Contacts of the strand formed by residues 55 - 62 (chain A) in PDB entry 1BKX
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 5.3 0.2 - - - -
52A GLY* 3.1 21.2 + - - +
53A SER 3.7 0.4 - - - -
54A PHE* 1.3 80.8 - - - +
56A ARG* 1.4 73.3 + - - +
72A LYS* 6.1 0.9 - - - -
73A ILE 2.9 17.5 - - - -
74A LEU* 3.8 2.9 - - - -
75A ASP* 4.5 3.1 - - - +
78A LYS* 5.7 1.0 - - - +
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Residues in contact with ARG 56 (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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48A THR* 2.7 35.1 + - + +
50A GLY 4.0 6.1 - - - +
51A THR* 4.7 19.1 - - + +
52A GLY* 4.9 0.8 - - - +
55A GLY* 1.4 82.7 - - - +
57A VAL* 1.3 62.8 + - - +
58A MET* 3.7 21.9 + - + +
71A MET 3.2 4.0 - - - +
72A LYS* 4.8 3.0 - - - +
73A ILE* 3.0 38.0 + - + +
330A TYR* 4.8 3.2 - - - +
331A GLU* 2.3 34.1 + - - +
332A GLU* 4.0 0.6 + - - +
333A GLU* 3.5 54.9 + - - +
334A GLU 6.1 0.4 - - - -
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Residues in contact with VAL 57 (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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48A THR* 4.0 0.6 - - - +
49A LEU* 2.6 43.4 + - + +
50A GLY 2.8 24.5 + - - +
51A THR* 4.8 1.2 - - - +
56A ARG* 1.3 68.9 - - - +
58A MET* 1.3 58.3 + - - +
70A ALA* 4.4 9.2 - - + -
71A MET 3.3 2.0 - - - +
72A LYS* 3.0 52.3 - - + +
120A MET* 5.4 2.5 - - - -
351A A 3.6 48.7 - - + +
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Residues in contact with MET 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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45A ARG* 4.4 19.7 - - - -
47A LYS 2.8 20.6 - - - +
48A THR* 3.1 28.3 - - - +
49A LEU* 3.6 7.0 - - - +
56A ARG* 3.7 31.1 + - + +
57A VAL* 1.3 73.3 - - - +
59A LEU* 1.3 66.3 + - - +
60A VAL* 3.6 9.6 - - + +
70A ALA* 3.6 1.9 - - - -
71A MET* 2.9 36.9 + - + +
73A ILE* 4.5 16.6 - - + -
332A GLU* 4.7 6.1 - - - +
333A GLU 5.1 6.3 - - - +
334A GLU 6.5 0.2 - - - -
335A ILE* 5.0 11.4 - - + -
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Residues in contact with LEU 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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45A ARG* 3.8 0.7 - - - -
46A ILE* 2.7 52.7 + - + -
47A LYS* 2.3 30.9 + - + +
49A LEU* 3.8 11.5 - - + +
58A MET* 1.3 70.9 - - - +
60A VAL* 1.3 61.9 + - - +
68A HIS* 4.1 15.9 - - + -
69A TYR 3.5 20.4 - - - +
122A TYR* 3.9 31.2 - - + -
322A GLY 4.4 10.8 - - - +
324A THR* 3.0 32.1 - - + -
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Residues in contact with VAL 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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43A PHE* 3.9 34.1 - - + -
44A ASP 3.4 9.6 - - - +
45A ARG* 4.5 10.5 - - + -
46A ILE* 4.2 3.1 - - - +
58A MET* 3.6 17.9 + - + +
59A LEU* 1.3 82.6 - - - +
61A LYS* 1.3 60.8 + - - +
62A HIS 3.9 0.4 + - - +
68A HIS* 3.2 6.9 - - - +
69A TYR* 3.2 38.6 + - + +
71A MET* 3.8 30.3 - - + -
119A VAL* 5.2 0.2 - - + -
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Residues in contact with LYS 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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43A PHE* 3.4 2.7 - - - -
44A ASP* 2.8 53.7 + - + +
46A ILE* 4.1 17.6 - - + +
60A VAL* 1.3 73.4 - - - +
62A HIS* 1.3 73.8 + - - +
63A LYS* 3.3 16.8 + - - +
66A GLY* 3.6 27.3 - - - -
67A ASN 4.2 1.3 - - - -
68A HIS* 4.0 28.0 - - + +
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Residues in contact with HIS 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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42A GLN* 3.8 28.1 + - + +
43A PHE* 3.7 24.8 - + + -
60A VAL 3.9 0.8 + - - -
61A LYS* 1.3 76.3 - - - +
63A LYS* 1.3 66.0 + - - +
64A GLU* 3.1 44.2 + - + +
65A SER* 2.7 52.2 + - - +
66A GLY* 3.5 6.4 - - - -
67A ASN 3.0 22.6 + - - +
69A TYR* 3.6 17.0 - + + -
108A PHE* 4.9 12.1 - + - -
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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