Contacts of the helix formed by residues 75 - 90 (chain K) in PDB entry 6NRB
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 PRO 75 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I MET* 6.0 3.4 - - - -
25K GLY* 3.2 29.4 - - - +
26K ASN* 4.7 7.6 - - - +
28K ASN* 6.2 0.4 - - + -
29K ALA* 3.9 10.3 - - + +
73K GLN* 2.8 23.8 - - + +
74K HIS* 1.4 116.2 - - + +
76K ALA* 1.3 52.9 + - - +
77K ALA 2.6 5.0 + - - -
78K LYS* 2.5 32.2 + - - +
79K SER* 4.4 2.2 - - - -
516K LEU* 6.2 0.2 - - - -
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Residues in contact with ALA 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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25K GLY 4.5 0.2 + - - -
26K ASN* 3.7 9.8 - - - +
29K ALA* 4.1 1.0 - - - +
30K ALA* 3.6 27.4 - - + +
33K ILE* 4.6 0.7 - - - -
75K PRO* 1.3 74.9 - - - +
77K ALA* 1.3 58.2 + - - +
78K LYS 3.0 0.7 - - - -
79K SER* 3.3 13.0 - - - +
80K MET* 2.3 44.0 + - + +
516K LEU* 3.6 29.1 - - + +
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Residues in contact with ALA 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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29K ALA* 3.3 24.2 - - + +
33K ILE* 3.7 17.5 - - + +
67K LEU* 4.0 9.8 - - + +
71K GLN 5.7 0.2 - - - +
72K VAL* 3.4 10.8 - - + +
73K GLN* 3.4 30.7 - - + +
75K PRO 2.6 4.9 + - - -
76K ALA* 1.3 72.9 - - - +
78K LYS* 1.3 59.1 + - - +
81K ILE* 3.3 24.1 + - - +
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Residues in contact with LYS 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ILE 3.0 27.0 + - - -
50I GLY* 4.1 11.8 - - - +
52I VAL* 3.8 35.5 - - + +
72K VAL* 3.7 11.4 - - + -
73K GLN 3.0 9.2 + - - +
74K HIS* 3.6 25.3 + - - +
75K PRO 2.5 16.6 + - - +
77K ALA* 1.3 71.5 - - - +
79K SER* 1.3 59.0 + - - +
81K ILE* 3.5 8.0 + - - +
82K GLU* 3.1 48.1 + - + +
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Residues in contact with SER 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I MET* 4.4 19.4 - - - +
74K HIS 5.1 1.2 + - - -
75K PRO 4.7 1.9 + - - -
76K ALA* 2.8 23.6 + - - +
78K LYS* 1.3 73.3 - - - +
80K MET* 1.3 58.3 + - - +
81K ILE 3.1 2.5 - - - -
82K GLU* 2.8 21.9 + - - +
83K ILE* 2.7 36.6 + - - +
512K THR* 4.6 14.6 - - - -
515K LEU* 5.9 0.6 - - - +
516K LEU* 4.5 5.2 - - - +
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Residues in contact with MET 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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30K ALA* 3.5 32.1 - - + -
33K ILE* 3.9 15.3 - - + -
64K ASN* 3.4 3.2 + - - -
76K ALA* 2.3 46.2 + - + +
79K SER 1.3 66.7 - - - -
81K ILE* 1.3 56.1 + - - +
83K ILE* 4.0 9.4 - - - -
84K SER* 2.9 29.3 + - - -
99K ILE* 3.2 24.6 - - + +
102K ALA* 3.5 34.1 - - + -
103K GLY* 3.8 4.0 - - - +
106K LEU* 5.6 1.8 - - + -
512K THR* 3.6 25.4 - - + -
516K LEU* 3.9 6.1 - - + -
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Residues in contact with ILE 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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64K ASN* 3.2 25.6 - - + +
67K LEU* 3.6 24.9 - - + -
68K ARG* 4.4 13.9 - - + +
72K VAL* 4.1 15.3 - - + -
77K ALA 3.3 19.4 + - - +
78K LYS* 3.5 8.7 + - - +
79K SER 3.1 0.2 - - - -
80K MET* 1.3 75.6 - - - +
82K GLU* 1.3 56.0 + - + +
84K SER* 3.1 2.8 + - - -
85K ARG* 2.5 68.9 + - + +
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Residues in contact with GLU 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I VAL* 5.5 3.3 - - - +
78K LYS* 3.1 39.5 + - + +
79K SER* 2.8 27.6 + - - +
81K ILE* 1.3 73.3 - - + +
83K ILE* 1.3 52.1 + - + +
85K ARG* 2.9 11.4 + - - +
86K THR* 2.6 36.6 + - - -
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Residues in contact with ILE 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K SER* 2.7 22.6 + - - +
80K MET* 4.0 17.9 - - - +
82K GLU* 1.3 74.5 - - + +
84K SER* 1.3 52.7 + - - +
86K THR* 3.1 23.1 - - + +
87K GLN* 2.7 31.0 + - - +
98K VAL* 3.9 15.0 - - + -
508K THR* 3.1 35.9 - - + +
511K GLU* 4.6 8.1 - - + -
512K THR* 3.0 29.6 - - + +
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Residues in contact with SER 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K ASN* 3.4 16.8 - - - -
80K MET 2.9 22.6 + - - -
81K ILE 3.1 2.3 + - - -
83K ILE* 1.3 78.6 - - - +
85K ARG* 1.3 54.4 + - - +
87K GLN* 2.8 7.2 + - - -
88K ASP* 2.3 33.4 + - - -
95K THR* 3.1 29.2 + - - +
98K VAL* 3.8 5.7 - - - +
99K ILE* 3.0 21.3 + - - +
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ASP* 4.2 5.0 + - - -
64K ASN* 3.2 42.5 + - - +
68K ARG* 3.1 52.0 - - - +
81K ILE* 2.5 40.4 + - + +
82K GLU* 3.2 10.1 - - - +
84K SER* 1.3 72.6 - - - +
86K THR* 1.3 53.6 + - - +
88K ASP* 3.4 22.2 + - - +
89K GLU* 2.7 46.9 + - + +
95K THR* 5.4 2.6 - - - -
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Residues in contact with THR 86 (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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82K GLU 2.6 20.2 + - - -
83K ILE* 3.1 32.9 - - + +
85K ARG* 1.3 73.9 - - - +
87K GLN* 1.3 57.6 + - - +
89K GLU* 3.5 16.9 + - - +
90K GLU* 3.3 36.3 + - + +
508K THR* 4.2 7.0 - - + -
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Residues in contact with GLN 87 (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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83K ILE 2.7 17.6 + - - +
84K SER* 2.8 13.4 + - - +
86K THR* 1.3 72.9 - - - +
88K ASP* 1.3 61.7 + - - +
89K GLU 3.6 0.3 + - - -
90K GLU* 3.7 7.2 + - - +
91K VAL* 3.2 21.0 + - - +
92K GLY 3.6 13.2 + - - -
93K ASP 3.2 28.7 + - - +
94K GLY 3.6 0.2 - - - -
95K THR* 3.5 10.3 - - + +
98K VAL* 3.2 21.3 - - + +
504K GLN* 3.2 27.9 - - - +
505K THR* 3.9 8.0 - - - +
508K THR* 2.5 32.3 + - - +
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Residues in contact with ASP 88 (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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84K SER 2.3 27.5 + - - +
85K ARG* 3.0 28.2 + - - +
87K GLN* 1.3 70.6 - - - +
89K GLU* 1.3 64.5 + - + +
92K GLY* 3.4 21.7 - - - -
95K THR* 3.4 14.9 - - + +
389K ARG* 4.2 13.0 + - - -
392K GLN* 4.8 7.1 + - - -
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Residues in contact with GLU 89 (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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85K ARG* 2.7 26.1 + - + +
86K THR* 3.9 13.4 + - - +
87K GLN 3.3 0.2 - - - -
88K ASP* 1.3 80.7 - - + +
90K GLU* 1.3 67.4 + - + +
92K GLY 4.8 0.2 + - - -
195K ILE* 5.8 5.4 - - - +
196K LYS* 5.8 4.3 - - - +
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Residues in contact with GLU 90 (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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86K THR* 3.3 34.3 + - + +
87K GLN* 3.7 3.9 + - - +
88K ASP 3.4 0.6 - - - -
89K GLU* 1.3 85.6 - - + +
91K VAL* 1.3 72.0 + - + +
195K ILE* 5.4 10.0 - - - +
196K LYS* 5.9 2.3 - - - -
399K ARG* 5.3 9.2 + - - -
504K GLN* 2.8 32.4 - - + +
507K LYS* 4.2 9.4 + - - -
508K THR* 4.3 8.8 - - - +
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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
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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