Contacts of the strand formed by residues 65 - 70 (chain A) in PDB entry 1BFD
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 ALA 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 5.9 0.2 - - - -
21A PHE* 4.2 9.0 - - + -
54A ALA* 3.5 34.5 - - + +
58A ALA* 3.8 10.8 - - + +
63A LYS* 3.7 12.3 + - - +
64A PRO* 1.3 73.9 - - - +
66A PHE* 1.3 60.4 + - - +
67A ILE* 4.1 1.6 + - - +
91A PRO 3.1 6.1 + - - -
92A LEU* 3.6 10.5 - - + +
93A ILE* 2.9 29.6 + - - +
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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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12A LEU* 4.0 24.9 - - + -
17A ILE* 3.7 26.1 - - + +
19A THR 3.7 7.2 + - - +
20A VAL* 3.6 27.1 - - + -
21A PHE* 3.0 30.6 + - - -
31A PHE* 3.8 33.9 - + - -
64A PRO 4.4 0.2 + - - -
65A ALA* 1.3 74.1 - - - +
67A ILE* 1.3 65.0 + - - +
68A ASN* 4.4 0.2 - - + -
93A ILE* 3.6 18.8 - - + -
95A THR* 3.6 39.9 - - + -
139A MET* 3.8 20.9 - - + -
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Residues in contact with ILE 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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21A PHE* 3.2 11.2 - - + +
50A VAL* 3.9 6.1 - - + -
51A VAL* 4.3 20.9 - - + -
54A ALA* 3.5 30.7 - - + -
65A ALA 4.7 1.1 - - - +
66A PHE* 1.3 83.4 - - - +
68A ASN* 1.3 63.3 + - - +
69A LEU* 3.7 34.1 - - + -
92A LEU* 4.1 19.1 - - + -
93A ILE 2.8 15.4 + - - +
94A VAL* 4.1 25.4 - - + -
95A THR* 2.8 30.7 + - - -
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Residues in contact with ASN 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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20A VAL* 4.0 20.0 - - + -
21A PHE 3.0 7.7 + - - -
22A GLY* 3.2 23.1 - - - -
23A ASN 3.4 9.4 + - - +
24A PRO* 5.5 0.2 - - - +
28A GLU* 3.4 37.2 - - - +
31A PHE* 3.9 22.9 - - - -
32A LEU* 3.9 14.3 - - - +
41A TYR* 4.8 2.6 + - + -
66A PHE* 4.4 2.7 - - + -
67A ILE* 1.3 74.3 - - - +
69A LEU* 1.3 61.6 + - - +
95A THR* 3.0 22.3 + - - +
96A ALA* 4.6 1.2 + - - -
97A GLY 4.8 0.7 + - - -
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Residues in contact with LEU 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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23A ASN 4.1 6.7 - - - +
28A GLU* 3.2 14.9 - - - +
47A GLU* 3.7 21.1 - - + -
50A VAL* 3.9 17.3 - - + -
51A VAL* 4.3 4.3 - - + -
67A ILE* 3.7 20.2 - - + -
68A ASN* 1.3 79.7 - - - +
70A HIS* 1.3 59.7 + - - +
71A SER 3.9 0.2 - - - -
74A GLY 3.7 15.9 - - - +
75A THR* 4.0 13.5 - - + +
78A ALA* 3.6 28.5 - - + -
82A LEU* 6.4 0.2 - - + -
94A VAL* 4.0 20.0 - - + -
95A THR 2.8 11.2 + - - +
96A ALA* 3.2 20.8 - - + -
97A GLY 3.3 0.9 + - - -
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Residues in contact with HIS 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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23A ASN* 4.1 7.8 + - - +
24A PRO 4.6 1.8 - - - +
25A GLY* 3.5 14.3 - - - +
26A SER* 3.7 25.1 + - - -
27A ASN* 3.9 19.1 - - - -
28A GLU* 2.7 28.2 + - - +
47A GLU* 5.0 5.0 + - - +
69A LEU* 1.3 73.1 - - - +
71A SER* 1.3 67.7 - - - +
72A ALA 3.6 0.2 + - - -
73A ALA* 3.8 6.0 + - + -
74A GLY* 2.7 38.4 + - - -
110A LEU* 3.7 30.3 - - + +
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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