Contacts of the helix formed by residues 58 - 70 (chain W) in PDB entry 1S72
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 SER 58 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57W PRO* 1.3 75.8 - - - +
59W GLN* 1.3 66.4 + - - +
60W GLU* 3.8 9.6 + - - +
61W THR* 3.0 16.3 + - - -
62W LEU* 3.0 22.3 + - - +
101W LEU* 4.2 1.1 - - - -
143W THR* 3.7 12.0 - - - +
147W ASP* 2.5 31.1 + - - -
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Residues in contact with GLN 59 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58W SER* 1.3 72.3 - - - +
60W GLU* 1.3 67.0 + - + +
62W LEU* 3.4 2.8 + - - +
63W GLU* 3.1 46.5 + - - +
94W SER* 3.2 9.5 + - - -
97W ALA* 3.2 8.0 - - - +
98W PHE* 3.1 53.5 - - - +
101W LEU* 3.7 18.9 - - + +
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Residues in contact with GLU 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58W SER* 3.2 8.5 - - - +
59W GLN* 1.3 81.4 - - + +
61W THR* 1.3 65.4 + - - +
63W GLU* 2.8 22.7 + - - +
64W THR* 2.9 17.8 + - - +
151W GLU* 5.7 1.1 - - - +
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Residues in contact with THR 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57W PRO* 4.5 0.4 - - + -
58W SER* 3.0 11.6 + - - -
60W GLU* 1.3 78.6 - - - +
62W LEU* 1.3 64.5 + - - +
64W THR* 3.1 9.2 + - - -
65W VAL* 3.0 22.7 + - + +
147W ASP* 2.8 32.1 + - - +
150W LEU* 3.7 42.2 - - + -
151W GLU* 2.6 32.9 + - + +
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Residues in contact with LEU 62 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W MET* 3.7 26.0 - - + -
34W LEU* 4.1 26.0 - - + -
57W PRO* 4.6 11.6 - - + +
58W SER 3.0 16.7 + - - +
59W GLN 3.7 4.9 - - - +
61W THR* 1.3 78.1 - - - +
63W GLU* 1.3 52.4 + - - +
65W VAL* 3.7 4.7 - - + +
66W LEU* 2.7 58.1 + - + +
97W ALA* 3.7 20.4 - - + +
100W LEU* 4.2 6.1 - - + -
101W LEU* 3.7 18.6 - - + -
116W LEU* 4.9 6.5 - - + -
150W LEU* 5.9 2.9 - - + -
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Residues in contact with GLU 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59W GLN* 3.1 43.8 + - - +
60W GLU* 2.8 14.6 + - - +
62W LEU* 1.3 75.7 - - - +
64W THR* 1.3 62.2 + - - +
66W LEU* 3.8 1.0 - - - +
67W ALA* 2.9 26.5 + - - +
93W ILE* 3.9 17.1 - - + +
94W SER* 2.7 36.1 + - - -
97W ALA* 3.7 15.9 - - + -
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Residues in contact with THR 64 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60W GLU* 2.9 14.1 + - - +
61W THR* 3.1 10.0 + - - -
63W GLU* 1.3 75.9 - - - +
65W VAL* 1.3 59.6 + - + +
67W ALA* 3.8 3.9 - - - +
68W THR* 2.9 31.2 + - - +
151W GLU* 5.1 12.8 + - + +
154W ARG* 4.2 27.4 - - + +
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Residues in contact with VAL 65 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W CYS* 5.8 0.2 - - - -
61W THR* 3.0 19.7 + - + +
62W LEU* 3.9 6.1 - - + +
64W THR* 1.3 76.2 - - + +
66W LEU* 1.3 57.9 + - - +
68W THR* 3.3 9.2 - - + -
69W ARG* 2.6 33.5 + - + +
70W ALA 3.8 0.5 + - - -
116W LEU* 3.6 28.9 - - + +
118W LEU* 4.0 21.3 - - + -
150W LEU* 3.8 44.6 - - + +
151W GLU* 5.3 0.9 - - + -
154W ARG* 4.8 5.2 - - + -
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Residues in contact with LEU 66 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34W LEU* 4.8 0.7 - - + -
62W LEU* 2.7 38.5 + - + +
63W GLU 3.8 3.4 - - - +
65W VAL* 1.3 72.1 - - - +
67W ALA* 1.3 65.2 + - - +
70W ALA* 2.8 41.3 + - + +
79W VAL* 4.1 4.8 - - + +
93W ILE* 4.0 15.0 - - + -
96W LEU* 4.4 11.2 - - + -
97W ALA* 3.9 26.0 - - + +
100W LEU* 3.7 24.5 - - + -
107W LEU* 4.1 26.0 - - + -
116W LEU* 4.3 11.7 - - + -
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Residues in contact with ALA 67 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63W GLU 2.9 18.4 + - - +
64W THR* 3.8 4.5 - - - +
66W LEU* 1.3 80.7 - - - +
68W THR* 1.3 61.8 + - - +
70W ALA 4.4 2.1 + - - +
78W ASP* 5.9 1.0 - - - +
79W VAL 3.7 15.8 + - - +
80W ASP* 5.6 0.7 - - - +
93W ILE* 3.4 28.2 - - + +
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Residues in contact with THR 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5670 U 5.1 1.4 + - - -
64W THR* 2.9 27.5 + - - +
65W VAL* 3.2 15.0 - - - +
67W ALA* 1.3 79.5 - - - +
69W ARG* 1.3 76.2 + - + +
70W ALA 5.3 0.7 - - - +
154W ARG* 3.1 45.9 + - + +
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Residues in contact with ARG 69 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5660 A 3.3 12.6 + - - -
5670 U 2.8 28.9 + - - -
12630 C 3.0 41.4 + - - -
12640 U 4.3 6.3 + - - -
65W VAL 2.6 18.0 + - - +
68W THR* 1.3 85.6 + - + +
70W ALA* 1.3 61.9 + - - +
71W GLU* 3.9 8.3 + - - +
115W THR 4.4 1.0 - - - +
116W LEU* 3.8 19.2 - - + -
117W ARG* 3.3 27.8 + - - +
118W LEU* 4.0 22.4 - - + +
119W HIS* 3.7 21.5 + - - +
153W MET 4.6 0.2 + - - -
154W ARG* 2.7 26.1 + - - +
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Residues in contact with ALA 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65W VAL 3.8 0.2 + - - -
66W LEU* 2.8 42.0 + - + +
67W ALA 4.4 1.2 + - - +
68W THR 3.8 0.9 - - - +
69W ARG* 1.3 79.6 - - - +
71W GLU* 1.3 65.6 + - - +
77W ALA 4.5 1.6 - - - +
78W ASP* 5.2 0.9 - - - -
79W VAL* 3.2 36.0 + - + +
107W LEU* 5.5 0.9 - - + -
112W LEU* 4.6 8.1 - - + -
116W LEU* 4.0 9.6 - - + -
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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