Contacts of the strand formed by residues 115 - 120 (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 ASN 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE* 5.1 7.8 - - - +
74A LEU 2.8 20.6 - - - +
75A ASP* 3.2 20.6 - - - +
76A LYS* 3.6 4.9 - - - -
111A LYS* 4.1 0.5 - - - +
112A ASP* 3.0 20.1 + - - +
114A SER* 1.3 77.6 - - - +
116A LEU* 1.4 59.3 + - - +
117A TYR* 2.5 48.6 + - - -
335A ILE* 4.9 7.9 - - - +
336A ARG* 3.7 22.0 + - - +
342A LYS* 5.5 0.2 - - - +
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Residues in contact with LEU 116 (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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73A ILE* 3.0 6.4 - - - +
74A LEU* 2.5 56.6 + - + +
76A LYS* 4.2 12.1 - - + -
79A VAL* 5.0 3.6 - - + -
88A THR* 3.9 20.2 - - + -
110A PHE 4.2 1.6 - - - -
111A LYS* 3.9 13.7 - - + -
115A ASN* 1.4 71.5 - - - +
117A TYR* 1.3 65.8 + - - +
347A PHE* 3.7 35.2 - - + -
350A PHE* 3.0 52.9 - - + -
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Residues in contact with TYR 117 (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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40A LEU* 3.9 15.1 - - + +
71A MET* 3.3 17.0 - - + -
72A LYS 3.3 5.4 - - - +
73A ILE* 3.0 31.4 - - + -
108A PHE 4.5 0.4 - - - -
109A SER* 3.2 29.6 - - - -
110A PHE* 3.1 52.9 + + + +
112A ASP* 2.8 35.4 + - - -
115A ASN* 2.5 40.5 + - - -
116A LEU* 1.3 76.0 - - - +
118A MET* 1.3 63.2 + - - +
335A ILE* 4.2 15.3 - - + +
337A VAL* 4.0 4.2 - - - +
350A PHE* 3.7 3.0 - - - -
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Residues in contact with MET 118 (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 ALA 3.7 0.3 - - - +
71A MET* 3.3 1.9 - - - -
72A LYS* 2.6 83.5 + - + +
74A LEU* 3.5 22.0 - - + -
88A THR* 5.2 3.4 - - + +
91A GLU* 3.9 26.5 - - - +
92A LYS* 4.4 17.5 - - + -
95A LEU* 4.9 4.0 - - + -
106A LEU* 4.4 19.3 - - + -
108A PHE 3.7 3.6 - - - -
109A SER* 4.7 2.0 - - - -
117A TYR* 1.3 75.9 - - - +
119A VAL* 1.3 60.3 + - - +
120A MET* 4.0 9.4 - - + +
350A PHE* 4.1 15.7 - - + -
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Residues in contact with VAL 119 (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* 4.6 7.2 - - + -
60A VAL* 5.2 0.7 - - + -
69A TYR* 3.6 27.6 - - + -
70A ALA 3.2 2.2 - - - -
71A MET* 3.2 46.4 - - + -
106A LEU* 3.1 5.4 - - - +
107A GLU* 2.7 31.5 + - - +
108A PHE* 3.0 43.0 + - + +
110A PHE* 4.6 11.0 - - + -
117A TYR* 5.1 0.2 - - + -
118A MET* 1.3 71.5 - - - +
120A MET* 1.4 52.2 + - - +
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Residues in contact with MET 120 (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 VAL* 5.4 2.5 - - + -
69A TYR* 3.3 13.1 - - - +
70A ALA 2.7 36.0 + - - +
72A LYS* 4.5 20.4 - - + -
91A GLU* 4.0 19.5 - - - +
95A LEU* 4.6 10.1 - - + -
104A VAL* 3.8 20.6 - - + -
105A LYS 2.9 18.6 - - - +
106A LEU* 4.5 8.3 - - + -
107A GLU* 4.7 1.3 - - - -
118A MET* 4.8 13.9 - - + +
119A VAL* 1.4 71.6 - - - +
121A GLU* 1.3 70.4 + - - +
183A THR* 3.5 25.4 - - - +
184A ASP 4.5 0.7 - - - +
351A A 3.7 18.2 - - - +
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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