Contacts of the helix formed by residues 34 - 46 (chain P) in PDB entry 2ZJQ
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 34 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ARG* 4.2 4.8 - - - +
33P MET* 1.3 72.9 - - - +
35P PRO* 1.3 74.5 - - - +
36P ARG* 2.9 26.3 + - - +
37P LYS* 3.0 12.6 + - - +
38P VAL* 3.4 9.5 + - - +
120P ARG* 4.0 18.0 + - - +
122P SER* 3.6 1.0 + - - -
1279X G 4.0 18.5 + - - +
1994X U 5.7 0.6 + - - -
1995X G 4.7 10.7 + - - -
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Residues in contact with PRO 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET 3.6 0.2 - - - +
34P SER* 1.3 85.2 - - - +
36P ARG* 1.3 59.5 + - - +
38P VAL* 3.3 1.6 + - - +
39P ARG* 2.6 54.9 + - - +
97P VAL* 4.3 6.3 - - + -
98P ASP 4.5 2.0 - - - +
99P ALA* 3.3 25.8 - - + +
120P ARG* 3.7 18.4 - - + -
121P THR 3.2 22.9 - - - +
122P SER* 2.9 17.2 - - - +
527X C 5.5 0.2 - - - +
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Residues in contact with ARG 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P SER* 2.9 12.6 + - - +
35P PRO* 1.3 81.9 - - - +
37P LYS* 1.3 63.9 + - - +
39P ARG* 3.8 19.5 + - - +
40P LEU* 3.9 15.1 + - + +
1278X A 3.2 24.2 + - - -
1279X G 2.3 59.4 + - + +
20Z ARG* 2.4 49.1 - - - +
23Z HIS* 4.9 1.8 + - - -
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Residues in contact with LYS 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 2.8 38.9 - - + +
34P SER* 3.0 11.7 + - - +
36P ARG* 1.3 76.4 - - - +
38P VAL* 1.3 68.2 + - - +
40P LEU* 2.8 26.1 + - - +
41P VAL* 4.0 1.9 + - - +
62P ARG* 4.9 2.6 + - - +
63P SER* 2.7 25.7 + - - -
64P ALA* 3.1 33.1 - - + +
1279X G 2.7 48.1 - - + +
1993X G 4.2 7.0 - - - +
1994X U 3.3 24.6 + - - +
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Residues in contact with VAL 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 3.6 35.9 - - + -
34P SER 3.6 12.1 - - - +
35P PRO 3.3 5.8 + - - +
37P LYS* 1.3 74.1 - - + +
39P ARG* 1.3 63.4 + - - +
40P LEU 2.9 1.7 + - - -
41P VAL* 2.9 13.7 + - - +
42P VAL* 3.1 10.5 + - + -
64P ALA* 3.9 13.0 - - + +
68P VAL* 3.8 26.0 - - + -
97P VAL* 3.8 24.0 - - + -
122P SER* 4.5 5.4 - - - +
124P ILE* 3.9 15.5 - - + -
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Residues in contact with ARG 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P PRO* 2.6 57.1 + - - +
36P ARG* 3.9 13.9 - - - +
37P LYS 3.0 0.6 + - - -
38P VAL* 1.3 71.6 - - - +
40P LEU* 1.3 62.9 + - + +
42P VAL* 4.5 2.7 - - + -
43P ASP* 2.8 42.3 + - - +
96P TYR* 6.2 0.2 - - - -
97P VAL* 3.4 41.8 + - + +
98P ASP* 5.2 1.8 - - - +
99P ALA* 5.7 1.0 - - - +
527X C 2.3 32.1 + - - +
528X G 2.8 47.6 + - - +
529X U 5.8 1.1 - - - +
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Residues in contact with LEU 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P ARG* 3.9 11.0 - - + +
37P LYS* 2.8 15.5 + - - +
39P ARG* 1.3 79.4 - - + +
41P VAL* 1.3 58.8 + - + +
43P ASP* 3.2 22.0 - - + +
44P VAL* 3.9 5.2 + - - +
62P ARG* 3.2 34.5 - - - +
1279X G 4.1 22.0 - - + +
23Z HIS* 3.4 37.7 - - + +
24Z ALA* 4.8 4.3 - - - -
25Z LEU* 3.9 17.2 + - + +
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Residues in contact with VAL 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LYS 4.6 2.2 - - - +
38P VAL* 2.9 6.4 + - - +
40P LEU* 1.3 70.0 - - + +
42P VAL* 1.3 72.0 + - - +
43P ASP 2.6 3.3 + - - -
44P VAL* 2.7 26.6 + - + +
45P ILE* 3.7 0.5 + - - +
57P LEU* 3.9 28.5 - - + -
60P ILE* 4.5 8.7 - - + -
62P ARG* 3.9 24.2 - - + +
64P ALA* 3.3 32.5 - - + -
65P SER* 4.1 8.3 - - - +
68P VAL* 4.2 12.6 - - + -
25Z LEU* 4.3 7.4 - - + -
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Residues in contact with VAL 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P VAL 3.1 4.8 + - - +
39P ARG* 4.0 6.1 - - - +
41P VAL* 1.3 80.7 - - - +
43P ASP* 1.3 63.4 + - - +
44P VAL 3.1 1.7 + - - -
45P ILE* 3.1 6.4 + - + +
46P ARG* 3.1 28.0 + - - +
68P VAL* 3.8 30.7 - - + -
95P ALA* 3.5 32.5 - - + -
96P TYR* 4.0 11.9 - - - +
97P VAL* 3.6 25.4 - - + -
124P ILE* 3.9 11.7 - - + -
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Residues in contact with ASP 43 (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 ARG* 2.8 37.4 + - - +
40P LEU* 3.2 16.6 + - + +
41P VAL 2.6 5.5 + - - -
42P VAL* 1.3 74.9 - - - +
44P VAL* 1.3 57.6 + - + -
46P ARG* 2.8 40.3 + - - +
529X U 4.5 6.8 + - - -
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Residues in contact with VAL 44 (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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40P LEU 4.4 2.9 - - - +
41P VAL* 2.7 23.5 + - - +
43P ASP* 1.3 73.9 - - + +
45P ILE* 1.3 69.9 + - + +
46P ARG 3.4 2.8 - - - +
48P LYS* 3.5 19.9 + - - +
56P LEU* 4.3 7.0 - - + +
60P ILE* 3.4 31.0 - - + -
25Z LEU* 4.2 32.1 - - + +
27Z ALA* 4.4 23.8 - - + +
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Residues in contact with ILE 45 (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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41P VAL* 5.1 1.3 - - + -
42P VAL* 3.1 11.4 + - - +
44P VAL* 1.3 89.3 - - + +
46P ARG* 1.3 69.4 + - - +
47P GLY 3.1 2.9 + - - -
48P LYS* 3.2 20.3 + - - +
53P ALA* 3.8 32.3 - - + +
56P LEU* 4.5 7.2 - - + -
57P LEU* 3.2 47.6 - - + -
68P VAL* 4.4 12.1 - - + -
72P LEU* 4.9 7.2 - - + -
92P VAL* 3.9 16.8 - - + +
95P ALA* 5.3 5.6 - - + -
126P ILE* 5.6 0.7 - - + -
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Residues in contact with ARG 46 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ARG* 6.2 0.2 - - - +
42P VAL* 3.1 17.4 + - - +
43P ASP* 2.8 39.3 + - - +
44P VAL 3.4 6.3 - - - +
45P ILE* 1.3 77.1 - - - +
47P GLY* 1.3 66.4 + - - +
48P LYS* 4.2 2.3 - - - +
92P VAL* 3.9 7.6 - - + -
93P LYS 5.0 2.7 - - - +
94P GLU* 4.3 8.7 - - - +
95P ALA* 2.6 47.3 + - + +
96P TYR* 4.8 2.0 - - - +
529X U 3.5 30.5 + - - -
530X G 3.2 27.5 + - - +
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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