Contacts of the helix formed by residues 88 - 96 (chain A) in PDB entry 4BZN
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 MET 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP* 3.0 34.9 + - + +
77A TRP 3.5 23.8 - - - +
78A GLY* 3.6 15.9 - - - +
86A VAL 3.5 1.2 + - - -
87A PRO* 1.3 70.5 - - - +
89A GLU* 1.3 64.6 + - - +
91A VAL* 2.9 18.0 + - + +
92A LEU* 2.8 58.2 + - + +
187A PHE 5.3 1.1 - - - +
188A GLY 5.9 2.7 - - - +
190A GLY 3.9 13.7 - - - +
191A ALA* 4.5 2.5 - - - -
192A LEU* 4.6 17.7 - - + +
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Residues in contact with GLU 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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67A LYS* 2.6 36.8 + - - +
69A VAL* 5.1 2.4 - - - +
87A PRO* 3.1 7.9 - - + +
88A MET* 1.3 78.5 - - - +
90A VAL* 1.3 56.5 + - - +
92A LEU* 3.8 0.6 - - - +
93A LEU* 2.8 47.6 + - + +
104A ILE* 5.8 0.3 - - - +
118A LEU* 3.7 19.5 - - + +
120A LEU* 5.5 2.6 - - - +
186A ASP* 3.4 6.9 + - - -
187A PHE* 2.8 50.3 + - + +
188A GLY* 3.8 9.3 + - - +
1306A UGX 4.0 1.4 - - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.1 9.6 - - + -
86A VAL* 3.8 18.8 - - + -
87A PRO* 2.9 26.2 + - + +
89A GLU* 1.3 74.4 - - - +
91A VAL* 1.3 66.2 + - - +
93A LEU* 3.9 0.9 - - - +
94A LYS* 3.0 28.1 + - + +
106A LEU* 4.1 8.9 - - + +
109A TRP* 4.0 39.0 - - + +
118A LEU* 3.9 33.7 - - + -
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Residues in contact with VAL 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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78A GLY* 4.0 7.9 - - - -
79A GLU 3.8 31.9 - - - +
80A LEU* 4.5 6.7 - - + -
81A PRO* 6.3 1.6 - - + -
86A VAL* 3.5 24.0 - - + -
87A PRO 3.5 1.8 + - - +
88A MET* 2.9 22.1 + - + +
90A VAL* 1.3 79.3 - - - +
92A LEU* 1.3 62.1 + - - +
94A LYS* 3.3 6.2 + - - +
95A LYS* 3.1 39.6 + - + +
192A LEU* 4.4 8.7 - - + -
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Residues in contact with LEU 92 (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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88A MET* 2.8 39.9 + - + +
89A GLU 3.8 2.9 - - - +
91A VAL* 1.3 72.8 - - - +
93A LEU* 1.3 62.8 + - - +
95A LYS* 3.1 13.4 + - - +
96A VAL* 3.2 15.2 + - - +
163A VAL* 3.7 34.0 - - + +
187A PHE* 3.7 21.3 - - + +
190A GLY* 3.4 15.5 - - - -
191A ALA 3.4 47.6 - - - +
192A LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 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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89A GLU* 2.8 48.1 + - + +
90A VAL 4.0 2.0 - - - +
92A LEU* 1.3 73.2 - - - +
94A LYS* 1.3 62.5 + - - +
96A VAL* 3.3 18.8 + - + +
97A SER* 3.4 14.4 + - - -
104A ILE* 3.5 30.0 - - + +
106A LEU* 3.7 28.9 + - + +
118A LEU* 4.3 2.0 - - + -
120A LEU* 3.8 29.2 - - + -
187A PHE* 3.6 29.8 - - + -
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Residues in contact with LYS 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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80A LEU* 3.5 35.7 - - + +
81A PRO* 5.2 10.1 - - + -
82A ASN* 6.4 0.2 - - - +
90A VAL* 3.0 24.3 + - + +
91A VAL* 3.7 4.7 - - - +
93A LEU* 1.3 75.5 - - - +
95A LYS* 1.3 64.3 + - + +
97A SER* 3.1 23.6 + - - +
106A LEU* 4.2 13.4 - - + +
109A TRP* 4.0 18.8 - - - +
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Residues in contact with LYS 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 VAL* 3.1 28.1 + - + +
92A LEU* 3.1 8.5 + - - +
94A LYS* 1.3 79.1 - - + +
96A VAL* 1.3 58.9 + - - +
97A SER 3.7 2.4 + - - +
161A CYS* 3.2 40.5 + - - +
162A GLY* 3.8 10.8 - - - -
163A VAL* 3.7 10.5 - - + -
192A LEU* 3.7 31.4 - - + +
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Residues in contact with VAL 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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92A LEU 3.2 6.9 + - - +
93A LEU* 3.4 22.0 - - + +
95A LYS* 1.3 76.9 - - - +
97A SER* 1.3 62.1 + - - +
98A SER 3.4 1.6 + - - -
100A PHE 5.5 1.6 - - - +
103A VAL* 3.6 27.9 - - + +
104A ILE 5.0 1.3 - - - +
157A HIS* 2.7 36.7 + - + +
158A CYS* 3.9 25.4 - - - -
161A CYS* 3.9 5.8 - - + -
163A VAL* 3.7 32.8 - - + -
187A PHE* 4.7 2.2 - - + -
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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