Contacts of the helix formed by residues 63 - 81 (chain g) in PDB entry 5M32
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 THR 63 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60g LEU 4.5 0.2 + - - -
62g VAL* 1.3 81.9 - - - +
64g HIS* 1.3 64.8 + - - +
65g GLU 3.5 1.6 - - - -
66g LEU* 3.4 14.3 - - - +
67g GLN* 3.3 22.7 + - - +
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Residues in contact with HIS 64 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60g LEU* 3.9 16.3 + - + +
62g VAL 3.9 0.2 - - - -
63g THR* 1.3 75.4 - - - +
65g GLU* 1.3 64.5 + - - +
66g LEU 3.1 1.7 + - - -
67g GLN* 3.5 11.8 + - - +
68g ALA* 3.5 12.8 + - - +
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Residues in contact with GLU 65 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60g LEU 4.8 2.2 + - - -
61g ARG* 5.0 15.6 + - + +
63g THR 4.9 0.4 - - - +
64g HIS* 1.3 75.0 - - - +
66g LEU* 1.3 63.8 + - - +
68g ALA* 4.1 7.1 + - - +
69g MET* 3.8 16.8 + - - +
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Residues in contact with LEU 66 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36f LEU* 5.7 9.0 - - + -
61g ARG 5.6 0.2 + - - -
62g VAL 4.4 5.3 + - - +
63g THR* 3.4 25.8 + - - +
64g HIS 3.1 0.4 - - - -
65g GLU* 1.3 78.5 - - - +
67g GLN* 1.3 57.9 + - - +
69g MET* 3.1 9.6 + - - +
70g LYS* 2.9 23.5 + - - +
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Residues in contact with GLN 67 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63g THR 3.3 12.7 + - - +
64g HIS* 3.5 5.3 + - - +
66g LEU* 1.3 77.2 - - - +
68g ALA* 1.3 60.0 + - - +
70g LYS* 3.5 11.1 - - + +
71g ASP* 2.9 28.8 + - - +
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Residues in contact with ALA 68 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64g HIS 3.5 13.0 + - - +
65g GLU* 4.5 6.5 - - - +
66g LEU 3.3 0.6 - - - -
67g GLN* 1.3 78.4 - - - +
69g MET* 1.3 56.8 + - - +
71g ASP* 4.1 4.5 - - - +
72g LYS* 2.9 30.5 + - - +
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Residues in contact with MET 69 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65g GLU 3.8 10.6 + - - +
66g LEU* 3.1 11.0 + - - +
68g ALA* 1.3 77.9 - - - +
70g LYS* 1.3 59.2 + - - +
71g ASP 3.3 0.2 - - - -
72g LYS* 4.7 1.1 - - - -
73g ILE* 2.6 45.5 + - + +
74g LYS* 3.1 1.9 + - - +
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Residues in contact with LYS 70 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66g LEU 2.9 12.2 + - - +
67g GLN* 3.3 15.0 + - + +
69g MET* 1.3 77.2 - - - +
71g ASP* 1.3 58.0 + - - +
74g LYS* 2.7 38.6 + - + +
75g GLU 3.2 2.1 + - - -
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Residues in contact with ASP 71 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67g GLN 2.9 16.6 + - - +
68g ALA* 4.1 5.4 - - - +
70g LYS* 1.3 78.6 - - - +
72g LYS* 1.3 55.0 + - - +
75g GLU* 2.5 37.1 + - - +
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Residues in contact with LYS 72 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47f LEU* 5.7 1.7 - - - +
68g ALA 2.9 18.9 + - - +
69g MET* 4.7 1.1 - - - -
71g ASP* 1.3 76.0 - - - +
73g ILE* 1.3 64.2 + - - +
75g GLU* 4.2 0.4 - - - +
76g ASN* 3.0 28.6 + - - +
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Residues in contact with ILE 73 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44f GLU* 5.9 9.0 - - + -
47f LEU* 5.1 19.9 - - + +
69g MET* 2.6 32.1 + - + +
72g LYS* 1.3 77.2 - - - +
74g LYS* 1.3 50.0 + - + +
76g ASN* 4.4 0.6 - - - +
77g SER* 2.7 40.4 + - - -
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Residues in contact with LYS 74 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69g MET 3.1 2.7 + - - +
70g LYS* 2.7 28.5 + - + +
73g ILE* 1.3 77.9 - - - +
75g GLU* 1.3 59.8 + - - +
76g ASN 3.4 0.4 - - - -
77g SER* 4.4 1.1 - - - -
78g GLU* 2.5 52.7 + - + +
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Residues in contact with GLU 75 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70g LYS 3.2 1.8 + - - -
71g ASP* 2.5 28.6 + - - +
72g LYS 4.2 0.4 - - - +
74g LYS* 1.3 76.2 - - - +
76g ASN* 1.3 51.3 + - - +
79g LYS* 2.5 39.0 + - - +
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Residues in contact with ASN 76 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47f LEU* 4.1 21.5 - - + -
50f LEU* 5.4 1.8 - - + -
72g LYS 3.0 17.4 + - - +
75g GLU* 1.3 74.7 - - - +
77g SER* 1.3 61.6 + - - +
79g LYS* 3.0 17.1 + - - +
80g ILE* 3.0 28.6 + - + +
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Residues in contact with SER 77 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46f ASP* 4.5 25.4 - - - -
47f LEU* 4.9 6.3 - - - -
50f LEU* 4.9 11.1 - - - +
73g ILE 2.7 25.9 + - - -
74g LYS* 4.4 0.9 - - - -
76g ASN* 1.3 74.1 - - - +
78g GLU* 1.3 57.3 + - - +
80g ILE* 3.6 2.6 + - - +
81g LYS* 2.9 44.4 + - - +
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Residues in contact with GLU 78 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74g LYS* 2.5 39.7 + - + +
75g GLU* 5.2 0.2 - - - -
77g SER* 1.3 74.9 - - - +
79g LYS* 1.3 59.7 + - - +
81g LYS* 2.9 42.0 + - - +
82g VAL* 2.9 31.6 + - + +
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Residues in contact with LYS 79 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75g GLU 2.5 25.6 + - - +
76g ASN* 3.0 6.5 + - - +
78g GLU* 1.3 75.4 - - - +
80g ILE* 1.3 66.0 + - + +
82g VAL* 2.9 31.4 + - + +
83g ASN* 3.0 38.7 + - - +
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Residues in contact with ILE 80 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50f LEU* 3.7 45.5 - - + -
76g ASN* 3.0 31.9 + - + +
77g SER 4.3 2.7 - - - +
79g LYS* 1.3 81.8 - - + +
81g LYS* 1.3 58.1 + - + +
83g ASN* 3.0 30.8 + - + +
84g LYS 3.2 8.3 + - - -
154g ASN* 4.4 20.4 - - - +
159g LEU* 5.2 0.2 - - + -
161g LEU* 3.3 20.6 - - + +
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Residues in contact with LYS 81 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46f ASP* 5.0 6.8 - - - +
77g SER* 2.9 36.3 + - - +
78g GLU* 2.9 44.4 + - - +
79g LYS 3.1 0.4 - - - -
80g ILE* 1.3 76.6 - - + +
82g VAL* 1.3 59.2 + - - +
84g LYS* 3.3 39.8 - - + +
85g THR* 5.6 0.2 + - - -
139g LEU* 3.7 41.3 - - + +
161g LEU* 5.2 4.7 - - + -
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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