Contacts of the helix formed by residues 61 - 82 (chain X) in PDB entry 5LMQ
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 61 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X LEU* 3.8 20.0 - - + +
44X ASP* 3.5 10.5 - - - +
60X MET* 1.3 67.7 - - - +
62X TYR* 1.3 53.9 + - - +
63X SER* 3.2 20.4 + - - -
64X LYS* 3.2 33.5 + - + +
65X TRP* 2.7 37.5 + - - +
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Residues in contact with TYR 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X GLU* 4.2 5.7 - - - +
5X TYR* 3.2 39.9 + - + -
7X THR* 3.4 29.2 - - + -
10X ARG* 4.1 14.4 + - - -
44X ASP* 2.6 31.3 + - + +
46X VAL* 3.8 14.1 - - + -
60X MET* 3.0 12.5 + - - -
61X ASP* 1.3 71.8 - - - +
63X SER* 1.3 62.3 + - - +
65X TRP* 3.2 30.7 + + - +
66X ARG* 2.9 46.8 + - + +
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Residues in contact with SER 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A A 4.4 31.5 + - - +
701A C 5.3 1.0 + - - -
44X ASP* 3.5 4.4 + - - -
61X ASP* 3.2 12.3 + - - -
62X TYR* 1.3 85.3 - - - +
64X LYS* 1.3 65.5 + - - +
66X ARG* 3.2 7.6 + - - +
67X TYR* 2.9 28.6 + - - +
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Residues in contact with LYS 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A C 4.3 24.0 - - + +
703A G 6.1 0.7 - - - +
61X ASP* 3.2 35.8 + - - +
63X SER* 1.3 82.6 + - - +
65X TRP* 1.3 58.3 + - - +
67X TYR* 3.2 17.3 + - + -
68X GLU* 2.8 57.9 + - - +
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Residues in contact with TRP 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X LYS* 3.6 11.4 - - - -
5X TYR* 3.4 35.4 - + - -
58X ARG* 6.3 0.9 - - - -
60X MET* 3.4 35.9 - - + +
61X ASP 2.7 22.6 + - - +
62X TYR* 3.3 28.3 - + - +
64X LYS* 1.3 74.8 - - - +
66X ARG* 1.3 86.8 + - + +
68X GLU* 3.2 12.9 + - + +
69X GLN* 2.9 60.5 + - + +
17Z U 4.9 12.0 + - - -
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Residues in contact with ARG 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LYS* 4.5 14.6 - - - +
3X LYS* 3.4 44.4 + - - +
4X GLU* 4.3 21.8 + - - +
62X TYR* 2.9 33.4 + - + +
63X SER* 3.2 11.0 + - - +
65X TRP* 1.3 96.9 - - + +
67X TYR* 1.3 58.4 + - - +
69X GLN* 3.2 9.4 + - - +
70X GLN* 2.9 53.9 + - - +
73X GLU* 3.6 20.8 + - - -
77X ARG* 5.2 2.0 - - - +
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Residues in contact with TYR 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A A 4.5 3.4 - - - +
688A G 5.8 0.2 - - - +
700A G 4.1 22.7 - + - +
701A C 3.4 81.7 + + + +
63X SER 2.9 13.2 + - - +
64X LYS* 3.2 22.4 + - + +
66X ARG* 1.3 75.5 - - - +
68X GLU* 1.3 81.5 + - - +
70X GLN* 3.2 13.4 + - - +
71X MET* 2.9 57.9 + - + +
74X LYS* 5.6 0.4 - - - -
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Residues in contact with GLU 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X LYS* 2.8 53.9 + - - +
65X TRP* 3.2 12.8 - - + +
67X TYR* 1.3 98.2 - - - +
69X GLN* 1.3 65.9 + - - +
71X MET* 3.2 8.5 + - - +
72X ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X LYS* 6.4 0.4 - - + -
65X TRP* 2.9 58.1 + - + +
66X ARG* 3.3 15.5 - - - +
68X GLU* 1.3 80.0 - - - +
70X GLN* 1.3 53.2 + - - +
72X ALA* 3.2 6.5 + - - +
73X GLU* 2.5 57.6 + - - +
17Z U 3.9 46.4 + - - +
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Residues in contact with GLN 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A G 4.7 23.1 + - - -
51K LYS* 3.3 31.2 - - - +
66X ARG* 2.9 45.5 + - - +
67X TYR* 3.5 12.7 + - - +
69X GLN* 1.3 75.5 - - - +
71X MET* 1.3 54.5 + - - +
73X GLU* 3.4 8.6 - - - +
74X LYS* 2.5 60.8 + - - +
77X ARG* 3.9 17.7 + - - +
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Residues in contact with MET 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A G 3.0 39.7 - - + +
67X TYR* 2.9 36.9 + - + +
68X GLU* 3.4 11.0 - - - +
70X GLN* 1.3 77.8 - - - +
72X ALA* 1.3 61.0 + - - +
74X LYS* 3.3 20.9 - - + +
75X GLU* 2.9 36.0 + - - +
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Residues in contact with ALA 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X GLU 2.9 13.1 + - - +
69X GLN* 3.5 11.4 - - - +
71X MET* 1.3 75.1 - - - +
73X GLU* 1.3 65.0 + - + +
75X GLU* 3.1 27.3 + - - +
76X ALA* 3.2 12.0 + - - +
17Z U 4.9 19.5 - - - +
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Residues in contact with GLU 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X LYS* 3.4 39.2 + - - +
66X ARG* 3.6 13.7 + - - -
69X GLN* 2.5 44.1 + - + +
70X GLN* 3.4 3.1 + - - +
72X ALA* 1.3 70.9 - - + +
74X LYS* 1.3 55.5 - - - +
76X ALA* 3.2 8.4 + - + +
77X ARG* 2.7 75.4 + - + +
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Residues in contact with LYS 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A G 3.4 15.2 + - - -
697A U 3.9 22.3 + - - +
698A G 5.9 0.4 - - - -
699A C 5.2 2.2 - - - +
700A G 2.7 30.9 + - - +
67X TYR* 4.9 1.2 + - - -
70X GLN* 2.5 48.7 + - - +
71X MET* 3.3 29.9 - - + +
72X ALA 3.2 0.2 - - - -
73X GLU* 1.3 72.7 - - - +
75X GLU* 1.3 55.9 + - + +
77X ARG* 3.7 20.4 - - - +
78X LYS* 2.8 37.9 + - - +
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Residues in contact with GLU 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X MET* 2.9 31.0 - - - +
72X ALA* 3.1 15.4 + - - +
74X LYS* 1.3 78.0 - - + +
76X ALA* 1.3 60.6 + - - +
78X LYS* 3.7 6.9 - - - +
79X LYS* 3.1 24.3 + - - +
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Residues in contact with ALA 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ALA 3.2 9.8 + - - +
73X GLU* 3.4 12.6 - - + +
75X GLU* 1.3 79.5 - - - +
77X ARG* 1.3 51.3 + - + +
79X LYS* 3.1 7.6 + - - +
80X ALA* 2.6 36.9 + - - +
14Z A 5.4 2.0 + - - +
15Z G 4.6 21.7 + - - +
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Residues in contact with ARG 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A A 5.0 10.6 + - - -
51K LYS* 5.2 8.9 - - - +
66X ARG* 5.2 2.0 - - - +
70X GLN* 3.9 19.1 - - - +
73X GLU* 2.7 67.5 + - + +
74X LYS* 3.7 21.0 - - - +
76X ALA* 1.3 69.5 - - + +
78X LYS* 1.3 64.4 + - - +
80X ALA* 3.4 20.9 + - + +
81X LYS* 3.7 7.6 + - - +
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Residues in contact with LYS 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A U 3.1 53.1 + - - +
698A G 4.0 8.3 + - - +
785A G 5.4 0.8 + - - -
786A G 5.6 8.5 - - - -
74X LYS 2.8 21.7 + - - +
75X GLU* 3.7 7.0 - - - +
77X ARG* 1.3 73.0 - - - +
79X LYS* 1.3 56.5 + - - +
81X LYS* 4.2 3.1 + - - +
82X ARG* 3.5 18.4 + - - +
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Residues in contact with LYS 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLU 3.1 17.3 + - - +
76X ALA* 3.1 7.7 + - - +
78X LYS* 1.3 74.9 - - - +
80X ALA* 1.3 60.0 + - - +
81X LYS 3.5 0.7 - - - -
82X ARG* 3.3 25.7 - - + +
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Residues in contact with ALA 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X ALA 2.6 18.3 + - - +
77X ARG* 3.4 16.2 - - + +
78X LYS 3.3 0.6 - - - -
79X LYS* 1.3 73.3 - - - +
81X LYS* 1.3 64.9 + - - +
13Z C 5.6 2.1 + - - -
14Z A 4.1 21.5 - - - +
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Residues in contact with LYS 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A A 5.0 9.6 - - - +
77X ARG 3.7 6.4 + - - +
78X LYS 4.5 4.7 - - - +
80X ALA* 1.3 79.5 - - - +
82X ARG* 1.3 71.1 + - - +
83X THR 3.0 15.0 + - - +
84X GLU* 3.3 30.1 - - - +
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Residues in contact with ARG 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X LYS 3.5 9.7 + - - +
79X LYS* 3.3 32.5 - - + +
81X LYS* 1.3 74.5 - - - +
83X THR* 1.3 77.2 + - - +
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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