Contacts of the helix formed by residues 78 - 91 (chain A) in PDB entry 2LAV
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 GLY 78 (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 3.7 1.7 + - - -
77A ASN* 1.3 78.1 - - - +
79A PRO* 1.3 72.7 - - - +
80A LEU 3.0 1.3 - - - -
81A PHE* 2.8 20.4 + - - +
82A THR* 3.1 10.2 + - - -
354A ILE* 4.5 5.2 - - - -
360A LYS* 6.0 2.6 - - - +
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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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77A ASN* 3.4 15.3 - - - +
78A GLY* 1.3 87.1 - - - +
80A LEU* 1.3 59.1 + - - +
82A THR* 3.1 10.7 + - - +
83A GLU 3.1 12.0 + - - -
352A LYS* 3.2 51.1 - - + +
354A ILE* 3.3 39.7 - - + -
357A LYS* 4.9 19.5 - - + +
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Residues in contact with LEU 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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71A LYS* 5.3 5.4 - - + +
73A GLU* 3.1 50.0 - - + +
74A PRO 3.2 25.6 - - - +
75A SER* 5.2 1.3 - - - +
77A ASN* 3.8 19.0 - - + +
78A GLY 2.8 4.6 + - - -
79A PRO* 1.3 73.9 - - - +
81A PHE* 1.3 64.4 + - + +
82A THR 3.0 5.9 + - - -
83A GLU* 3.0 12.6 + - - +
84A LEU* 3.1 17.5 + - + +
127A ARG* 4.4 20.6 - - + +
128A PHE* 6.1 0.4 - - - -
129A MET* 5.2 2.1 - - + +
351A ALA* 3.6 23.3 + - + +
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Residues in contact with PHE 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 SER 5.0 10.3 - - - +
77A ASN 4.1 10.0 + - - +
78A GLY* 2.8 15.2 + - - +
80A LEU* 1.3 78.8 - - + +
82A THR* 1.3 57.1 + - - +
84A LEU* 4.2 8.9 - - + +
85A LYS* 2.9 51.3 + - + +
127A ARG* 3.0 43.7 - - - +
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Residues in contact with THR 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 GLY 3.1 9.4 + - - -
79A PRO 3.1 5.5 + - - -
80A LEU 3.0 0.4 - - - -
81A PHE* 1.3 76.1 - - - +
83A GLU* 1.3 56.3 + - - +
84A LEU 3.2 0.2 - - - -
85A LYS* 3.8 6.0 - - + +
86A PHE* 2.7 40.1 + - + +
201A ALA 4.8 2.7 - - - +
202A TYR* 4.6 8.1 - - + -
353A THR* 2.8 26.9 - - + -
354A ILE* 2.7 39.2 - - + +
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Residues in contact with GLU 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 3.1 1.2 + - - -
80A LEU 3.0 5.9 + - - +
82A THR* 1.3 76.4 - - - +
84A LEU* 1.3 57.3 + - - +
86A PHE* 4.6 2.0 - - - -
87A TYR* 2.8 74.4 + - + -
129A MET* 2.8 29.4 - - + +
131A MET* 4.5 7.2 - - - +
197A ASP* 4.3 9.6 - - - +
198A TYR* 5.2 1.1 - - + +
350A LYS 3.7 3.5 - - - +
351A ALA* 2.7 33.2 - - + +
352A LYS* 3.3 35.2 - - - +
353A THR* 2.6 11.6 + - + +
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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 LEU* 3.1 18.3 + - + +
81A PHE* 4.2 9.4 - - + +
83A GLU* 1.3 75.7 - - - +
85A LYS* 1.3 70.4 + - + +
87A TYR* 3.9 1.0 - - - +
88A GLN* 3.2 24.8 + - + +
113A TYR* 4.2 8.1 - - - +
116A SER* 3.3 35.2 - - - +
127A ARG* 3.6 40.2 - - + +
128A PHE 4.2 0.9 - - - +
129A MET* 3.3 37.6 - - + +
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Residues in contact with LYS 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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81A PHE* 2.9 45.3 + - + +
82A THR* 3.2 6.5 + - + +
84A LEU* 1.3 81.6 - - + +
86A PHE* 1.3 58.7 + - - +
88A GLN* 5.0 2.0 - - - -
89A ARG* 3.0 62.3 + - + +
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Residues in contact with PHE 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 THR* 2.7 23.7 + - + +
83A GLU* 4.1 3.8 - - - +
85A LYS* 1.3 72.3 - - - +
87A TYR* 1.3 64.1 + + - +
89A ARG* 4.6 2.0 - - + -
90A ALA* 2.6 58.9 + - + +
91A ALA* 3.2 0.8 + - + -
168A ILE* 4.4 11.4 - - + -
173A TYR* 3.4 58.1 - + + -
198A TYR* 3.8 42.0 - + - -
201A ALA* 4.2 12.8 - - + -
353A THR* 4.1 14.4 - - + -
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Residues in contact with TYR 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 GLU* 2.8 51.1 + - + +
84A LEU 3.9 2.7 - - - +
85A LYS 3.2 0.2 - - - -
86A PHE* 1.3 85.9 - + - +
88A GLN* 1.3 59.4 + - - +
89A ARG 3.0 4.3 - - - -
91A ALA* 2.6 51.5 + - + -
111A PRO* 3.1 38.1 - - + +
112A LYS 4.4 9.2 - - - -
113A TYR* 3.6 17.3 - + + -
129A MET* 4.0 10.3 - - - -
131A MET* 3.2 34.2 - - + -
196A VAL* 3.5 13.7 - - - +
197A ASP 3.8 8.3 + - - -
198A TYR* 5.4 7.4 - + - -
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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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32A MET* 4.1 23.2 - - + +
84A LEU* 3.2 18.4 + - + +
85A LYS* 4.5 3.6 - - - +
87A TYR* 1.3 78.1 - - - +
89A ARG* 1.3 65.2 + - + +
91A ALA 4.9 0.2 - - - -
92A LYS* 2.9 40.1 + - - +
113A TYR* 3.1 43.6 + - + +
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Residues in contact with ARG 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 LYS* 3.0 47.8 + - + +
86A PHE* 4.3 2.2 - - + +
87A TYR 3.0 0.6 - - - -
88A GLN* 1.3 90.4 - - + +
90A ALA* 1.3 53.4 + - + +
92A LYS* 4.0 3.1 - - - +
95A GLN* 2.5 38.7 + - - +
173A TYR* 6.1 1.6 - - + -
203A ARG* 5.5 6.7 - - - +
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Residues in contact with ALA 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 PHE* 2.6 56.7 + - + +
89A ARG* 1.3 74.1 - - - +
91A ALA* 1.3 55.4 + - - +
92A LYS 3.1 10.4 + - - -
95A GLN* 3.6 11.3 + - - +
96A ILE* 4.4 2.1 - - - +
110A VAL* 5.4 2.3 - - - +
167A TYR* 3.4 31.2 + - + -
171A HIS* 6.4 1.3 - - + -
173A TYR* 5.8 2.7 - - + -
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Residues in contact with ALA 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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86A PHE* 3.2 1.5 + - + +
87A TYR* 2.6 51.7 + - + +
90A ALA* 1.3 71.5 - - - +
92A LYS* 1.3 60.0 + - - +
96A ILE* 3.5 10.3 - - - +
110A VAL* 4.8 7.9 - - + -
111A PRO* 3.3 22.2 - - + +
113A TYR* 3.0 24.8 + - + +
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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