Contacts of the helix formed by residues 84 - 97 (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 GLN 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A PHE* 3.6 35.0 - - + -
79A VAL* 2.7 12.6 + - + +
82A LEU* 2.3 55.2 + - + +
83A LYS* 1.4 61.3 - - - +
85A ILE* 1.3 49.0 + - - -
86A GLU* 3.5 1.6 - - - -
87A HIS* 2.9 42.9 + - - +
88A THR* 2.5 43.8 + - - +
186A GLY 5.3 0.6 + - - -
187A PHE* 4.7 12.7 - - - -
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Residues in contact with ILE 85 (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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79A VAL* 3.7 11.1 + - + +
80A VAL* 4.1 25.4 - - + -
83A LYS* 2.3 36.7 + - + +
84A GLN* 1.3 62.3 - - - +
86A GLU* 1.3 78.3 + - - +
87A HIS 2.7 2.6 + - - -
88A THR* 3.1 15.7 + - - -
89A LEU* 2.9 37.9 + - + +
346A GLU* 3.9 33.9 - - + +
347A PHE* 3.8 17.7 - - + -
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Residues in contact with GLU 86 (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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83A LYS* 3.4 26.5 - - + +
85A ILE* 1.3 86.4 - - - +
87A HIS* 1.3 58.4 + - + +
89A LEU* 3.9 8.1 + - - +
90A ASN* 2.3 30.9 + - - -
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Residues in contact with HIS 87 (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 PHE* 6.0 1.3 - - + -
84A GLN* 2.9 37.0 + - - +
85A ILE 2.7 1.2 + - - -
86A GLU* 1.3 80.0 - - + +
88A THR* 1.3 53.8 + - - +
89A LEU 2.3 20.4 + - - -
90A ASN* 2.5 33.6 + - - +
91A GLU* 3.5 4.3 + - - -
165A ARG* 3.5 14.7 + - - -
186A GLY* 3.8 22.3 + - - +
187A PHE* 4.8 10.2 - + - -
188A ALA 4.7 3.6 - - - -
189A LYS* 6.1 2.5 - - + -
197A TPO 3.2 35.2 + - + -
199A CYS* 5.0 1.8 - - + -
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Residues in contact with THR 88 (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 PHE* 4.7 4.5 - - - -
74A LEU* 3.5 35.9 - - + +
79A VAL* 4.2 9.1 - - + +
84A GLN* 2.5 37.2 + - - +
85A ILE* 3.1 6.7 + - - -
87A HIS* 1.3 67.9 - - - +
89A LEU* 1.3 61.4 + - + +
90A ASN 3.6 0.2 - - - -
91A GLU* 4.3 10.5 - - - +
92A LYS 4.1 8.0 + - - -
116A LEU* 3.9 24.5 - - + -
118A MET* 5.2 3.1 - - + +
186A GLY* 6.1 1.3 - - - -
347A PHE* 5.1 2.7 - - + -
350A PHE* 4.1 15.9 - - + -
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Residues in contact with LEU 89 (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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85A ILE* 2.9 45.8 - - + +
86A GLU* 4.0 7.9 - - - +
87A HIS 2.3 15.2 + - - -
88A THR* 1.3 73.6 - - - +
90A ASN* 1.3 58.2 + - - +
91A GLU 3.4 0.4 - - - -
92A LYS* 3.6 2.9 + - - +
93A ARG* 3.0 21.5 + - - +
346A GLU 4.4 11.9 - - - +
347A PHE* 4.9 6.5 - - + -
349A GLU* 3.0 61.6 - - + +
350A PHE* 3.9 18.8 - - + +
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Residues in contact with ASN 90 (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 TRP* 4.5 11.2 - - + -
86A GLU 2.3 32.9 + - - -
87A HIS* 2.5 22.4 + - - +
89A LEU* 1.3 68.2 - - - +
91A GLU* 1.4 55.1 + - - -
92A LYS 3.1 1.8 - - - -
93A ARG* 4.0 7.2 - - - +
94A ILE* 2.5 53.4 + - + +
185A PHE 5.4 1.4 - - - +
186A GLY 5.4 1.6 - - - +
188A ALA 3.9 18.7 - - - +
189A LYS* 5.0 4.2 - - - +
190A ARG 6.0 0.7 - - - +
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Residues in contact with GLU 91 (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 PHE* 5.5 0.9 - - - -
72A LYS* 2.7 38.1 + - - -
74A LEU* 5.3 2.4 - - - +
87A HIS 3.5 6.8 + - - +
88A THR* 4.8 9.1 - - - +
89A LEU 3.4 0.8 - - - +
90A ASN* 1.4 77.1 + - - +
92A LYS* 1.3 62.4 + - - +
94A ILE* 3.8 1.0 - - - +
95A LEU* 2.9 52.8 + - + +
118A MET* 3.9 14.5 - - - +
120A MET* 4.0 4.0 - - - +
184A ASP* 3.4 6.2 + - - -
185A PHE* 2.9 43.2 + - + +
186A GLY* 3.4 19.2 - - - -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO* 3.3 36.8 + - - +
34A SER 3.3 13.2 + - - -
35A GLN* 4.1 0.8 - - - +
88A THR 4.1 4.2 + - - +
89A LEU 3.6 8.1 + - - +
90A ASN 3.1 0.4 - - - -
91A GLU* 1.3 76.1 - - - +
93A ARG* 1.3 72.6 + - - +
94A ILE 2.9 0.3 + - - -
95A LEU* 3.9 2.9 - - - +
96A GLN* 2.8 31.7 + - + +
106A LEU* 4.8 5.3 - - + +
109A SER* 3.9 23.1 - - - +
118A MET* 4.4 12.0 - - + -
349A GLU* 3.4 28.0 + - - +
350A PHE* 3.1 56.7 + - + +
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Residues in contact with ARG 93 (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 TRP* 2.6 85.6 + - + +
31A GLU* 3.1 24.7 - - - +
32A THR 4.0 0.4 - - - +
33A PRO* 4.0 16.5 - - + +
89A LEU 3.0 17.5 + - - +
90A ASN* 3.0 8.1 + - - +
92A LYS* 1.3 77.4 - - - +
94A ILE* 1.3 59.2 + - - +
96A GLN* 2.5 41.3 + - - +
97A ALA* 3.3 3.6 + - - +
349A GLU* 4.6 13.7 - - - +
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Residues in contact with ILE 94 (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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26A PHE* 5.2 1.6 - - + -
30A TRP* 3.5 22.4 - - + -
90A ASN* 2.5 40.2 + - + +
91A GLU* 3.8 5.6 - - - +
92A LYS 2.9 0.4 + - - -
93A ARG* 1.3 69.2 - - - +
95A LEU* 1.3 56.1 + - - +
96A GLN 2.9 1.6 - - - -
97A ALA* 2.7 6.3 + - - -
98A VAL* 2.4 51.5 + - + +
157A LEU* 5.7 0.4 - - + -
162A LEU* 4.3 25.4 - - + -
185A PHE* 4.0 22.2 - - + +
188A ALA* 3.5 31.0 - - + -
189A LYS* 4.4 4.3 - - - +
190A ARG 5.1 0.4 - - - +
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Residues in contact with LEU 95 (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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91A GLU* 2.9 56.5 + - + +
92A LYS 4.0 0.2 - - - +
94A ILE* 1.3 79.8 - - - +
96A GLN* 1.4 60.7 + - - +
97A ALA 3.6 0.2 + - - -
98A VAL* 3.6 26.2 - - + +
104A VAL* 4.3 17.3 - - + +
106A LEU* 3.8 36.2 + - + +
118A MET* 4.9 5.8 - - + -
120A MET* 4.6 10.5 - - + -
185A PHE* 3.0 38.4 - - + -
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Residues in contact with GLN 96 (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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29A LYS* 2.6 56.4 + - + +
30A TRP 3.5 0.5 + - - -
32A THR 3.9 0.6 - - - +
33A PRO* 3.1 34.9 - - + +
34A SER 4.6 5.6 - - - +
92A LYS* 2.8 24.3 + - + +
93A ARG* 2.5 55.5 + - - +
95A LEU* 1.4 79.4 - - - +
97A ALA* 1.4 54.5 + - - +
98A VAL 4.6 0.8 - - - +
106A LEU* 4.5 9.8 - - + +
109A SER* 5.9 0.7 - - - +
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Residues in contact with ALA 97 (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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26A PHE* 3.4 34.8 - - + +
29A LYS* 3.4 20.0 - - + +
30A TRP* 3.3 31.4 - - - +
93A ARG 3.3 10.8 + - - +
94A ILE 2.7 9.1 + - - -
96A GLN* 1.4 75.5 - - - +
98A VAL* 1.3 68.9 + - - +
99A ASN* 3.5 4.7 + - - +
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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