Contacts of the helix formed by residues 59 - 71 (chain O) in PDB entry 5D4D
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 ASN 59 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696N HIS 3.4 12.2 + - - +
697N GLY* 3.2 32.2 - - - -
698N LYS* 3.5 14.5 - - - +
756N GLN* 5.3 0.6 + - - +
760N ARG* 3.0 15.6 + - - +
57O ASP* 3.0 16.4 + - - +
58O PRO* 1.3 76.4 - - - +
60O ALA* 1.3 60.7 + - - +
61O VAL* 2.9 19.2 + - - +
62O THR* 3.1 16.8 + - - +
63O TRP* 3.0 29.9 + - - -
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Residues in contact with ALA 60 (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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753N SER* 4.6 2.0 - - - +
27O ALA* 3.6 34.3 - - + +
30O LEU* 4.1 1.5 - - + +
31O LEU* 3.7 26.9 - - + -
35O PHE* 3.9 18.8 - - + -
58O PRO 3.3 3.0 + - - -
59O ASN* 1.3 72.3 + - - +
61O VAL* 1.3 61.1 + - - +
63O TRP* 3.3 3.4 - - - +
64O ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753N SER* 3.7 29.8 - - - +
756N GLN* 4.6 6.7 - - + -
757N ALA* 4.4 15.5 - - + +
760N ARG* 3.4 26.0 - - + +
761N ILE* 6.1 0.4 - - + -
23O VAL* 3.9 16.6 - - + -
27O ALA* 4.0 16.2 - - + -
59O ASN* 2.9 9.7 + - - +
60O ALA* 1.3 75.3 - - - +
62O THR* 1.3 63.9 + - - +
64O ALA* 3.1 4.8 + - - +
65O MET* 2.9 36.6 + - - +
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Residues in contact with THR 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697N GLY* 4.6 4.0 - - - -
760N ARG* 3.2 22.7 + - - +
3O GLU* 5.6 1.3 - - - +
46O PRO* 4.6 10.3 - - + -
57O ASP* 4.3 17.1 + - - +
59O ASN* 3.1 31.8 + - - +
61O VAL* 1.3 76.1 - - - +
63O TRP* 1.3 64.0 + - - +
65O MET* 3.2 6.4 + - - +
66O LYS* 3.0 25.8 + - + +
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Residues in contact with TRP 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O LEU* 3.6 13.2 - - + -
35O PHE* 3.9 30.3 - + + -
38O THR* 3.2 34.5 - - + -
40O LEU* 3.6 22.3 - - + +
45O ARG* 3.6 47.3 - - + -
46O PRO* 3.5 31.9 - - + +
56O ASP* 4.3 13.0 - - + -
57O ASP* 2.8 27.8 + - + +
59O ASN 3.0 22.3 + - - -
60O ALA* 3.3 10.3 - - - +
62O THR* 1.3 80.5 - - - +
64O ALA* 1.3 57.1 + - - +
66O LYS* 3.2 1.7 + - - +
67O GLU* 2.8 37.0 + - - +
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Residues in contact with ALA 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O VAL* 3.5 31.6 - - + +
26O ARG* 3.7 18.1 - - + +
27O ALA* 3.9 2.7 - - - +
30O LEU* 4.1 0.9 - - + +
60O ALA 2.9 15.2 + - - +
61O VAL 3.1 8.5 + - - +
63O TRP* 1.3 76.2 - - - +
65O MET* 1.3 58.6 + - - +
67O GLU* 3.5 13.6 - - - +
68O LEU* 2.9 31.7 + - - +
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Residues in contact with MET 65 (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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760N ARG* 4.8 2.7 - - - -
761N ILE* 4.5 17.5 - - + -
3O GLU* 3.6 47.1 - - + +
4O PRO 5.1 3.6 - - - +
6O ILE* 4.8 3.1 - - + -
9O LEU* 3.6 26.9 - - + +
23O VAL* 3.8 23.3 - - + -
61O VAL* 2.9 36.8 + - - +
62O THR* 3.8 4.7 - - - +
64O ALA* 1.3 75.7 - - - +
66O LYS* 1.3 66.4 + - - +
68O LEU* 3.2 6.6 + - - +
69O LEU* 3.0 31.5 + - + +
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Residues in contact with LYS 66 (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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40O LEU* 4.3 13.0 - - + -
44O GLU* 3.6 29.6 + - - +
45O ARG 5.4 1.0 + - - -
46O PRO* 4.3 19.4 - - + +
62O THR* 3.0 18.5 + - + +
63O TRP 3.7 3.1 - - - +
65O MET* 1.3 75.8 - - - +
67O GLU* 1.3 64.2 + - - +
69O LEU* 3.3 25.2 + - + +
70O THR* 3.3 15.6 - - + +
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Residues in contact with GLU 67 (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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26O ARG* 2.3 56.0 + - - +
30O LEU* 3.4 15.4 - - - +
38O THR* 3.1 12.9 + - - -
39O VAL* 3.0 25.8 + - + +
40O LEU* 3.6 27.1 - - + -
63O TRP* 2.8 20.9 + - - +
64O ALA* 3.5 4.2 - - - +
66O LYS* 1.3 77.3 - - - +
68O LEU* 1.3 61.4 + - - +
70O THR* 2.6 27.9 + - - -
71O GLY 3.9 0.5 + - - -
72O ARG 4.6 1.0 + - - -
73O LEU* 4.2 7.7 - - + +
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Residues in contact with LEU 68 (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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9O LEU* 3.8 11.9 - - + -
12O MET* 3.3 26.0 - - - +
19O LEU* 3.6 31.2 - - + -
22O VAL* 3.8 25.6 - - + -
23O VAL* 3.8 16.4 - - + -
26O ARG* 5.8 0.9 - - + -
64O ALA 2.9 15.1 + - - +
65O MET 3.2 5.6 + - - +
67O GLU* 1.3 75.5 - - - +
69O LEU* 1.3 62.3 + - - +
70O THR 3.2 0.7 + - - -
71O GLY* 3.4 10.7 + - - -
73O LEU* 3.8 33.1 + - + +
75O PHE* 4.4 14.1 - - + -
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Residues in contact with LEU 69 (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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4O PRO* 4.0 23.3 - - + +
5O GLY* 4.0 25.4 - - - +
8O LYS* 3.2 50.6 + - + +
9O LEU* 4.4 11.2 - - + -
12O MET* 3.9 7.0 - - + +
65O MET* 3.0 20.9 + - + +
66O LYS* 3.4 21.1 - - + +
67O GLU 3.1 0.2 - - - -
68O LEU* 1.3 78.1 - - - +
70O THR* 1.3 61.2 + - + +
71O GLY* 3.5 0.5 + - - -
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Residues in contact with THR 70 (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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8O LYS* 5.6 0.2 + - - -
39O VAL* 4.4 1.2 - - - +
40O LEU* 3.8 21.3 - - + -
44O GLU* 4.9 2.9 - - - +
66O LYS* 3.3 18.4 - - + +
67O GLU 2.6 15.7 + - - +
69O LEU* 1.3 78.1 - - + +
71O GLY* 1.3 58.8 + - - +
72O ARG* 3.1 46.6 + - - +
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Residues in contact with GLY 71 (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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1489N GLN* 5.4 3.1 + - - -
12O MET* 5.7 2.5 - - - -
67O GLU 3.9 0.2 + - - -
68O LEU 3.4 10.6 + - - -
69O LEU 3.4 3.7 - - - -
70O THR* 1.3 78.4 + - - +
72O ARG* 1.3 62.7 + - - +
73O LEU 3.3 14.0 - - - +
74O VAL* 5.6 0.2 - - - +
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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