Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 3BX7
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.8 4.3 - + - -
24A ASP* 2.7 47.0 + - + -
27A PHE* 3.5 20.0 - + - +
28A HIS* 4.2 8.5 - - - -
56A TYR* 3.8 27.4 - + + -
57A GLU 3.3 21.5 - - - +
58A LEU* 3.8 20.4 - - + -
59A LYS* 4.4 3.1 - - - -
62A LYS 4.7 1.1 - - - -
63A SER* 1.3 75.9 - - - +
65A ASN* 1.3 66.0 + - - +
66A VAL* 3.6 12.0 + - + +
82A THR* 3.4 6.7 - - - +
83A PHE* 2.9 35.3 + - + +
92A PHE* 3.6 38.4 - + - -
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Residues in contact with ASN 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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55A ILE 3.4 0.9 - - - +
56A TYR* 3.7 1.7 - - - -
57A GLU* 2.7 68.4 + - + +
59A LYS* 4.1 15.7 - - + +
64A TYR* 1.3 73.4 - - - +
66A VAL* 1.3 58.5 + - - +
67A THR* 2.9 18.0 + - - -
80A ILE* 3.5 30.1 - - - +
81A ALA 3.7 4.1 - - - +
82A THR* 4.8 5.3 + - - +
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Residues in contact with VAL 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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54A THR* 3.4 30.1 - - + -
55A ILE 3.5 3.1 - - - +
56A TYR* 4.0 19.5 - - + +
64A TYR* 4.0 7.2 - - + +
65A ASN* 1.3 79.2 - - - +
67A THR* 1.3 58.5 + - - +
68A SER* 4.0 2.3 + - - +
79A THR* 3.7 1.2 + - - +
80A ILE* 3.6 4.3 + - - -
81A ALA* 2.7 41.7 + - + +
83A PHE* 3.6 46.7 - - + -
102C PRO* 4.7 10.5 - - + -
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Residues in contact with THR 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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54A THR* 3.3 1.6 - - - -
55A ILE* 2.7 47.7 + - + +
57A GLU* 3.1 14.8 + - - +
65A ASN* 2.9 24.6 + - - -
66A VAL* 1.3 71.2 - - - +
68A SER* 1.3 63.1 + - - +
69A VAL* 3.8 3.3 + - + -
78A TYR* 3.3 38.6 - - + -
79A THR 3.4 12.3 - - - +
80A ILE* 3.5 9.4 - - + +
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Residues in contact with SER 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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52A TYR* 3.9 10.1 - - - -
53A ALA 3.2 5.8 - - - -
54A THR* 3.0 24.8 + - - +
66A VAL* 4.0 3.5 + - - +
67A THR* 1.3 72.6 - - - +
69A VAL* 1.3 60.9 + - - +
70A ILE* 3.5 17.4 - - - +
78A TYR* 3.2 6.6 - - - -
79A THR* 3.0 45.3 + - - -
102C PRO* 5.8 4.2 - - - +
104C TYR* 4.8 7.4 + - - +
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Residues in contact with VAL 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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30A LYS* 5.1 1.8 - - - -
52A TYR* 3.3 8.1 - - - +
53A ALA* 2.7 37.8 + - + +
55A ILE* 4.0 24.9 - - + -
67A THR 4.4 1.1 - - - +
68A SER* 1.3 73.7 - - - +
70A ILE* 1.3 63.1 + - - +
76A CYS* 5.3 1.1 - - + -
77A GLU 3.5 5.8 - - - +
78A TYR* 3.5 39.9 - - + +
175A CYS* 3.1 34.5 - - + +
176A ILE* 3.7 9.4 - - - +
178A GLY 5.1 5.4 - - - +
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Residues in contact with ILE 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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52A TYR* 4.0 10.5 - - + -
68A SER* 3.5 31.0 - - - +
69A VAL* 1.3 81.7 - - - +
71A SER* 1.3 74.2 + - - +
72A SER* 3.9 11.4 - - - +
76A CYS* 3.5 5.7 - - - +
77A GLU* 2.9 40.2 + - + +
79A THR* 4.3 12.8 - - + -
175A CYS* 4.1 5.1 - - - +
176A ILE* 5.0 0.4 - - - -
35C ARG* 6.1 0.2 - - - +
97C GLU* 4.7 2.0 - - - +
104C TYR* 3.6 52.7 - - + +
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Residues in contact with SER 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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50A ASN* 5.0 10.4 + - - +
51A MET 5.6 1.0 + - - -
70A ILE* 1.3 78.8 - - - +
72A SER* 1.3 65.9 + - - +
172A ILE* 3.7 28.2 - - - +
174A GLN* 3.3 33.7 - - - +
175A CYS* 3.8 9.2 - - - +
176A ILE* 5.0 2.4 - - - +
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Residues in contact with SER 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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70A ILE* 3.6 13.1 + - - +
71A SER* 1.3 80.4 + - - +
73A HIS* 1.3 66.5 - - - +
74A LYS 3.0 4.0 + - - -
75A LYS* 2.8 30.1 + - - +
77A GLU* 2.4 39.9 + - - +
35C ARG* 4.2 2.1 + - - -
95C LYS* 4.6 12.2 + - - +
97C GLU* 4.8 2.6 + - - -
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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