Contacts of the helix formed by residues 59 - 74 (chain P) in PDB entry 6P18
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26P TRP* 3.1 19.0 + - - -
58P CYS* 1.3 79.7 - - - +
60P ASP* 1.3 61.2 + - - +
61P ASP* 2.8 26.9 - - - +
62P ASP* 2.9 40.9 + - - +
63P GLY 3.8 0.2 + - - -
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Residues in contact with ASP 60 (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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26P TRP* 3.8 23.7 - - - +
31P ARG* 5.4 7.3 - - - +
59P ASN* 1.3 80.2 + - - +
61P ASP* 1.3 64.5 + - + +
63P GLY* 3.3 3.8 + - - -
64P MET* 2.9 29.5 + - - +
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Residues in contact with ASP 61 (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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59P ASN* 2.8 19.1 - - - +
60P ASP* 1.3 74.4 + - + +
62P ASP* 1.3 60.2 + - - +
63P GLY 3.3 0.2 - - - -
64P MET* 3.3 11.7 + - + +
65P LEU* 2.9 26.9 + - - +
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Residues in contact with ASP 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P TRP* 4.3 22.2 - - + -
58P CYS* 3.7 11.7 - - - +
59P ASN* 2.9 50.8 + - - +
61P ASP* 1.3 77.3 + - - +
63P GLY* 1.3 71.8 + - - -
65P LEU* 3.2 13.4 + - + +
66P ILE* 3.0 33.6 + - - +
149P PHE* 6.2 2.5 - - + -
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Residues in contact with GLY 63 (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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23P TRP* 3.6 18.0 + - - -
26P TRP* 4.4 12.1 - - - -
58P CYS* 4.0 17.7 - - - -
59P ASN 4.2 0.4 - - - -
60P ASP 3.3 5.2 + - - -
62P ASP* 1.3 84.5 + - - +
64P MET* 1.3 59.0 + - - +
66P ILE* 4.4 1.8 - - - -
67P SER* 2.9 29.9 + - - -
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Residues in contact with MET 64 (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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26P TRP* 4.5 10.9 - - + -
32P LEU* 4.1 24.5 - - + -
33P GLU* 5.1 9.0 - - + +
36P MET* 4.6 17.9 - - + -
60P ASP* 2.9 19.0 + - - +
61P ASP* 3.4 15.0 - - + +
62P ASP 3.2 0.2 - - - -
63P GLY* 1.3 78.3 - - - +
65P LEU* 1.3 56.4 + - - +
67P SER* 2.8 19.2 + - - -
68P GLN* 3.0 24.1 + - + +
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Residues in contact with LEU 65 (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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61P ASP 2.9 14.5 + - - +
62P ASP* 3.2 13.2 + - + +
64P MET* 1.3 75.3 - - - +
66P ILE* 1.3 64.4 + - + +
68P GLN* 3.2 31.4 + - + +
69P VAL* 3.1 22.9 + - + +
148P ALA* 4.0 26.2 - - + +
149P PHE* 3.7 35.9 - - + -
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Residues in contact with ILE 66 (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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19P TRP* 4.9 22.0 - - + +
20P LEU* 5.2 11.7 - - + -
23P TRP* 3.5 41.3 - - + -
62P ASP 3.0 21.2 + - - +
63P GLY* 4.4 0.9 - - - -
64P MET 3.4 0.2 - - - -
65P LEU* 1.3 78.2 - - + +
67P SER* 1.3 61.5 + - - +
69P VAL* 3.2 10.1 - - + +
70P VAL* 3.1 25.2 + - + +
145P LEU* 4.2 18.6 - - + -
149P PHE* 3.7 35.0 - - + -
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Residues in contact with SER 67 (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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23P TRP* 3.4 23.9 - - - +
26P TRP* 4.7 1.9 - - - -
32P LEU* 4.1 25.0 - - - +
36P MET* 4.0 6.0 - - - +
40P ILE* 5.7 1.5 - - - +
63P GLY 2.9 11.8 + - - -
64P MET* 2.8 28.4 + - - -
66P ILE* 1.3 77.1 - - - +
68P GLN* 1.3 58.2 + - - +
70P VAL* 3.3 8.5 - - - +
71P ASP* 2.9 27.9 + - - +
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Residues in contact with GLN 68 (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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36P MET* 4.6 13.6 - - - +
64P MET* 3.0 23.3 + - + +
65P LEU* 3.2 37.6 + - + +
67P SER* 1.3 77.6 + - - +
69P VAL* 1.3 82.4 + - - +
71P ASP* 2.9 17.1 - - - +
72P SER* 3.2 18.2 + - - -
148P ALA* 4.5 4.6 - - - +
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Residues in contact with VAL 69 (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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65P LEU* 3.1 13.0 + - + +
66P ILE* 3.2 30.5 - - + +
68P GLN* 1.3 89.3 - - - +
70P VAL* 1.3 62.9 + - + +
72P SER* 2.8 20.1 + - - +
73P VAL* 3.2 14.9 + - + +
141P ILE* 5.2 5.8 - - + +
144P VAL* 3.7 40.2 - - + +
145P LEU* 4.4 12.6 - - + +
148P ALA* 4.1 14.1 - - + -
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Residues in contact with VAL 70 (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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20P LEU* 5.6 3.6 - - + -
23P TRP* 3.6 32.3 - - + -
40P ILE* 5.8 1.1 - - + -
66P ILE* 3.1 21.7 + - + +
67P SER 3.3 10.5 - - - +
69P VAL* 1.3 79.5 - - + +
71P ASP* 1.3 56.9 + - + +
73P VAL* 4.1 4.5 - - - -
74P MET* 3.0 33.6 + - + +
81P PHE* 3.6 25.5 - - + -
84P LEU* 4.3 10.5 - - + -
141P ILE* 3.7 24.0 - - + -
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Residues in contact with ASP 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P MET* 3.3 19.8 - - - +
37P SER* 3.3 31.5 - - - +
39P VAL* 5.4 3.4 - - + -
40P ILE* 4.6 9.9 - - + -
67P SER 2.9 18.1 + - - +
68P GLN* 2.9 31.0 - - - +
70P VAL* 1.3 76.5 - - + +
72P SER* 1.3 59.8 + - - +
74P MET 4.3 7.6 - - - +
75P TYR* 3.4 22.0 - - + +
81P PHE* 5.1 4.5 - - + -
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Residues in contact with SER 72 (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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68P GLN* 3.2 18.1 + - - -
69P VAL* 2.8 28.1 + - - +
71P ASP* 1.3 79.5 - - - +
73P VAL* 1.3 59.1 + - - +
74P MET 3.6 0.2 - - - -
75P TYR* 3.2 24.6 - - - -
144P VAL* 5.0 3.3 - - - +
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Residues in contact with VAL 73 (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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69P VAL* 3.3 16.4 - - + +
70P VAL 3.7 5.4 - - - +
72P SER* 1.3 81.0 + - - +
74P MET* 1.3 84.5 + - + +
75P TYR* 3.5 6.1 + - - -
76P ILE* 4.5 11.1 - - - +
140P MET* 3.6 26.2 - - + +
141P ILE* 3.8 19.1 - - + -
144P VAL* 4.3 22.9 - - + -
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Residues in contact with MET 74 (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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39P VAL* 5.6 2.9 - - - +
70P VAL* 3.0 31.3 + - + +
71P ASP* 4.6 3.7 - - - -
73P VAL* 1.3 101.5 - - + +
75P TYR* 1.3 57.6 + - - +
76P ILE* 3.4 11.2 - - + +
77P ASP* 3.5 22.4 - - + +
80P ALA* 4.9 15.0 - - + -
81P PHE* 4.0 30.6 - - + +
84P LEU* 5.2 4.5 - - + -
137P SER* 4.8 19.5 - - - +
140P MET* 4.0 28.0 - - + -
141P ILE* 4.7 4.3 - - + -
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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