Contacts of the helix formed by residues 53 - 67 (chain C) in PDB entry 3O9Z
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 GLU 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B HIS* 2.9 37.0 + - + +
82B LEU* 3.8 32.3 - - + +
174B LYS* 4.2 9.4 + - - -
311B NAD 4.6 7.4 + - - -
32C LEU* 3.7 2.7 - - - -
51C PHE* 4.0 1.0 - - - +
52C THR* 1.3 92.5 + - - +
54C PRO* 1.3 71.4 - - - +
55C GLU* 4.0 1.7 - - - +
56C ALA* 3.1 10.3 + - + +
57C PHE* 3.0 20.4 + - - +
313C EDO 3.7 2.5 - - - -
314C CL 3.4 19.1 - - + +
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Residues in contact with PRO 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 4.4 15.0 - - + -
55B GLU* 3.4 45.5 - - + +
311B NAD 6.0 0.2 - - - +
32C LEU* 3.8 20.4 - - + -
34C PRO* 5.5 3.8 - - + -
52C THR 3.6 8.5 - - - +
53C GLU* 1.3 84.0 - - - +
55C GLU* 1.3 66.7 + - - +
57C PHE* 3.3 4.5 + - - +
58C GLU* 2.9 29.4 + - - +
89C MET* 4.5 3.3 - - + +
311C NAD 4.1 10.3 - - + +
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 4.0 0.3 - - - +
54B PRO* 3.3 22.6 - - + +
82B LEU* 3.7 13.1 - - + +
85B PRO* 3.5 34.9 - - + +
86B GLN* 2.8 33.6 + - + -
89B MET* 3.7 26.7 - - + -
92B ARG* 5.4 3.5 + - - +
311B NAD 2.9 16.2 + - - -
53C GLU* 4.0 0.5 - - - +
54C PRO* 1.3 87.9 - - - +
56C ALA* 1.3 57.3 + - - +
58C GLU* 3.4 9.0 + - - +
59C ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PRO* 3.9 18.0 - - + +
51C PHE* 3.8 20.9 - - + -
53C GLU* 3.1 16.9 + - + +
55C GLU* 1.3 77.1 - - - +
57C PHE* 1.3 63.4 + - - +
59C ALA* 3.3 2.8 + - - +
60C TYR* 3.0 24.9 + - - +
314C CL 3.9 11.4 - - + -
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 3.9 4.0 - - + -
6C LEU 4.1 5.8 - - - -
7C THR* 3.9 17.5 - - + -
30C ALA* 4.1 9.0 - - + -
31C SER* 3.7 25.8 - - - -
32C LEU* 3.8 26.7 - - + -
51C PHE* 3.7 34.9 - + + -
53C GLU 3.0 11.7 + - - +
54C PRO* 3.4 9.9 - - + +
56C ALA* 1.3 74.5 - - - +
58C GLU* 1.3 66.0 + - - +
60C TYR* 3.2 3.1 + - - +
61C LEU* 3.0 52.6 + - + +
74C LEU* 3.8 20.2 - - + -
89C MET* 4.0 17.5 - - - -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU* 5.7 0.2 - - - +
58B GLU* 2.5 27.9 - - - +
89B MET* 4.7 1.9 - - - +
92B ARG* 3.3 26.8 + - - +
54C PRO 2.9 16.7 + - - +
55C GLU* 3.8 6.4 - - - +
57C PHE* 1.3 78.7 - - - +
59C ALA* 1.3 57.7 + - - +
61C LEU* 3.2 5.7 + - - +
62C GLU* 2.8 32.0 + - - +
89C MET* 3.7 32.4 - - + +
92C ARG* 2.7 35.3 + - - +
93C LEU* 4.0 8.9 - - + +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TYR* 4.8 5.8 - - + -
85B PRO* 4.3 12.8 - - + -
88B ARG* 3.4 34.9 + - + +
92B ARG* 5.5 2.2 - - - +
55C GLU 3.0 18.0 + - - +
56C ALA* 3.8 4.3 - - - +
58C GLU* 1.3 78.3 - - - +
60C TYR* 1.3 55.5 + - - +
62C GLU* 3.4 3.5 + - - -
63C ASP* 2.9 37.5 + - - +
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.0 8.2 - - + +
30C ALA* 3.9 20.6 - - + -
49C GLU* 3.3 28.2 + - + +
51C PHE* 3.4 35.4 - + + -
56C ALA 3.0 11.2 + - - +
57C PHE 3.2 2.9 + - - +
59C ALA* 1.3 76.0 - - - +
61C LEU* 1.3 76.5 + - + +
63C ASP* 3.2 12.0 + - + +
64C LEU* 3.1 57.9 + - + +
67C ARG* 5.3 7.4 - - - -
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 4.2 13.2 - - + -
30C ALA* 4.5 4.9 - - + -
57C PHE* 3.0 53.2 + - + +
58C GLU 3.8 1.1 - - - +
60C TYR* 1.3 94.1 - - + +
62C GLU* 1.3 57.5 + - - +
64C LEU* 3.4 9.4 + - + +
65C ARG* 3.0 28.6 + - - +
70C GLY* 5.0 1.7 - - - -
71C VAL* 4.0 34.9 + - + -
74C LEU* 4.8 3.6 - - + -
93C LEU* 3.7 34.6 - - + +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG* 2.7 34.9 + - - +
92B ARG* 3.1 41.3 + - - +
116B LEU* 6.3 1.6 - - - -
58C GLU* 2.8 17.0 + - - +
59C ALA* 4.3 2.8 - - - -
61C LEU* 1.3 73.9 - - - +
63C ASP* 1.3 59.3 + - - +
65C ARG* 3.0 33.9 + - - +
66C ASP* 2.9 39.2 + - - +
93C LEU* 3.6 13.5 - - + +
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 5.5 0.7 - - - -
88B ARG* 2.7 31.8 + - - -
112B ARG* 2.9 33.4 + - - +
59C ALA* 2.9 19.4 + - - +
60C TYR* 3.2 13.0 + - + +
62C GLU* 1.3 77.2 - - - +
64C LEU* 1.3 61.5 + - - +
66C ASP* 3.2 8.8 + - - +
67C ARG* 3.2 44.5 + - - +
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ARG* 4.0 4.0 - - - +
29C VAL* 3.8 18.8 - - + -
60C TYR* 3.1 54.4 + - + +
61C LEU* 3.5 17.3 - - + +
62C GLU 3.3 0.2 - - - -
63C ASP* 1.3 74.6 - - - +
65C ARG* 1.3 62.2 + - - +
67C ARG* 3.2 35.0 + - - +
68C GLY 3.2 4.7 + - - -
69C GLU* 2.8 50.6 + - + +
70C GLY* 3.7 5.2 - - - -
71C VAL* 4.7 4.3 - - + +
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Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU 3.0 14.5 + - - +
62C GLU* 3.0 42.0 + - - +
64C LEU* 1.3 74.5 - - - +
66C ASP* 1.3 84.9 + - - +
68C GLY* 3.0 14.9 + - - -
70C GLY* 3.9 15.4 - - - +
92C ARG 2.9 28.7 + - - -
93C LEU* 3.3 35.5 - - + +
94C GLY* 5.3 2.5 - - - +
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG* 4.7 4.3 + - - -
116B LEU* 5.1 10.4 - - - +
62C GLU* 2.9 28.3 + - - +
63C ASP* 3.7 8.5 - - - +
64C LEU 3.2 0.4 - - - -
65C ARG* 1.3 103.6 + - - +
67C ARG* 1.3 58.9 + - + +
68C GLY 3.3 1.8 + - - -
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 5.3 8.3 - - - +
60C TYR* 5.3 6.7 - - - -
63C ASP* 3.2 32.1 + - - +
64C LEU* 3.4 32.8 - - - +
66C ASP* 1.3 77.0 - - + +
68C GLY* 1.3 61.4 + - - +
69C GLU* 3.2 33.9 + - - +
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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