* 1.3 69.6 + - - +
75K ALA* 2.8 17.1 + - + +
76K LEU* 2.8 29.6 + - + +
101K LEU* 4.8 2.5 - - + -
121K LEU* 5.2 6.7 - - + -
124K LEU* 5.0 14.8 - - + -
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Residues in contact with GLY 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ASP 3.8 5.3 + - - -
70K HIS 3.4 2.8 + - - -
72K LEU* 1.3 80.3 - - - +
74K ASN* 1.3 63.1 + - - +
75K ALA 2.9 1.7 + - - -
76K LEU* 3.0 6.9 + - - -
77K ARG* 2.9 27.4 + - - +
91K TYR* 3.4 22.7 - - - -
101K LEU* 4.1 15.9 - - - +
103K ILE* 5.5 2.9 - - - -
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Residues in contact with ASN 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A GLN* 4.8 3.3 + - - +
1008B ILE 3.3 12.6 + - - +
1009B THR* 2.6 45.1 + - - +
62C SER* 3.2 33.1 + - - +
65C ASN* 4.0 2.6 - - - +
66C ALA* 5.9 0.9 - - + +
69C ARG* 6.6 0.2 - - - -
70K HIS 3.1 16.2 + - - +
71K THR 5.3 0.4 - - - +
73K GLY* 1.3 73.9 - - - +
75K ALA* 1.3 57.8 - - - +
77K ARG* 3.9 19.6 + - - +
78K TYR* 4.1 0.9 - - - +
91K TYR* 3.0 30.0 + - - +
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Residues in contact with ALA 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER* 4.6 2.0 - - - -
63C ILE* 3.8 21.7 - - + +
66C ALA* 4.5 10.7 - - + +
321C LEU* 4.8 6.7 - - + -
71K THR 4.1 11.7 + - - +
72K LEU* 2.8 11.0 + - + +
74K ASN* 1.3 76.3 - - - +
76K LEU* 1.3 58.8 + - - +
77K ARG 3.2 2.0 - - - -
78K TYR* 2.6 32.1 + - - +
79K VAL* 3.3 4.5 + - - +
124K LEU* 3.7 19.9 - - + +
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Residues in contact with LEU 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU* 4.9 4.9 - - + -
65K ILE* 5.1 3.1 - - + -
72K LEU* 2.8 37.4 + - + +
73K GLY* 3.9 4.7 - - - +
75K ALA* 1.3 70.8 - - - +
77K ARG* 1.3 62.4 + - - +
79K VAL* 3.1 4.3 + - - +
80K ILE* 2.9 35.7 + - + +
101K LEU* 6.5 0.4 - - + -
103K ILE* 3.8 24.7 - - + -
117K LEU* 4.1 18.8 - - + +
120K GLY 4.4 2.0 - - - +
121K LEU* 3.7 48.5 - - + +
124K LEU* 3.6 12.9 - - + +
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Residues in contact with ARG 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A ALA* 3.4 43.8 + - - +
575A THR* 5.1 0.2 - - - +
578A GLN* 3.4 26.2 + - - +
62C SER* 4.9 5.5 + - - -
73K GLY 2.9 18.1 + - - +
74K ASN* 3.9 16.8 + - - +
76K LEU* 1.3 76.6 - - - +
78K TYR* 1.3 68.4 + - - +
80K ILE* 3.6 12.7 - - + +
81K MET* 2.8 43.8 + - - +
89K CYS* 3.9 22.1 + - + +
90K GLY* 5.1 1.3 - - - -
91K TYR* 3.5 30.5 - - + -
103K ILE* 5.3 5.5 - - + +
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Residues in contact with TYR 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER* 4.7 9.6 - - - -
19C ASP* 2.4 40.1 + - - -
20C PHE* 6.4 0.2 - - + -
31C TRP* 5.8 2.2 - + - -
60C ASP* 2.9 43.1 + - + +
62C SER* 4.1 17.9 - - - +
63C ILE* 4.6 13.0 - - + -
74K ASN 4.1 1.1 - - - +
75K ALA* 2.6 17.5 + - - +
77K ARG* 1.3 86.2 - - + +
79K VAL* 1.3 67.3 + - + +
81K MET* 4.0 6.9 + - + +
82K LYS* 2.5 39.8 + - + +
127K LEU* 5.2 9.4 - - + -
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Residues in contact with VAL 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 4.8 11.5 - - + -
63C ILE* 5.5 0.7 - - + -
75K ALA 3.3 2.2 + - - +
76K LEU 3.1 7.4 + - - +
78K TYR* 1.3 82.8 - - + +
80K ILE* 1.3 67.6 + - - +
82K LYS* 3.3 21.1 - - - +
83K ASN* 3.8 4.7 + - - +
120K GLY* 3.2 31.5 - - - +
123K ASP* 3.6 20.2 - - + +
124K LEU* 3.8 32.3 - - + -
127K LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K LEU* 2.9 49.5 + - + +
77K ARG* 3.1 8.0 + - - +
79K VAL* 1.3 77.1 - - - +
81K MET* 1.3 56.5 + - - +
83K ASN* 2.8 30.5 + - - +
86K VAL* 3.5 24.5 - - + +
89K CYS* 3.5 24.0 - - + -
103K ILE* 4.2 14.4 - - + -
105K ILE* 4.5 15.9 - - + -
116K ALA* 5.3 4.5 - - + +
117K LEU* 4.7 12.1 - - + -
120K GLY* 4.8 13.5 - - - -
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Residues in contact with MET 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A ARG* 4.6 4.5 - - - +
574A ALA* 3.5 40.8 - - + -
577A THR* 3.7 16.2 - - + -
20C PHE* 4.2 20.0 - - + +
21C PRO 4.2 9.4 - - - +
77K ARG* 2.8 28.9 + - - +
78K TYR* 4.6 5.4 - - + +
79K VAL 3.4 0.2 - - - -
80K ILE* 1.3 73.8 - - - +
82K LYS* 1.3 58.8 + - - +
83K ASN 3.2 6.6 + - - +
86K VAL* 4.2 10.2 - - - +
87K GLU 3.6 18.2 - - - +
89K CYS* 3.3 36.8 - - - +
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Residues in contact with LYS 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASP* 3.4 15.0 + - - -
20C PHE* 4.1 4.9 - - + +
21C PRO* 3.3 25.4 - - + +
29C ASN* 5.0 6.7 + - - -
30C GLU* 3.2 25.2 - - - +
31C TRP* 3.7 46.4 - - + +
78K TYR* 2.5 56.1 + - - +
79K VAL* 3.3 16.4 - - - +
81K MET* 1.3 78.0 - - - +
83K ASN* 1.3 63.3 + - - +
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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
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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