Contacts of the helix formed by residues 31 - 42 (chain Z) in PDB entry 5V09
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 THR 31 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29Z VAL* 3.0 12.6 + - - +
30Z ASP* 1.3 71.2 - - - +
32Z TYR* 1.3 57.3 + - - +
33Z CYS 3.1 0.7 + - - -
34Z TRP* 3.1 12.2 + - + +
35Z LEU* 2.9 30.0 + - + +
59Z CYS* 4.8 6.5 - - + -
75Z LEU* 3.3 36.3 - - + +
76Z VAL 3.2 16.9 + - - -
77Z PHE* 3.3 31.6 - - + -
133Z VAL* 4.4 10.3 - - + -
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Residues in contact with TYR 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A 3.7 35.7 - - - +
30Z ASP* 3.2 5.8 + - - +
31Z THR* 1.3 77.8 - - - +
33Z CYS* 1.3 57.8 + - - +
35Z LEU* 3.5 13.4 - - + +
36Z HIS* 2.9 36.8 + - - -
77Z PHE* 3.8 21.8 - + + -
78Z ASP* 3.2 65.0 + - + +
125Z ILE* 3.6 46.0 + - + -
126Z THR 4.3 4.2 + - - -
127Z HIS* 4.8 4.5 + - - +
130Z ALA* 4.3 11.0 - - + +
332Z ILE* 5.9 0.9 - - - +
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Residues in contact with CYS 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B A 4.4 27.8 - - + +
2B C 5.7 0.9 - - - -
30Z ASP* 3.6 28.7 - - - +
31Z THR 3.1 0.6 + - - -
32Z TYR* 1.3 75.4 - - - +
34Z TRP* 1.3 66.4 + - + +
36Z HIS* 3.2 2.6 + - - +
37Z LYS* 2.9 38.1 + - + +
169Z THR* 4.1 2.0 - - - -
170Z GLU* 3.9 43.7 - - + -
171Z ASP* 4.9 2.7 - - - -
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Residues in contact with TRP 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Z VAL* 3.6 30.1 - - + -
30Z ASP 5.2 0.9 - - - -
31Z THR* 3.1 13.1 + - + +
33Z CYS* 1.3 86.4 - - + +
35Z LEU* 1.3 56.5 + - - +
37Z LYS* 4.3 19.8 - - - +
38Z GLY* 2.9 27.0 + - - -
58Z PHE* 3.6 10.5 - - + -
59Z CYS* 3.8 29.1 - - + -
62Z PHE* 3.5 47.3 - + + -
63Z VAL* 4.3 17.5 - - + -
66Z LEU* 3.9 20.9 - - + -
75Z LEU* 4.3 8.1 - - + -
168Z ILE* 3.9 16.3 - - + +
170Z GLU* 5.5 4.9 + - + +
186Z MET* 3.6 26.9 + - + +
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Residues in contact with LEU 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Z THR* 2.9 14.6 + - + +
32Z TYR* 3.5 19.5 - - + +
33Z CYS 3.1 0.2 - - - -
34Z TRP* 1.3 75.3 - - - +
36Z HIS* 1.3 60.4 + - - +
38Z GLY* 3.8 0.4 - - - -
39Z ALA* 2.9 31.9 + - - +
55Z TYR* 3.8 22.1 - - + +
59Z CYS* 4.3 5.2 - - - -
77Z PHE* 4.1 16.6 - - + -
125Z ILE* 3.6 34.2 - - + +
129Z MET* 4.7 5.8 - - + +
130Z ALA* 4.0 23.3 - - + -
133Z VAL* 3.6 26.0 - - + -
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Residues in contact with HIS 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 5.5 0.2 - - - +
1B A 3.3 85.1 + + + +
32Z TYR* 2.9 28.1 + + - +
33Z CYS 3.7 3.6 - - - +
35Z LEU* 1.3 75.3 - - - +
37Z LYS* 1.3 66.2 + - - +
39Z ALA* 3.1 2.8 + - - +
40Z ILE* 2.9 32.5 + - + +
96Z ARG* 4.4 8.1 - - - -
123Z ILE* 4.2 23.5 + - - +
125Z ILE* 3.4 29.5 - - + +
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Residues in contact with LYS 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 3.8 37.5 - - - +
11A C 3.2 41.1 + - - +
1B A 5.3 1.6 - - + -
33Z CYS* 2.9 23.0 + - + +
34Z TRP* 4.3 17.6 - - - -
36Z HIS* 1.3 76.8 - - + +
38Z GLY* 1.3 60.1 + - - +
40Z ILE* 3.5 13.9 + - - +
58Z PHE* 3.9 17.9 - - + -
62Z PHE* 4.6 9.9 - - - -
170Z GLU* 4.4 24.2 + - + -
186Z MET 4.5 11.5 + - - -
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Residues in contact with GLY 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Z TRP 2.9 14.2 + - - -
35Z LEU 4.0 0.4 - - - -
37Z LYS* 1.3 76.2 - - - +
39Z ALA* 1.3 61.8 + - - +
40Z ILE 3.2 0.4 - - - -
41Z ALA* 3.3 20.0 + - - +
42Z CYS* 4.0 4.2 - - - -
54Z ARG 4.8 0.3 - - - -
55Z TYR* 3.6 17.5 + - - +
58Z PHE* 3.5 32.3 - - - +
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Residues in contact with ALA 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z LEU 2.9 19.5 + - - +
36Z HIS 3.1 4.0 + - - +
38Z GLY* 1.3 73.5 - - - +
40Z ILE* 1.3 66.8 + - - +
41Z ALA 3.2 0.2 - - - -
42Z CYS* 3.3 14.7 + - - +
43Z ALA* 3.3 13.3 + - - +
46Z LEU* 3.8 17.9 - - + +
55Z TYR* 3.8 6.0 - - + +
123Z ILE* 3.7 26.0 - - + +
125Z ILE* 3.9 7.9 - - + -
129Z MET* 4.1 6.5 - - + -
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Residues in contact with ILE 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 3.5 56.5 - - + +
11A C 3.6 35.6 - - + +
36Z HIS* 2.9 22.4 + - + +
37Z LYS* 3.5 11.7 - - - +
38Z GLY 3.2 0.2 - - - -
39Z ALA* 1.3 78.4 - - - +
41Z ALA* 1.3 61.7 + - - +
42Z CYS 3.2 0.7 + - - -
43Z ALA* 3.2 20.0 + - - +
44Z GLU* 5.6 0.2 - - - +
120Z THR* 3.3 30.6 + - - +
123Z ILE* 5.0 6.7 - - + -
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Residues in contact with ALA 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A C 3.5 37.6 + - - +
12A A 3.9 13.8 - - - +
101A MN 3.8 13.0 + - - -
38Z GLY* 3.3 15.6 + - - +
39Z ALA 3.2 0.6 - - - -
40Z ILE* 1.3 79.6 - - - +
42Z CYS* 1.3 57.4 + - - +
43Z ALA 3.9 0.2 + - - -
44Z GLU* 3.6 7.3 - - - +
54Z ARG* 4.1 28.9 + - + +
58Z PHE* 5.6 0.7 - - + -
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Residues in contact with CYS 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Z GLY 4.0 5.8 - - - -
39Z ALA* 3.4 12.6 - - - -
40Z ILE 3.1 0.4 - - - -
41Z ALA* 1.3 77.1 - - - +
43Z ALA* 1.3 62.8 + - - +
44Z GLU* 3.1 13.2 - - - +
45Z LYS* 3.5 7.0 + - + -
46Z LEU* 3.3 21.7 + - - +
52Z THR* 3.5 36.6 - - - +
54Z ARG* 3.9 23.8 - - + +
55Z TYR* 4.0 14.8 - - - -
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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