Contacts of the helix formed by residues 78 - 89 (chain A) in PDB entry 2L28
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 ASP 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.6 16.8 - - - +
64A HIS* 5.8 4.0 - - - -
76A VAL 3.8 0.4 - - - -
77A HIS* 1.3 92.2 - - + +
79A VAL* 1.3 64.0 + - - +
80A ALA* 3.0 14.3 + - + +
81A ALA* 3.2 11.4 + - + +
82A VAL* 3.1 21.1 + - - +
105A ALA* 4.9 9.0 - - - +
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Residues in contact with VAL 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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78A ASP* 1.3 77.0 - - - +
80A ALA* 1.3 59.5 + - - +
81A ALA 3.5 0.2 - - - -
82A VAL 4.1 1.3 - - - -
83A PHE* 2.8 55.7 + - + -
105A ALA* 2.7 43.3 - - + +
106A PHE* 3.0 43.5 - - + -
109A ASP* 3.5 17.5 - - + +
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Residues in contact with ALA 80 (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 ASP* 3.0 7.9 - - + +
79A VAL* 1.3 78.7 - - - +
81A ALA* 1.3 63.4 + - - +
82A VAL 3.3 0.4 - - - -
83A PHE* 3.7 5.8 + - - +
84A ALA* 3.2 21.3 + - - +
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Residues in contact with ALA 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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75A VAL 5.3 0.2 - - - +
76A VAL* 3.4 33.4 - - + +
77A HIS* 3.6 19.3 - - + +
78A ASP* 3.2 6.4 + - - +
80A ALA* 1.3 77.6 - - - +
82A VAL* 1.3 62.6 + - - +
84A ALA* 3.3 18.6 - - - +
85A TYR* 3.4 6.4 + - - +
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Residues in contact with VAL 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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38A ILE* 5.4 0.9 - - + -
40A VAL* 3.2 31.9 - - + -
60A VAL* 4.6 7.0 - - + -
62A LEU* 3.8 0.7 - - + -
76A VAL* 3.3 27.8 - - + -
78A ASP 3.1 18.3 + - - +
79A VAL 4.3 0.4 - - - +
80A ALA 3.3 0.2 - - - -
81A ALA* 1.3 73.6 - - - +
83A PHE* 1.3 66.8 + - - +
84A ALA 3.0 1.8 - - - -
85A TYR* 2.9 17.7 + - + +
86A ALA* 3.0 11.3 + - - +
94A LEU* 3.2 22.2 - - + -
106A PHE* 3.4 27.1 - - + -
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Residues in contact with PHE 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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1A THR* 3.1 31.6 - - + -
79A VAL* 2.8 37.2 + - + +
80A ALA* 3.7 6.9 + - - +
82A VAL* 1.3 78.8 - - - +
84A ALA* 1.3 56.0 + - - +
86A ALA* 3.7 5.6 - - + +
87A LYS* 2.8 46.5 + - + +
94A LEU* 3.5 20.0 - - + -
109A ASP* 3.2 38.4 - - + -
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Residues in contact with ALA 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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80A ALA 3.2 15.1 + - - +
81A ALA* 3.3 15.0 - - - +
82A VAL 3.0 0.6 - - - -
83A PHE* 1.3 74.7 - - - +
85A TYR* 1.3 60.2 + - - +
87A LYS* 3.2 19.7 - - - +
88A GLN* 2.6 28.3 + - - +
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Residues in contact with TYR 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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38A ILE* 3.5 42.6 - - + -
58A THR* 4.3 10.5 - - + +
60A VAL* 5.6 2.5 - - + -
74A VAL* 3.5 47.7 - - + +
76A VAL* 5.3 0.4 - - + -
81A ALA 3.4 7.8 + - - +
82A VAL* 2.9 13.8 + - + +
84A ALA* 1.3 74.0 - - - +
86A ALA* 1.3 57.4 + - - +
87A LYS 2.9 4.0 - - - -
88A GLN* 2.8 26.8 + - - +
89A HIS* 2.9 55.6 + + - -
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Residues in contact with ALA 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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38A ILE* 4.4 7.6 - - + +
82A VAL 3.0 10.7 + - - +
83A PHE* 4.0 6.3 - - + +
85A TYR* 1.3 84.6 - - - +
87A LYS* 1.3 65.5 + - - +
89A HIS 3.2 24.9 - - - +
90A PRO* 3.5 6.2 - - - +
92A GLN 5.2 3.0 - - - +
94A LEU* 4.1 34.8 - - + +
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Residues in contact with LYS 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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83A PHE* 2.8 33.4 + - + +
84A ALA* 3.2 11.7 - - - +
85A TYR 2.9 0.2 + - - -
86A ALA* 1.3 82.8 - - - +
88A GLN* 1.3 61.8 + - + +
89A HIS 3.2 0.8 + - - -
90A PRO* 3.6 12.0 - - - +
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Residues in contact with GLN 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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84A ALA* 2.6 34.0 + - - +
85A TYR* 2.8 11.7 + - - +
87A LYS* 1.3 74.8 - - + +
89A HIS* 1.3 71.4 + - + +
90A PRO* 3.2 12.2 - - - +
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Residues in contact with HIS 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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38A ILE* 3.8 17.4 - - + +
85A TYR* 2.9 68.2 + + - +
86A ALA 3.2 10.6 - - - +
87A LYS 3.2 0.4 - - - -
88A GLN* 1.3 93.3 + - + +
90A PRO* 1.3 56.3 - - - +
91A ASP* 3.0 23.0 + - - +
92A GLN* 3.3 16.2 + - - +
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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