Contacts of the helix formed by residues 57 - 66 (chain A) in PDB entry 3BNF
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 TYR 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 3.8 10.0 - - - +
39A ALA 5.3 0.2 + - - -
40A HIS* 2.8 34.4 + + - -
53A TRP* 3.1 24.2 + + - +
54A ALA* 3.8 2.4 - - - -
56A TYR* 1.3 99.2 - + + +
58A PRO* 1.3 67.9 - - - +
59A ARG 3.2 2.6 + - - -
60A GLN* 3.3 14.9 + - - +
61A PHE* 2.9 21.7 + - - +
177A ALA* 3.6 15.6 - - + +
509A HEM 3.4 58.6 - - + -
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Residues in contact with PRO 58 (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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54A ALA* 3.4 16.4 - - + +
55A ARG 4.6 3.6 - - - +
56A TYR* 3.4 9.6 - - - +
57A TYR* 1.3 90.5 - - - +
59A ARG* 1.3 59.5 + - + +
61A PHE* 3.8 6.1 - - + +
62A ASP* 2.9 30.3 + - - +
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Residues in contact with ARG 59 (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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57A TYR 3.2 0.4 - - - -
58A PRO* 1.3 81.0 - - + +
60A GLN* 1.3 71.1 + - + +
62A ASP* 3.3 6.5 + - - +
63A SER* 3.2 23.4 + - - -
303A THR* 4.3 13.3 - - - +
305A GLU* 2.6 41.7 + - - -
310A TYR* 3.2 56.0 - - + +
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Residues in contact with GLN 60 (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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57A TYR* 3.3 23.9 + - - +
59A ARG* 1.3 84.0 - - + +
61A PHE* 1.3 60.3 + - - +
63A SER* 3.5 6.9 + - - -
64A TRP* 2.9 33.0 + - - +
310A TYR* 4.2 15.7 - - + -
311A SER 4.5 3.8 - - - +
313A HIS* 3.6 28.6 - - + +
509A HEM 2.6 74.0 + - + +
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Residues in contact with PHE 61 (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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50A SER 3.9 5.2 - - - -
51A GLU* 3.5 35.2 - - + -
54A ALA* 3.6 29.8 - - + -
57A TYR 2.9 17.7 + - - +
58A PRO* 3.8 5.6 - - + +
60A GLN* 1.3 77.6 - - - +
62A ASP* 1.3 66.8 + - + +
64A TRP* 3.3 28.0 + + - +
65A LYS* 3.1 51.0 + - + +
509A HEM 3.7 25.2 - - + +
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Residues in contact with ASP 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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58A PRO 2.9 19.8 + - - +
59A ARG* 3.3 5.6 + - - +
61A PHE* 1.3 84.2 - - + +
63A SER* 1.3 60.2 + - - +
65A LYS* 3.6 6.0 + - - +
66A LYS* 3.1 53.7 + - - +
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Residues in contact with SER 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 ARG 3.2 15.6 + - - -
60A GLN* 3.5 3.3 + - - -
62A ASP* 1.3 75.1 + - - +
64A TRP* 1.3 65.8 + - - +
66A LYS* 3.0 22.3 + - - +
311A SER 4.2 3.3 + - - -
312A ASP* 3.4 23.6 - - - -
313A HIS* 2.9 25.4 + - - +
314A LYS* 3.3 21.9 - - - +
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Residues in contact with TRP 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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50A SER* 3.5 26.0 - - - -
51A GLU* 5.2 4.0 - - - -
60A GLN 2.9 20.8 + - - +
61A PHE* 3.3 33.8 + + - +
63A SER* 1.3 78.5 + - - +
65A LYS* 1.3 87.4 + - + +
66A LYS 3.3 0.5 + - - -
67A THR* 3.4 22.8 + - + +
102A HIS* 5.6 7.0 - - + +
103A TYR* 5.7 6.7 - + - -
165A THR* 4.3 15.5 - - + -
166A ILE* 2.8 34.2 + - + +
167A GLY* 3.9 4.8 - - - -
313A HIS* 3.6 21.1 - + + +
491A SER* 6.4 2.2 - - - -
509A HEM 3.6 42.1 - + + +
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Residues in contact with LYS 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 PHE* 3.1 43.8 + - + +
62A ASP* 3.8 7.2 - - - +
64A TRP* 1.3 90.5 - - + +
66A LYS* 1.3 56.0 + - + +
67A THR* 3.1 6.0 + - - -
68A LYS* 3.1 28.8 + - + +
103A TYR* 3.8 27.8 - - + -
490A GLU* 3.7 35.4 + - - +
491A SER* 6.2 1.1 - - - +
493A LYS* 6.3 1.1 - - - -
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Residues in contact with LYS 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 ASP* 3.1 41.2 + - - +
63A SER* 3.0 19.1 + - - +
65A LYS* 1.3 71.7 - - + +
67A THR* 1.3 56.1 + - - +
68A LYS* 2.9 6.7 - - - -
69A GLU* 2.8 53.7 + - - +
314A LYS* 3.6 22.3 - - + -
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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