Contacts of the helix formed by residues 77 - 86 (chain A) in PDB entry 4B7B
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 LYS 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.1 5.2 - - - +
75A SER 3.9 9.0 + - - +
76A THR* 1.3 79.1 - - - +
78A GLN* 1.3 68.3 + - - +
79A ILE* 3.2 18.9 - - + +
80A ASP* 2.9 46.9 + - - +
81A VAL* 3.3 5.5 + - - +
131A PRO* 5.3 4.7 - - + +
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Residues in contact with GLN 78 (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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24A ARG* 2.9 35.7 + - - +
77A LYS* 1.3 75.7 - - - +
79A ILE* 1.3 57.7 + - - +
81A VAL* 3.4 6.9 + - - +
82A TYR* 3.0 26.5 + - - +
113A PHE* 2.8 49.1 + - + +
114A THR* 4.4 1.9 - - - +
131A PRO 3.2 16.2 + - - +
132A LEU* 3.3 24.0 + - + -
133A ASP 3.1 22.8 + - - +
134A GLY* 3.6 6.2 - - - -
138A ARG* 3.3 11.9 + - - +
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Residues in contact with ILE 79 (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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77A LYS* 3.2 26.1 - - + +
78A GLN* 1.3 78.7 - - - +
80A ASP* 1.3 66.3 + - - +
82A TYR* 3.4 12.7 + - + -
83A ARG* 2.9 63.1 + - + +
131A PRO 5.0 0.2 + - - -
138A ARG* 3.4 36.8 - - - +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.3 5.8 - - + -
75A SER 4.3 1.0 - - - +
76A THR* 4.0 14.2 - - + +
77A LYS* 2.9 59.1 + - - +
79A ILE* 1.3 80.7 - - - +
81A VAL* 1.3 61.4 + - - +
83A ARG* 3.6 4.7 + - - +
84A SER* 3.1 27.5 + - - -
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Residues in contact with VAL 81 (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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24A ARG* 3.7 38.1 - - - +
72A PHE* 4.2 19.5 - - + -
76A THR* 3.8 16.2 - - + -
77A LYS 3.3 3.4 + - - +
78A GLN* 3.7 7.9 - - - +
80A ASP* 1.3 71.6 - - - +
82A TYR* 1.3 67.1 + - - +
85A VAL* 2.9 30.7 + - + +
86A VAL* 4.4 0.2 - - - +
114A THR* 4.6 8.5 - - + -
135A ILE* 4.5 12.3 - - + -
333A ILE* 4.3 25.4 - - + -
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Residues in contact with TYR 82 (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 GLN 3.0 14.8 + - - +
79A ILE* 3.6 18.8 - - + +
80A ASP 3.2 0.2 - - - -
81A VAL* 1.3 77.6 - - - +
83A ARG* 1.3 65.3 + - + +
86A VAL* 2.9 61.8 + - + +
87A CYS* 3.1 17.8 + - + -
90A LEU* 3.6 12.3 - - - +
134A GLY 6.3 0.2 - - - -
135A ILE* 4.4 9.4 - - + +
138A ARG* 3.7 41.3 - - + -
139A THR* 3.7 14.7 - - - -
142A GLN* 2.6 45.7 + - + +
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Residues in contact with ARG 83 (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 ILE* 2.9 53.7 + - + +
80A ASP* 4.3 4.0 - - - +
82A TYR* 1.3 80.2 - - + +
84A SER* 1.3 61.8 + - - +
87A CYS* 3.7 11.7 - - + +
88A PRO* 3.7 15.4 - - - +
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Residues in contact with SER 84 (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 MET* 2.5 49.3 - - - +
72A PHE* 3.8 7.5 - - - -
80A ASP 3.1 19.2 + - - -
81A VAL 4.1 0.9 - - - -
82A TYR 3.1 0.4 - - - -
83A ARG* 1.3 80.8 - - - +
85A VAL* 1.3 61.8 + - - +
88A PRO* 3.8 13.9 - - - +
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Residues in contact with VAL 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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20A GLN* 6.4 0.7 - - + -
22A VAL* 4.1 34.1 - - + -
70A MET* 4.6 0.9 - - + -
72A PHE* 4.4 9.2 - - + -
81A VAL* 2.9 22.3 + - + +
84A SER* 1.3 81.7 - - - +
86A VAL* 1.3 67.0 + - + +
87A CYS 3.8 0.2 - - - -
88A PRO* 3.8 5.5 - - - +
89A ILE* 3.5 19.1 - - - +
101A ILE* 4.1 21.1 - - + -
331A SER* 4.1 25.6 + - - +
333A ILE* 4.3 12.8 - - + -
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Residues in contact with VAL 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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81A VAL 4.4 0.9 - - - +
82A TYR* 2.9 57.7 + - + +
85A VAL* 1.3 73.2 - - + +
87A CYS* 1.3 59.0 + - - +
88A PRO* 3.3 3.6 - - - -
89A ILE* 2.8 21.3 + - - +
90A LEU* 2.9 18.4 + - + +
101A ILE* 4.0 18.4 - - + -
135A ILE* 3.8 35.9 - - + -
139A THR* 3.7 13.7 - - - +
261A LEU* 4.9 6.3 - - + -
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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