Contacts of the helix formed by residues 38 - 50 (chain P) in PDB entry 6Y5D
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 TYR 38 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O PHE* 3.4 28.5 - + + -
27O PRO* 3.7 18.8 - - + -
30O ARG* 3.3 38.4 - - - +
31O VAL* 4.4 10.8 - - + +
34O LEU* 3.4 19.6 - - + +
56O LEU* 4.9 4.4 - - + +
37P SER* 1.3 76.9 - - - +
39P SER* 1.3 65.1 + - - +
40P VAL 3.1 3.4 - - - -
41P TYR* 2.9 25.7 + + - -
42P VAL* 3.0 19.3 + - + +
64P ASN* 3.3 17.4 + - + +
67P VAL* 3.6 28.7 - - + +
68P ASN* 3.6 24.9 - - - -
71P PHE* 5.1 1.9 - - + -
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Residues in contact with SER 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P SER* 3.3 14.6 + - - -
38P TYR* 1.3 77.5 - - - +
40P VAL* 1.3 62.2 + - - +
43P TYR* 3.2 8.7 + - - +
60P MET* 3.2 40.9 - - - +
64P ASN* 2.8 28.3 + - - -
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Residues in contact with VAL 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P SER 4.9 1.3 - - - +
38P TYR 4.7 1.1 - - - -
39P SER* 1.3 81.7 - - - +
41P TYR* 1.3 95.1 + - + +
43P TYR* 3.7 7.4 + - + +
44P LYS* 3.2 41.4 + - + +
125V G 5.3 5.2 - - + -
126V C 3.8 22.0 - - - +
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Residues in contact with TYR 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O SER* 5.8 0.2 - - - -
25O GLN* 3.1 25.5 - - - +
26O PHE* 3.6 25.3 - - + -
27O PRO* 3.5 36.7 - - + +
30O ARG* 4.0 20.6 + - - -
37P SER 4.1 1.3 - - - -
38P TYR* 2.9 20.9 + + - +
40P VAL* 1.3 96.3 - - + +
42P VAL* 1.3 65.4 + - - +
43P TYR 3.2 0.2 - - - -
44P LYS* 3.3 17.6 + - + +
45P VAL* 3.0 27.2 + - - +
125V G 3.2 44.6 + - - -
126V C 4.7 0.6 + - - -
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Residues in contact with VAL 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O PHE* 3.8 20.6 - - + -
60O THR* 4.5 4.7 - - + -
64O LEU* 3.4 21.0 - - + +
38P TYR* 3.0 13.9 + - + +
41P TYR* 1.3 76.3 - - - +
43P TYR* 1.3 63.5 + - - +
45P VAL 3.2 1.0 + - - -
46P LEU* 3.1 18.7 + - - +
55P ILE* 4.6 2.5 - - + -
60P MET* 3.6 19.3 - - + -
63P MET* 3.6 38.1 - - + +
64P ASN* 3.9 13.5 - - - +
67P VAL* 4.3 11.4 - - + -
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Residues in contact with TYR 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P SER 3.2 15.8 + - - +
40P VAL* 3.7 9.0 - - + +
41P TYR 3.2 0.2 - - - -
42P VAL* 1.3 80.4 - - - +
44P LYS* 1.3 70.0 + - + +
46P LEU* 3.2 22.1 + - + +
47P LYS* 3.1 44.8 + - + +
53P THR 5.1 0.4 - - - -
54P GLY* 4.8 1.3 - - - -
55P ILE* 3.7 24.7 - - + -
60P MET* 3.7 9.4 - - + +
24U G 3.3 53.2 + - + -
25U G 4.6 12.1 + - - -
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Residues in contact with LYS 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O GLN* 3.8 33.1 + - + +
40P VAL* 3.2 32.6 + - + +
41P TYR* 3.3 21.7 + - + +
42P VAL 3.3 0.2 - - - -
43P TYR* 1.3 81.5 - - + +
45P VAL* 1.3 67.5 + - - +
47P LYS* 3.0 17.4 + - - +
48P GLN* 3.1 17.4 + - - +
125V G 4.6 13.1 + - - -
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Residues in contact with VAL 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O GLN* 4.1 6.5 - - + -
26O PHE* 3.4 27.4 - - + -
57O GLU* 3.8 19.7 - - + +
60O THR* 4.2 1.6 - - + -
61O ALA* 3.5 44.2 - - + +
64O LEU* 3.8 8.3 - - + -
41P TYR 3.0 14.8 + - - +
42P VAL 3.2 7.4 + - - +
44P LYS* 1.3 75.5 - - - +
46P LEU* 1.3 64.5 + - - +
48P GLN* 2.8 22.0 + - + +
49P VAL* 3.2 11.2 + - + +
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Residues in contact with LEU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O LEU* 3.5 25.9 - - + +
79O ILE* 3.2 28.7 - - + -
42P VAL 3.1 11.5 + - - +
43P TYR* 3.3 13.7 - - + +
44P LYS 3.2 0.2 - - - -
45P VAL* 1.3 76.1 - - - +
47P LYS* 1.3 52.5 + - + +
49P VAL* 3.2 8.0 - - + +
50P HIS* 2.7 40.9 + - + +
53P THR* 3.3 35.2 - - + +
54P GLY 3.4 23.6 - - - +
55P ILE* 3.8 18.6 - - + -
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Residues in contact with LYS 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P TYR* 3.1 51.0 + - + +
44P LYS* 3.0 11.4 + - - +
46P LEU* 1.3 77.3 - - - +
48P GLN* 1.3 68.1 + - - +
50P HIS 3.8 1.8 - - - -
51P PRO* 3.2 55.9 + - + +
52P ASP* 3.9 3.0 - - - +
53P THR 2.9 32.9 + - - +
54P GLY* 4.2 1.8 - - - +
24U G 5.1 0.2 + - - -
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Residues in contact with GLN 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O GLN* 3.4 43.2 + - + +
57O GLU* 5.4 2.0 - - - +
44P LYS* 3.1 13.6 + - - +
45P VAL* 2.8 13.2 + - + +
47P LYS* 1.3 79.3 - - - +
49P VAL* 1.3 65.6 + - + +
51P PRO* 4.9 2.6 - - - +
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Residues in contact with VAL 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ALA* 4.1 24.7 - - + -
64O LEU* 4.2 4.0 - - + -
65O GLU* 3.8 42.4 - - + +
45P VAL 3.2 11.2 + - - +
46P LEU* 3.2 21.1 - - - +
48P GLN* 1.3 85.5 - - + +
50P HIS* 1.3 79.9 + - + +
51P PRO* 3.7 6.4 - - - +
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Residues in contact with HIS 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O LEU 3.9 1.1 - - - -
65O GLU* 2.9 48.1 + - + +
68O GLY* 3.7 14.6 - - - -
69O ASN* 3.1 23.8 + - - -
72O ARG* 3.3 32.5 + - - +
46P LEU* 2.7 23.8 + - + +
47P LYS* 3.8 2.3 - - - -
49P VAL* 1.3 81.0 + - + +
51P PRO* 1.3 64.0 - - - +
52P ASP* 3.1 2.7 - - - -
53P THR* 3.0 43.4 + - - +
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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