Contacts of the helix formed by residues 53 - 64 (chain H) in PDB entry 5W97
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 CYS 53 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36H PHE* 3.4 31.8 - - + -
39H CYS* 2.0 69.5 - - + -
40H GLU* 3.2 7.2 - - + +
43H MET* 3.9 10.1 - - - -
50H VAL 3.0 17.0 + - - +
52H VAL* 1.3 77.9 - - - +
54H GLU* 1.3 60.6 + - - +
55H TRP 3.3 1.6 - - - -
56H TYR* 3.2 19.9 + - - +
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LYS* 6.1 7.2 - - + -
36H PHE* 5.0 2.2 - - - -
50H VAL 4.2 0.6 + - - -
51H SER* 3.5 24.4 + - - +
52H VAL 3.2 2.2 - - - -
53H CYS* 1.3 75.5 - - - +
55H TRP* 1.3 65.8 + - - +
57H ARG* 2.7 51.5 + - - +
58H ARG* 3.0 36.6 + - + +
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Residues in contact with TRP 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE 4.8 4.3 - - - -
9H LYS* 4.0 35.0 - - + -
11H TYR* 3.8 26.9 - + - -
15H PRO* 3.6 38.1 - - + -
32H ASN* 5.0 2.2 + - - -
52H VAL 4.4 5.5 + - - +
53H CYS 3.3 1.2 + - - -
54H GLU* 1.3 76.8 - - - +
56H TYR* 1.3 88.6 + + + +
58H ARG* 3.1 8.6 + - + +
59H VAL* 3.1 36.8 + - + +
46h LYS* 5.6 13.9 - - - +
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ARG* 6.1 2.2 - - - -
32H ASN* 3.8 24.5 - - - +
35H ASP* 3.9 42.0 + - + -
36H PHE* 3.8 20.2 - - + +
39H CYS* 4.5 15.0 - - + -
52H VAL 5.2 3.8 - - - -
53H CYS* 3.2 21.2 + - - +
55H TRP* 1.3 95.3 - + + +
57H ARG* 1.3 56.9 + - - +
59H VAL* 3.4 2.1 + - - +
60H TYR* 3.0 31.0 + - - +
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Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H PHE* 3.5 34.0 - - + -
53H CYS 3.5 2.4 + - - -
54H GLU* 2.7 45.2 + - - +
56H TYR* 1.3 78.1 - - - +
58H ARG* 1.3 73.0 + - - +
60H TYR* 3.6 30.8 - - + +
61H LYS* 2.9 64.7 + - + +
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Residues in contact with ARG 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP 2.8 28.7 + - - +
113B TYR* 3.6 19.4 - - - +
9H LYS* 4.8 14.0 - - + +
11H TYR* 3.0 57.4 + - + +
54H GLU* 3.0 40.9 + - + +
55H TRP* 3.1 8.7 + - + +
57H ARG* 1.3 86.8 - - - +
59H VAL* 1.3 60.3 + - - +
61H LYS* 3.4 11.4 + - - +
62H SER* 3.0 27.2 + - - -
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H TYR* 3.3 15.0 - - + +
14H ALA* 4.1 12.3 - - + -
15H PRO* 5.0 0.7 - - + -
28H ASN* 4.4 1.8 - - - +
32H ASN* 3.4 34.3 - - + +
55H TRP* 3.1 44.4 + - + +
56H TYR 3.7 6.5 - - - +
58H ARG* 1.3 76.7 - - - +
60H TYR* 1.3 62.0 + - - +
62H SER* 3.3 2.5 + - - -
63H LEU* 3.0 40.1 + - + +
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Residues in contact with TYR 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H CYS* 4.8 0.9 - - - +
32H ASN* 3.9 4.9 - - + -
33H TYR* 3.7 47.5 - + - +
36H PHE* 3.7 21.1 - + + -
37H HIS* 3.8 15.0 + - - -
56H TYR 3.0 11.4 + - - +
57H ARG* 3.6 42.5 - - + +
59H VAL* 1.3 75.8 - - - +
61H LYS* 1.3 70.1 + - + +
63H LEU* 4.7 1.3 - - - +
64H CYS* 3.0 47.4 + - - +
69H VAL* 3.5 38.6 - - + +
73H ASP* 4.7 3.1 + - - -
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Residues in contact with LYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.9 0.2 + - - -
111B THR* 2.5 57.7 + - - +
112B ASP 5.4 0.9 - - - -
113B TYR 3.8 21.0 + - - +
114B GLU 4.3 0.8 + - - -
115B ASP* 3.1 31.3 + - - +
57H ARG* 2.9 49.4 + - - +
58H ARG* 3.9 11.7 - - - +
60H TYR* 1.3 95.6 - - + +
62H SER* 1.3 54.7 + - - +
64H CYS 3.8 8.5 - - - +
69H VAL* 5.6 3.8 - - + -
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Residues in contact with SER 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 3.5 16.6 - - - +
98B LYS* 3.5 18.9 - - - -
111B THR* 3.6 9.3 + - - -
112B ASP* 2.5 32.0 + - - -
11H TYR* 2.8 33.4 + - - -
13H THR* 4.1 5.6 - - - -
14H ALA* 4.4 6.3 - - - -
58H ARG 3.0 9.7 + - - -
59H VAL 3.4 3.6 - - - -
61H LYS* 1.3 76.8 - - - +
63H LEU* 1.3 59.9 + - - -
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 4.4 2.5 - - - +
98B LYS* 3.6 5.7 - - - +
151B ARG* 4.0 22.4 - - - +
153B LEU* 3.2 35.3 - - + +
179B LEU* 3.3 13.1 - - + +
14H ALA* 3.8 21.1 - - + -
25H GLN* 5.0 4.3 - - + +
28H ASN* 3.4 47.6 - - + +
29H CYS* 4.4 10.5 - - + -
59H VAL* 3.0 30.5 + - + +
60H TYR 4.5 0.7 - - - +
62H SER* 1.3 75.3 - - - +
64H CYS* 1.3 62.4 + - - +
65H PRO* 3.7 0.3 - - - +
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Residues in contact with CYS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LYS* 2.8 24.7 + - - -
29H CYS* 2.1 59.7 - - - -
33H TYR* 4.9 0.2 - - - -
60H TYR* 3.0 34.5 + - - +
61H LYS 3.8 5.7 - - - +
63H LEU* 1.3 75.9 - - - +
65H PRO* 1.4 64.2 - - + +
66H ILE* 3.5 0.7 + - - +
68H TRP* 5.1 0.2 - - + -
69H VAL* 3.4 21.7 - - + +
72H TRP* 4.3 4.9 - - + -
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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