Contacts of the helix formed by residues 77 - 88 (chain O) in PDB entry 5LN3
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 VAL 77 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73O PRO 3.1 20.0 + - - +
74O LEU* 3.9 11.2 - - + +
75O SER 3.8 0.2 - - - -
76O LEU* 1.4 75.7 - - - +
78O GLU* 1.3 80.9 + - - +
80O ILE* 3.2 15.1 - - - +
81O LEU* 3.4 11.9 - - + +
96O PHE* 4.0 23.6 - - + -
100O THR* 4.9 4.7 - - + -
109O GLU* 5.0 2.0 - - + -
110O ALA* 3.7 42.2 - - + +
113O LEU* 3.7 15.3 - - + +
114O CYS* 5.0 1.8 - - - -
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Residues in contact with GLU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O PHE* 5.1 15.4 - - + -
74O LEU 5.2 0.9 - - - +
75O SER 3.9 17.7 - - - +
76O LEU* 3.2 6.0 + - + -
77O VAL* 1.3 96.2 - - - +
79O ILE* 1.3 65.2 + - + +
80O ILE 3.8 0.2 - - - -
81O LEU* 4.2 2.1 - - - +
82O HIS* 3.5 21.7 + - - +
109O GLU* 3.8 18.9 - - - +
113O LEU* 3.7 20.6 - - + +
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Residues in contact with ILE 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR* 5.8 1.6 - - - +
43O ASP* 3.6 38.3 - - + +
44O PHE* 3.9 30.3 - - + +
46O GLN 5.0 0.9 - - - +
47O ASP* 3.6 23.3 - - - +
60O TYR* 4.8 2.1 + - - -
76O LEU* 3.8 19.9 + - + +
77O VAL 3.7 0.4 - - - -
78O GLU* 1.3 84.7 - - + +
80O ILE* 1.3 65.6 - - - +
82O HIS* 4.1 16.8 - - + -
83O VAL* 3.8 15.7 - - + -
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Residues in contact with ILE 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O ILE* 5.5 0.5 - - - +
60O TYR* 4.2 23.6 - - + +
64O ILE* 3.7 33.9 - - + -
67O PHE* 5.9 2.7 - - + -
73O PRO* 4.4 20.0 - - + -
76O LEU 3.3 18.2 - - - +
77O VAL* 3.2 23.3 - - - +
79O ILE* 1.3 71.9 - - - +
81O LEU* 1.4 69.0 + - - +
82O HIS 3.3 2.1 - - - +
83O VAL* 3.4 15.2 + - - +
84O VAL* 3.3 25.5 + - + +
96O PHE* 3.8 30.3 - - + -
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O VAL* 3.4 17.5 - - + +
78O GLU 4.2 2.5 - - - +
80O ILE* 1.4 77.0 - - - +
82O HIS* 1.3 64.3 + - - +
84O VAL* 3.2 20.2 + - + +
85O ARG* 3.3 13.8 + - - +
93O ALA* 5.7 2.5 - - - +
96O PHE* 3.4 40.4 - - + -
113O LEU* 3.7 37.9 - - + +
114O CYS* 4.1 7.6 - - - +
117O ALA* 3.7 31.9 - - + -
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Residues in contact with HIS 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O ASP* 3.7 33.1 + - - +
78O GLU 3.5 17.3 + - - +
79O ILE* 4.1 16.4 - - + -
80O ILE 3.3 0.2 - - - -
81O LEU* 1.3 78.2 - - - +
83O VAL* 1.3 69.2 + - + +
85O ARG* 3.5 7.1 + - - +
86O GLN* 2.9 64.7 + - + +
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Residues in contact with VAL 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR* 6.2 0.4 - - - +
47O ASP* 4.8 0.9 - - - +
48O PRO* 4.4 22.7 - - + -
51O ALA* 3.9 27.7 - - + +
57O ILE* 3.9 16.2 - - + -
60O TYR* 5.2 13.9 - - + -
79O ILE* 3.8 27.1 - - + -
80O ILE* 3.4 15.8 + - - +
81O LEU 3.3 0.4 - - - -
82O HIS* 1.3 82.3 - - + +
84O VAL* 1.4 60.7 + - - +
86O GLN* 3.8 10.5 + - - +
87O MET* 3.6 20.1 + - - +
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Residues in contact with VAL 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O ILE* 4.5 15.5 - - + -
80O ILE* 3.3 17.7 + - + +
81O LEU* 3.2 16.0 + - + +
83O VAL* 1.4 75.9 - - - +
85O ARG* 1.4 62.3 - - - +
87O MET* 3.4 16.9 + - + +
88O THR* 3.6 4.0 + - - -
89O ASP* 4.5 7.0 + - + +
92O VAL* 3.7 24.5 - - + -
93O ALA* 3.6 37.2 - - + +
96O PHE* 5.2 14.4 - - + -
121O LEU* 5.9 0.2 - - - +
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Residues in contact with ARG 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O LEU 3.3 10.1 + - - +
82O HIS* 3.5 10.5 + - - +
84O VAL* 1.4 62.8 - - - +
86O GLN* 1.4 62.2 + - + +
88O THR* 3.3 34.5 + - - +
93O ALA* 6.5 0.4 - - - -
117O ALA* 4.0 21.8 - - + +
120O ALA* 3.0 36.4 + - - +
121O LEU* 3.5 39.7 + - - +
124O ASN* 3.2 27.7 + - - +
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Residues in contact with GLN 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O ASP* 4.8 6.0 - - - +
48O PRO* 6.1 0.3 - - - +
51O ALA 4.7 4.7 - - - +
52O GLN* 3.6 38.3 + - - +
53O GLY* 3.4 15.0 - - - -
82O HIS* 2.9 55.4 + - + +
83O VAL* 4.0 9.7 - - + +
84O VAL 3.3 0.4 - - - -
85O ARG* 1.4 77.8 - - + +
87O MET* 1.3 60.3 + - - +
88O THR* 3.2 8.9 + - - +
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Residues in contact with MET 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ALA* 3.6 32.8 - - + -
52O GLN 4.2 0.4 - - - -
53O GLY 3.4 31.6 - - - +
54O ASP* 4.6 0.2 - - - -
55O GLY 3.7 31.0 - - - +
57O ILE* 3.8 32.3 - - + -
83O VAL 3.6 15.0 + - - +
84O VAL* 3.4 8.9 + - + +
85O ARG 3.3 0.6 - - - -
86O GLN* 1.3 78.2 - - + +
88O THR* 1.4 67.9 + - - +
89O ASP* 3.3 22.2 - - - +
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Residues in contact with THR 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O GLY* 5.0 1.7 + - - -
84O VAL 3.6 1.4 + - - -
85O ARG* 3.3 35.5 + - - +
86O GLN 3.2 8.1 + - - +
87O MET* 1.4 81.3 + - - +
89O ASP* 1.3 64.7 + - - +
90O PRO* 4.2 4.0 - - - +
121O LEU* 4.4 11.7 - - + -
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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