Contacts of the helix formed by residues 35 - 55 (chain B) in PDB entry 1ZN7
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 ASP 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 5.2 2.3 - - - +
11B GLN* 5.1 1.6 - - - +
12B ARG* 3.0 36.7 + - - +
31B PRO 3.1 16.0 + - - +
32B VAL 3.0 13.4 - - - +
33B LEU 4.4 0.7 - - - -
34B LYS* 1.3 75.4 - - - +
36B PRO* 1.3 71.5 - - - +
37B ALA* 3.1 20.4 + - - +
38B SER* 3.0 26.0 + - - -
39B PHE 3.0 1.6 + - - -
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Residues in contact with PRO 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 6.1 0.2 - - + -
77A GLN* 2.9 30.6 + - - +
80A GLY 3.9 21.1 - - - +
81A LEU* 3.6 21.3 - - - +
82A GLY* 3.8 8.3 - - - +
33B LEU 5.1 0.7 - - - +
34B LYS 3.5 10.5 - - - +
35B ASP* 1.3 86.3 - - - +
37B ALA* 1.3 57.7 + - + +
39B PHE* 4.6 1.6 - - + -
40B ARG* 3.0 32.3 + - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 5.0 0.2 - - - +
8B LEU* 4.0 17.8 - - + +
35B ASP* 3.1 12.2 + - - +
36B PRO* 1.3 82.0 - - + +
38B SER* 1.3 57.8 + - - +
40B ARG* 3.6 18.4 + - - +
41B ALA* 3.0 29.3 + - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 2.9 29.7 + - - +
9B VAL* 3.6 6.2 - - - +
12B ARG* 3.3 17.7 - - - +
32B VAL* 3.6 15.3 - - - +
35B ASP* 3.0 27.9 + - - -
37B ALA* 1.3 76.0 - - - +
39B PHE* 1.3 60.3 + - - +
41B ALA* 3.3 7.1 + - - +
42B ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 3.6 10.3 - - + -
77A GLN* 3.4 38.1 - - + +
32B VAL* 3.2 18.5 + - - +
33B LEU* 3.8 29.2 - - + +
35B ASP 3.0 7.7 + - - +
36B PRO* 4.6 0.9 - - + -
38B SER* 1.3 79.6 - - - +
40B ARG* 1.3 61.9 + - - +
42B ALA* 3.1 2.6 + - - +
43B ILE* 3.0 43.3 + - + +
70B LEU 3.5 23.8 - - - -
71B PHE* 3.6 28.5 - + - -
74B SER* 3.4 32.3 - - - -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 3.1 44.7 + - - +
80A GLY* 5.5 4.6 - - - -
5B GLU* 6.1 0.2 - - - +
36B PRO* 3.0 27.3 + - - +
37B ALA* 3.7 28.4 - - - +
39B PHE* 1.3 77.1 - - - +
41B ALA* 1.3 57.0 + - - +
43B ILE* 3.5 4.7 + - - +
44B GLY* 2.9 27.4 + - - -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 3.5 50.0 + - + +
8B LEU* 4.0 7.4 - - + -
9B VAL* 4.0 4.0 - - + -
37B ALA 3.0 18.5 + - - +
38B SER 3.4 5.2 - - - +
39B PHE 3.3 0.2 - - - -
40B ARG* 1.3 74.0 - - - +
42B ALA* 1.3 59.2 + - - +
44B GLY* 3.2 1.5 + - - -
45B LEU* 2.9 35.8 + - - +
48B ARG* 5.6 0.4 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.6 16.7 - - + +
32B VAL* 4.2 7.4 - - + -
38B SER 2.9 13.7 + - - +
39B PHE* 3.1 8.0 + - - +
41B ALA* 1.3 76.2 - - - +
43B ILE* 1.3 62.0 + - + +
45B LEU 3.5 0.2 + - - -
46B LEU* 3.1 31.5 + - - +
71B PHE* 4.9 6.3 - - + -
156B LEU* 4.1 26.7 - - + -
176B LEU* 3.8 10.2 - - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.0 53.4 + - + +
40B ARG* 3.9 4.7 - - - +
42B ALA* 1.3 76.1 - - - +
44B GLY* 1.3 58.2 + - - +
46B LEU* 3.4 9.2 + - + +
47B ALA* 2.9 28.1 + - - +
71B PHE* 3.9 37.7 - - + +
74B SER* 3.7 27.6 - - - +
75B LEU* 4.0 10.0 - - + +
78B GLU* 3.9 18.2 - - + -
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Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 2.9 18.4 + - - -
41B ALA* 3.7 1.6 - - - -
43B ILE* 1.3 77.0 - - - +
45B LEU* 1.3 56.5 + - - +
47B ALA* 3.8 4.7 - - - +
48B ARG* 2.9 49.9 + - - +
78B GLU* 5.1 7.6 - - - -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 3.9 19.5 - - + +
6B LEU* 3.7 46.9 - - + +
9B VAL* 4.2 8.5 - - + -
41B ALA 2.9 21.0 + - - +
42B ALA 3.9 1.6 - - - +
44B GLY* 1.3 76.6 - - - +
46B LEU* 1.3 62.0 + - - +
48B ARG* 3.5 22.7 - - - +
49B HIS* 3.1 23.9 + - - +
174B PHE* 4.9 1.0 - - - -
176B LEU* 3.6 21.5 - - + +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA 3.1 21.4 + - - +
43B ILE* 3.7 13.5 - - + +
44B GLY 3.4 0.2 - - - -
45B LEU* 1.3 78.1 - - - +
47B ALA* 1.3 57.1 + - - +
49B HIS* 3.4 4.4 + - - +
50B LEU* 3.0 34.3 + - + +
71B PHE* 5.3 1.1 - - + -
75B LEU* 3.8 26.2 - - + -
126B VAL* 4.7 10.1 - - + -
154B VAL* 4.1 19.3 - - + -
155B SER 4.1 11.4 - - - +
156B LEU* 4.1 24.9 - - + -
174B PHE* 4.0 14.6 - - + -
176B LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE 2.9 18.0 + - - +
44B GLY* 3.8 3.1 - - - +
46B LEU* 1.3 77.0 - - - +
48B ARG* 1.3 58.2 + - - +
50B LEU* 3.3 1.8 + - - -
51B LYS* 2.9 39.3 + - - +
75B LEU* 3.6 15.5 - - + +
78B GLU* 3.5 27.8 - - + -
79B LEU* 3.7 14.8 - - + +
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 5.0 14.5 + - - +
41B ALA* 5.6 0.6 + - - +
44B GLY* 2.9 34.3 + - - +
45B LEU* 3.5 32.5 - - - +
47B ALA* 1.3 73.9 - - - +
49B HIS* 1.3 60.5 + - - +
51B LYS* 3.9 11.4 - - - +
52B ALA* 2.9 34.5 + - - +
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 3.1 18.0 + - - +
46B LEU 3.7 3.1 - - - +
48B ARG* 1.3 75.2 - - - +
50B LEU* 1.3 64.8 + - + +
52B ALA* 3.8 4.0 - - - +
53B THR* 2.8 56.6 + - + -
152B GLU* 2.5 39.4 + - - -
154B VAL* 4.5 0.9 - - + -
174B PHE* 3.4 53.4 - + + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU 3.0 21.7 + - - +
47B ALA 3.8 3.6 - - - +
48B ARG 3.3 0.2 - - - -
49B HIS* 1.3 78.8 - - + +
51B LYS* 1.3 57.5 + - - +
53B THR 3.3 0.2 + - - -
54B HIS* 2.9 46.7 + - + +
58B ILE* 3.9 13.3 - - + +
61B ILE* 4.5 2.0 - - + -
75B LEU* 3.9 24.0 - - + -
79B LEU* 4.1 15.9 - - + -
124B VAL* 3.8 35.2 - - + -
152B GLU* 3.5 24.2 - - - +
154B VAL* 3.9 15.3 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA* 2.9 25.1 + - - +
48B ARG* 4.1 11.0 - - - +
50B LEU* 1.3 73.6 - - - +
52B ALA* 1.3 60.6 + - - +
55B GLY* 3.0 39.1 + - - +
58B ILE* 5.4 0.7 - - - -
78B GLU* 4.6 18.0 + - - -
79B LEU* 3.2 31.4 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG 2.9 20.3 + - - +
49B HIS* 3.8 5.2 - - - +
51B LYS* 1.3 76.2 - - - +
53B THR* 1.3 62.2 + - - +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 2.8 43.7 + - + -
52B ALA* 1.3 79.8 - - - +
54B HIS* 1.3 89.2 + - + +
55B GLY 3.7 0.2 - - - -
152B GLU* 3.9 6.3 - - - +
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Residues in contact with HIS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 2.9 37.9 + - + +
53B THR* 1.3 90.9 + - + +
55B GLY* 1.3 65.9 + - - +
56B GLY 3.2 0.3 + - - -
57B ARG* 2.8 31.9 + - + +
58B ILE* 3.8 24.5 - - + -
124B VAL* 4.4 2.2 - - + -
151B LEU* 3.7 42.5 - - + +
152B GLU* 2.5 35.8 + - + +
172B PRO* 5.7 2.5 - - + -
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 4.0 0.2 + - - -
51B LYS* 3.0 32.3 + - - +
52B ALA 4.7 0.2 - - - -
53B THR 3.7 0.8 - - - -
54B HIS* 1.3 78.7 - - - +
56B GLY* 1.3 58.8 + - - -
57B ARG 3.5 0.5 + - - -
58B ILE* 4.5 8.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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