Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 2BBV
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 GLN 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LEU 4.1 1.0 + - - -
60A SER* 1.3 77.8 - - - +
62A PRO* 1.3 95.8 - - + +
64A LEU* 3.0 15.7 + - - +
65A ALA* 3.3 12.0 + - - +
82A LYS* 4.4 12.1 + - - +
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER* 3.3 10.8 - - - +
61A GLN* 1.3 119.8 - - + +
63A GLY* 1.3 59.2 + - - +
65A ALA* 3.6 3.2 + - + +
66A PHE* 3.2 21.7 + - - +
82A LYS* 4.0 28.5 - - + +
83A GLY 4.5 4.5 - - - +
85A PRO* 4.7 4.8 - - + +
337A PRO* 3.7 29.4 - - + -
338A PRO* 5.1 9.9 - - + +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.8 2.0 - - - -
60A SER* 2.8 14.5 + - - -
62A PRO* 1.3 78.6 - - - +
64A LEU* 1.3 61.3 + - - +
66A PHE* 3.3 15.6 - - - +
67A LEU* 3.5 8.3 + - - +
85A PRO* 4.2 9.2 - - - +
340A ASP* 3.2 19.3 - - - -
343A ALA* 3.4 21.6 - - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.9 31.6 - - + -
59A LEU* 4.4 16.1 - - + +
60A SER 2.8 10.8 + - - +
61A GLN* 3.4 12.1 - - - +
63A GLY* 1.3 76.2 - - - +
65A ALA* 1.3 63.9 + - - +
67A LEU* 3.2 12.6 + - + +
68A LYS* 3.1 48.0 + - - +
367D TRP* 3.9 20.0 - - + -
371D LYS* 6.1 2.0 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN 3.3 6.6 + - - +
62A PRO 3.7 9.0 - - - +
64A LEU* 1.3 76.2 - - - +
66A PHE* 1.3 59.8 - - - +
68A LYS* 2.7 36.8 + - - +
69A CYS* 2.8 15.1 + - - +
80A PRO* 3.3 30.7 - - + +
81A GLY* 4.2 4.7 - - - -
82A LYS* 3.8 17.9 - - + -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO 3.2 11.3 + - - +
63A GLY 3.3 14.1 - - - +
65A ALA* 1.3 78.5 - - - +
67A LEU* 1.3 64.0 + - + +
69A CYS* 4.3 4.2 - - - +
70A ALA* 3.0 29.8 + - - +
81A GLY* 5.3 2.0 - - - -
82A LYS 5.2 0.4 - - - +
83A GLY 4.0 11.9 + - - +
84A ILE* 4.4 12.8 - - + -
85A PRO* 3.4 37.2 - - + -
169A ALA* 4.3 16.6 - - + -
250A PHE* 4.0 20.0 - + - -
343A ALA* 4.1 9.9 - - + -
344A LEU* 4.7 3.8 - - + -
347A TYR* 3.2 55.2 - + + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.3 19.1 - - + -
63A GLY 3.7 13.5 - - - +
64A LEU* 3.2 13.4 + - + +
65A ALA 3.0 0.2 - - - -
66A PHE* 1.3 82.1 - - + +
68A LYS* 1.3 60.6 + - - +
70A ALA* 4.1 2.2 - - - -
71A PHE* 3.1 49.4 + - + +
343A ALA* 4.0 11.9 - - - +
346A GLU* 4.5 9.2 - - + +
347A TYR* 3.9 33.0 - - + +
350A VAL* 5.0 0.7 - - + -
367D TRP* 4.4 12.1 - - + -
370D VAL* 5.5 0.2 - - + -
374D ILE* 3.5 30.3 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.1 37.0 + - - +
65A ALA* 2.7 17.1 + - - +
67A LEU* 1.3 70.5 - - - +
69A CYS* 1.3 60.3 + - - +
72A ALA 2.8 36.8 + - - +
73A PRO* 4.2 0.2 - - - +
76A PHE* 3.0 41.4 - - + -
80A PRO* 3.5 29.8 - - + -
367D TRP* 3.5 29.2 - - + +
371D LYS* 5.7 1.4 - - - +
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Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 2.8 10.7 + - - +
66A PHE* 4.3 3.6 - - - +
68A LYS* 1.3 73.3 - - - +
70A ALA* 1.3 65.7 + - - +
71A PHE 3.4 0.5 + - - -
73A PRO* 3.7 17.2 - - - +
79A ASP* 3.5 26.2 - - - +
80A PRO* 4.4 2.8 - - - +
81A GLY* 3.7 22.9 - - - +
169A ALA* 5.9 1.3 - - + -
170A SER* 3.4 20.0 - - - -
172A ASN* 3.5 13.3 - - - +
316A TRP* 6.3 2.0 - - - -
318A CYS* 3.4 24.2 - - - -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.0 19.5 + - + +
67A LEU* 3.6 7.2 - - - +
68A LYS 3.3 0.2 - - - -
69A CYS* 1.3 82.0 - - - +
71A PHE* 1.3 77.0 + - + +
169A ALA 4.4 7.0 - - - +
170A SER* 3.8 13.5 - - - -
172A ASN* 3.6 15.8 + - - +
242A GLN* 4.0 4.3 - - - +
243A SER 4.6 5.9 - - - +
244A VAL* 5.8 0.2 - - - +
347A TYR* 3.9 24.0 - - + -
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.1 36.1 + - + +
70A ALA* 1.3 86.5 - - + +
72A ALA* 1.3 59.6 + - - +
73A PRO* 3.2 10.9 - - - +
240A PHE* 3.5 5.7 - - - -
242A GLN* 2.8 37.0 + - + +
244A VAL* 3.8 26.5 - - + -
347A TYR* 3.5 38.1 - + - -
350A VAL* 3.3 34.1 - - + -
351A ALA* 3.9 5.8 - - - -
354A LEU* 3.6 23.8 - - + -
366D MET* 3.7 5.4 - - - +
370D VAL* 4.7 17.9 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU 4.3 0.2 + - - -
68A LYS 2.8 14.6 + - - +
71A PHE* 1.3 74.3 - - - +
73A PRO* 1.3 63.9 - - - +
74A PRO* 3.4 3.6 - - - -
75A ASP* 3.0 30.9 + - - +
76A PHE* 2.9 32.3 - - + -
240A PHE* 4.9 0.2 - - - -
366D MET* 3.9 4.3 - - + -
367D TRP* 3.9 22.9 - - + +
370D VAL* 4.9 0.9 - - + -
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Residues in contact with PRO 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS 3.6 4.2 - - - +
69A CYS* 3.7 16.2 - - - +
71A PHE 3.2 9.9 - - - +
72A ALA* 1.3 92.1 - - - +
74A PRO* 1.3 69.5 - - + +
75A ASP 2.9 6.2 + - - -
76A PHE* 3.6 18.0 + - + +
79A ASP* 5.3 9.7 + - - +
80A PRO* 5.4 4.1 - - + +
172A ASN* 3.4 37.5 - - + +
240A PHE* 3.6 0.7 - - + -
316A TRP* 3.7 30.9 + - + -
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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