Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 3LHD
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 HIS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLN* 6.4 0.6 - - - +
76A ILE* 3.8 31.6 + - + +
77A VAL* 1.3 77.4 - - - +
79A PRO* 1.4 67.8 - - + +
80A LYS* 3.2 12.6 - - + -
81A ASP* 2.7 41.6 + - - +
82A ALA* 3.0 10.5 + - - +
193A TYR* 5.1 0.9 + - - -
241A LEU* 3.8 23.6 - - + +
244A THR* 3.6 25.8 - - + +
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Residues in contact with PRO 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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67A LEU* 6.1 4.7 - - + -
76A ILE* 5.0 5.8 - - + -
77A VAL 4.0 4.3 - - - +
78A HIS* 1.4 91.2 - - + +
80A LYS* 1.3 57.8 + - - +
81A ASP 3.2 0.2 + - - -
82A ALA* 3.3 10.2 + - + +
83A ALA* 2.9 29.9 + - - +
110A PHE* 5.4 6.1 - - + -
87B ALA* 4.0 10.4 - - + +
88B TYR* 3.9 25.6 - - + +
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Residues in contact with LYS 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 HIS* 4.1 6.5 - - + -
79A PRO* 1.3 79.5 - - + +
81A ASP* 1.3 88.6 + - - +
83A ALA* 3.4 9.4 - - - +
84A LEU* 3.3 26.9 - - - +
221A ASN* 5.7 0.4 - - - +
222A VAL* 2.8 35.7 + - + +
223A LEU* 5.0 0.4 - - - +
224A VAL* 3.9 37.0 - - + +
241A LEU* 4.2 23.1 - - + -
242A VAL 6.0 0.7 - - - -
243A HIS* 5.5 0.4 - - - +
244A THR* 3.1 34.6 + - - +
245A GLY 5.4 0.8 + - - -
84B LEU* 4.3 10.5 - - + -
88B TYR* 4.4 7.6 - - - +
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Residues in contact with ASP 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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77A VAL* 3.9 13.7 - - + -
78A HIS* 2.7 37.1 + - - +
80A LYS* 1.3 92.5 + - - +
82A ALA* 1.3 64.6 + - - +
83A ALA 3.2 0.4 + - - -
84A LEU 3.3 1.4 + - - -
85A ILE* 3.1 29.8 + - + +
193A TYR* 3.8 12.1 - - + -
222A VAL* 3.2 11.9 - - - +
244A THR* 2.7 23.1 + - - -
245A GLY 4.5 3.5 - - - +
247A ILE* 3.8 20.7 - - + +
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Residues in contact with ALA 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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77A VAL* 4.6 4.2 - - + +
78A HIS 3.0 9.7 + - - +
79A PRO* 3.4 12.3 - - + +
81A ASP* 1.3 77.1 - - - +
83A ALA* 1.3 62.4 + - - +
85A ILE* 3.3 12.7 + - - +
86A VAL* 3.0 27.2 + - - +
107A LEU* 4.2 17.0 - - + -
110A PHE* 3.5 33.7 - - + -
111A LEU* 5.6 0.3 - - - +
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Residues in contact with ALA 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 PRO 2.9 13.6 + - - +
80A LYS* 3.4 13.0 - - - +
81A ASP 3.2 0.2 - - - -
82A ALA* 1.3 76.1 - - - +
84A LEU* 1.3 60.2 + - + +
86A VAL* 3.3 6.3 + - - +
87A ALA 2.8 22.3 + - - -
110A PHE* 4.2 4.7 - - - -
83B ALA* 3.3 40.7 - - + +
84B LEU* 4.2 6.3 - - + -
87B ALA* 3.6 13.7 - - + -
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Residues in contact with LEU 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 LYS 3.3 17.0 - - - +
81A ASP 3.3 6.7 + - - +
83A ALA* 1.3 77.7 - - + +
85A ILE* 1.3 58.8 + - - +
87A ALA* 4.0 4.7 - - + -
88A TYR* 2.7 72.5 + - + +
220A ILE* 3.9 19.7 - - + -
222A VAL* 4.0 15.3 - - + -
247A ILE* 4.6 5.4 - - + -
249A PHE* 4.0 2.2 - - - -
80B LYS* 4.2 14.1 - - + +
83B ALA* 4.5 2.9 - - + -
84B LEU* 3.8 24.9 - - + -
222B VAL* 5.2 0.2 - - + -
224B VAL* 3.9 19.1 - - + -
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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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77A VAL* 4.9 9.6 - - + -
81A ASP* 3.1 21.9 + - + +
82A ALA* 3.5 11.4 - - - +
84A LEU* 1.3 75.0 - - - +
86A VAL* 1.3 64.0 + - - +
89A ALA* 3.0 30.7 + - - +
91A ILE* 3.8 17.0 - - + -
107A LEU* 4.9 12.6 - - + -
111A LEU* 4.7 4.9 - - + -
167A ILE* 4.2 20.2 - - + -
191A VAL* 3.8 22.0 - - + -
193A TYR* 5.1 8.3 - - + -
247A ILE* 3.7 31.4 - - + -
249A PHE* 3.7 6.7 - - - -
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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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82A ALA 3.0 17.6 + - - +
83A ALA* 3.4 9.6 - - - +
85A ILE* 1.3 74.6 - - - +
87A ALA* 1.3 59.0 + - - +
90A GLY* 2.9 26.3 + - - -
91A ILE* 3.1 43.7 + - + +
110A PHE* 3.4 25.8 - - + -
111A LEU* 4.5 5.4 - - + -
114A ILE* 4.2 16.4 - - + -
83B ALA* 6.1 0.7 - - + -
86B VAL* 5.3 5.4 - - + -
110B PHE* 5.0 6.5 - - + -
114B ILE* 4.2 20.0 - - + -
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Residues in contact with ALA 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 ALA 2.8 20.6 + - - +
84A LEU* 3.2 7.4 + - + +
86A VAL* 1.3 77.4 - - - +
88A TYR* 1.3 72.5 + - + +
90A GLY* 3.4 1.6 + - - -
63B ILE* 5.6 0.3 - - - +
64B VAL* 3.4 18.0 - - - +
67B LEU* 5.8 1.2 - - - +
79B PRO* 3.9 15.8 - - + +
83B ALA* 3.5 20.6 - - + -
110B PHE* 4.2 21.2 - - + -
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Residues in contact with TYR 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 LEU* 2.7 42.5 + - + +
87A ALA* 1.3 80.7 - - + +
89A ALA* 1.3 60.2 + - - +
90A GLY 3.3 0.2 - - - -
189A PHE* 3.7 16.1 - - - -
218A ARG* 4.0 39.4 + - + +
220A ILE* 3.7 28.0 - - + -
249A PHE* 3.6 22.6 - + + -
64B VAL* 3.7 12.3 - - + +
79B PRO* 4.3 24.2 - - + +
80B LYS* 4.2 14.0 + - - +
224B VAL* 4.2 11.3 - - + +
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Residues in contact with ALA 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 3.0 19.5 + - - +
88A TYR* 1.3 77.6 - - - +
90A GLY* 1.3 63.7 + - - +
91A ILE* 3.9 13.5 - - + -
165A HIS* 3.4 10.1 - - - +
189A PHE* 3.4 42.5 - - + -
191A VAL* 4.1 13.2 - - + -
249A PHE* 3.7 10.4 - - + -
62B ARG* 4.5 2.9 + - - +
64B VAL* 4.3 2.4 - - - +
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Residues in contact with GLY 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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86A VAL 2.9 9.9 + - - -
87A ALA 3.4 2.2 + - - -
88A TYR 3.3 3.0 - - - -
89A ALA* 1.3 77.8 - - - +
91A ILE* 1.3 56.8 + - - +
92A SER* 3.0 11.2 + - - -
62B ARG* 2.7 31.0 + - - -
63B ILE* 3.5 22.9 - - - +
64B VAL* 3.7 12.1 - - - +
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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