Contacts of the helix formed by residues 70 - 83 (chain I) in PDB entry 5BRR
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 GLY 70 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68I ASP 3.5 0.8 + - - -
69I LYS* 1.3 79.5 - - - +
71I MET* 1.3 62.1 + - - +
72I ALA 3.3 2.9 - - - -
73I PRO* 3.3 22.6 - - - +
74I ALA* 3.0 23.4 + - - +
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Residues in contact with MET 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 5.3 17.0 - - + +
11I LEU* 5.5 5.6 - - + -
64I PHE* 3.7 46.0 - - + -
65I LYS 3.7 8.3 - - - +
66I ILE* 3.8 11.7 - - - +
68I ASP* 3.4 36.1 + - + +
69I LYS 2.9 10.6 + - - +
70I GLY* 1.3 78.1 - - - +
72I ALA* 1.3 61.4 + - - +
74I ALA* 3.4 17.5 - - - +
75I LEU* 3.8 8.5 + - - +
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Residues in contact with ALA 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I ILE* 3.6 26.7 + - + +
68I ASP 4.5 0.4 + - - +
71I MET* 1.3 78.2 - - - +
73I PRO* 1.3 78.6 - - + +
74I ALA 3.0 0.9 + - - -
75I LEU* 3.2 12.3 + - - +
76I ARG* 3.3 14.9 + - - +
116I LEU* 3.8 43.1 - - + +
117I PHE* 5.3 1.3 - - + -
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Residues in contact with PRO 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I ASP 5.7 0.2 - - - +
70I GLY* 3.3 27.6 - - - +
71I MET 3.9 0.2 - - - +
72I ALA* 1.3 95.4 - - + +
74I ALA* 1.3 63.9 + - - +
76I ARG* 3.2 21.3 - - - +
77I HIS* 2.6 49.5 + - + +
116I LEU* 5.5 1.8 - - + -
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 3.5 31.0 - - + -
9I ALA* 6.4 0.2 - - + -
70I GLY 3.0 10.8 + - - +
71I MET 3.4 12.8 - - - +
72I ALA 3.0 0.4 + - - -
73I PRO* 1.3 76.3 - - - +
75I LEU* 1.3 62.1 + - + +
77I HIS* 2.9 9.9 + - - +
78I LEU* 2.9 28.3 + - - +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 5.7 7.0 - - + +
9I ALA* 5.8 3.8 - - + -
12I ALA* 5.1 15.7 - - + -
37I TYR* 4.4 10.0 + - + +
40I ALA 5.3 0.4 - - - +
41I SER* 4.8 19.5 - - - +
44I ALA* 3.9 19.5 - - + -
64I PHE* 5.0 9.2 - - + -
66I ILE* 3.7 26.7 - - + -
71I MET 3.8 8.0 + - - +
72I ALA* 3.2 8.2 + - - +
74I ALA* 1.3 80.0 - - + +
76I ARG* 1.3 56.6 + - - +
78I LEU* 2.9 16.5 + - + +
79I TYR* 2.7 36.4 + - - +
117I PHE* 5.0 8.7 - - + -
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Residues in contact with ARG 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ALA* 3.3 7.8 + - - +
73I PRO* 3.2 36.2 - - - +
75I LEU* 1.3 78.2 - - - +
77I HIS* 1.3 74.1 - - + +
79I TYR* 3.1 10.2 + - - +
80I LYS* 2.7 41.2 + - + +
115I ARG 3.7 14.2 + - - -
116I LEU* 3.0 33.3 + - - +
117I PHE* 4.7 11.9 - - + +
118I ARG* 4.8 19.0 - - + +
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Residues in contact with HIS 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I PRO* 2.6 32.5 + - + +
74I ALA* 2.9 10.8 + - - +
76I ARG* 1.3 106.5 - - - +
78I LEU* 1.3 65.4 + - - +
80I LYS* 3.2 24.5 - - + +
81I GLU* 3.4 9.4 + - - +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ALA* 4.2 13.2 - - + -
37I TYR* 4.0 21.1 - - + -
74I ALA 2.9 10.9 + - - +
75I LEU* 3.1 18.8 - - + +
77I HIS* 1.3 75.7 - - - +
79I TYR* 1.3 62.1 + - - +
81I GLU* 2.7 14.9 + - - +
82I LEU* 2.7 40.7 + - + +
364I HIS* 4.4 19.5 - - + +
367I THR* 4.6 11.0 - - + +
369I THR* 3.4 33.0 - - + +
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Residues in contact with TYR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I TYR* 3.6 14.9 + - - +
75I LEU 2.7 15.4 + - - +
76I ARG* 3.3 12.8 - - - +
78I LEU* 1.3 72.8 - - - +
80I LYS* 1.3 67.5 + - + +
82I LEU* 2.9 23.1 + - + +
83I MET* 3.4 45.7 + - + +
93I THR* 3.2 35.6 + - + +
95I ASP* 6.0 2.0 - - - -
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Residues in contact with LYS 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ARG* 2.7 21.9 + - + +
77I HIS* 3.2 24.2 - - + +
79I TYR* 1.3 78.6 - - + +
81I GLU* 1.3 62.4 + - - +
83I MET 3.2 21.6 - - - +
84I GLY 4.0 0.3 + - - -
85I PRO* 5.5 0.9 - - - +
118I ARG* 4.9 14.1 - - - +
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Residues in contact with GLU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I HIS 3.4 8.4 + - - +
78I LEU* 2.7 14.4 + - - +
80I LYS* 1.3 77.0 - - - +
82I LEU* 1.3 66.3 + - + +
83I MET 2.9 1.4 + - - -
84I GLY* 3.8 5.5 + - - -
85I PRO* 4.3 2.8 - - - +
86I TRP* 2.4 48.8 + - - -
232I THR* 4.5 5.7 - - - +
364I HIS* 3.6 33.2 + - + +
366I PRO* 4.7 6.9 - - - +
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Residues in contact with LEU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I TYR* 4.3 15.0 - - + +
78I LEU* 2.7 52.0 - - + +
79I TYR* 2.9 16.4 + - + +
81I GLU* 1.3 78.5 - - + +
83I MET* 1.3 65.7 + - + +
84I GLY* 3.9 0.2 - - - -
86I TRP* 4.3 11.4 - - + -
87I ASN* 2.9 28.4 + - - +
91I ILE* 3.8 20.0 - - + +
93I THR* 6.1 4.3 - - + -
169I LEU* 6.5 1.3 - - + -
233I LEU* 6.1 0.9 - - + -
364I HIS* 5.5 7.6 - - + -
371I LEU* 3.5 40.8 - - + -
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Residues in contact with MET 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I TYR* 3.4 45.6 + - + +
80I LYS* 3.2 16.6 - - - +
81I GLU 3.0 0.2 - - - -
82I LEU* 1.3 85.0 - - + +
84I GLY* 1.3 52.3 + - - +
87I ASN* 4.0 5.2 - - - +
91I ILE* 4.1 9.9 - - - -
92I SER* 4.0 9.9 - - - -
93I THR* 3.9 28.5 - - + +
143I HIS 5.7 0.9 - - - +
145I LYS* 4.4 17.3 - - - +
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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