Contacts of the helix formed by residues 35 - 55 (chain A) in PDB entry 1ZN8
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 5.1 4.5 - - - +
12A ARG* 3.0 37.9 + - - +
31A PRO 3.2 15.1 + - - +
32A VAL 3.0 13.1 - - - +
33A LEU 4.5 0.7 - - - -
34A LYS* 1.4 75.2 - - + +
36A PRO* 1.3 71.7 - - - +
37A ALA* 2.9 21.9 + - - +
38A SER* 3.0 24.9 + - - -
39A PHE* 3.0 1.2 + - - +
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Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 5.1 0.9 - - - +
34A LYS 3.4 10.3 - - - +
35A ASP* 1.3 86.9 - - - +
37A ALA* 1.3 55.7 + - + +
39A PHE* 4.5 2.2 - - + -
40A ARG* 3.1 18.2 + - - +
60B TYR* 5.9 0.4 - - + -
77B GLN* 2.8 29.7 + - - +
80B GLY* 3.9 23.1 - - - +
81B LEU* 3.6 21.8 - - - +
82B GLY* 3.9 8.1 - - - +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.1 20.5 - - + +
35A ASP* 2.9 12.3 + - - +
36A PRO* 1.3 77.6 - - - +
38A SER* 1.3 60.0 + - - +
40A ARG* 3.6 8.7 + - - +
41A ALA* 3.0 28.1 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 2.7 33.9 + - - +
9A VAL* 3.6 7.4 - - - +
12A ARG* 3.4 15.3 - - - +
32A VAL* 3.6 12.0 - - - +
35A ASP* 3.0 28.2 + - - -
37A ALA* 1.3 75.1 - - - +
39A PHE* 1.3 66.8 + - - +
41A ALA* 3.2 7.1 + - - +
42A ALA* 2.9 23.9 + - - +
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.2 18.1 + - + +
33A LEU* 3.6 32.1 - - + +
35A ASP 3.0 8.4 + - - +
36A PRO* 3.9 2.7 - - + +
38A SER* 1.3 76.8 - - - +
40A ARG* 1.3 63.0 + - - +
42A ALA* 3.2 2.3 + - - +
43A ILE* 3.1 33.1 + - + +
70A LEU 3.5 23.1 - - - -
71A PHE* 3.6 28.0 - + - -
74A SER* 3.4 35.4 - - - -
73B PRO* 3.6 11.2 - - + -
77B GLN* 3.4 39.9 - - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PRO 3.1 16.6 + - - +
37A ALA* 3.8 7.9 - - - +
39A PHE* 1.3 82.4 - - - +
41A ALA* 1.3 56.4 + - - +
43A ILE* 4.0 4.5 - - - +
44A GLY* 2.9 26.3 + - - -
77B GLN* 3.5 19.5 - - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.6 35.2 - - + +
8A LEU* 4.1 15.3 - - + -
9A VAL* 4.1 1.1 - - + -
37A ALA 3.0 19.6 + - - +
38A SER 3.2 5.4 + - - +
40A ARG* 1.3 77.0 - - - +
42A ALA* 1.4 55.8 + - - +
44A GLY* 3.4 1.1 + - - -
45A LEU* 2.9 37.4 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.8 17.4 - - + +
32A VAL* 4.3 6.3 - - + -
38A SER 2.9 15.7 + - - +
39A PHE* 3.7 4.7 - - - +
41A ALA* 1.4 72.0 - - - +
43A ILE* 1.3 63.9 + - + +
45A LEU* 3.3 2.8 + - - +
46A LEU* 3.1 30.0 + - - +
71A PHE* 4.7 7.0 - - + -
156A LEU* 3.9 29.6 - - + -
176A LEU* 4.1 8.1 - - + -
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.1 36.7 + - + +
40A ARG* 4.0 4.3 - - - +
42A ALA* 1.3 76.9 - - - +
44A GLY* 1.3 56.1 + - - +
46A LEU* 3.4 8.7 + - + +
47A ALA* 2.9 31.9 + - - +
71A PHE* 3.7 48.0 - - + +
74A SER* 3.6 29.8 - - - +
75A LEU* 3.9 12.9 - - + +
78A GLU* 4.0 15.0 - - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG 2.9 18.6 + - - -
41A ALA* 3.8 1.6 - - - -
43A ILE* 1.3 74.8 - - - +
45A LEU* 1.3 59.4 + - - +
47A ALA* 3.9 5.0 - - - +
48A ARG* 2.9 38.9 + - - +
78A GLU* 5.2 7.6 - - - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 4.1 15.7 - - - +
5A GLU* 3.7 32.5 - - + +
6A LEU* 3.7 42.4 - - + +
9A VAL* 4.1 9.4 - - + -
41A ALA 2.9 21.9 + - - +
42A ALA 3.8 1.3 - - - +
43A ILE 3.3 0.2 - - - -
44A GLY* 1.3 77.0 - - - +
46A LEU* 1.3 57.9 + - - +
48A ARG* 3.8 11.8 - - - +
49A HIS* 3.0 27.9 + - - +
174A PHE* 4.7 0.9 - - - -
176A LEU* 3.5 21.4 - - + +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.1 22.8 + - + +
43A ILE* 3.8 12.8 - - + +
45A LEU* 1.3 78.3 - - - +
47A ALA* 1.3 56.7 + - - +
49A HIS* 3.4 5.0 + - - +
50A LEU* 3.0 33.3 + - - +
71A PHE* 5.4 1.3 - - + -
75A LEU* 3.9 26.7 - - + -
126A VAL* 4.7 9.2 - - + -
154A VAL* 4.1 22.2 - - + -
155A SER 3.8 21.3 - - - +
156A LEU* 4.5 20.2 - - + -
174A PHE* 4.2 9.0 - - + -
176A LEU* 4.1 16.6 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE 2.9 18.8 + - - +
44A GLY* 3.9 3.6 - - - +
46A LEU* 1.3 78.3 - - - +
48A ARG* 1.4 56.3 + - - +
50A LEU* 3.3 2.5 + - - +
51A LYS* 3.0 40.6 + - - +
75A LEU* 3.7 15.5 - - + -
78A GLU* 3.6 27.4 - - + +
79A LEU* 3.8 12.9 - - + +
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 2.8 39.7 + - - -
44A GLY* 2.9 25.6 + - - +
45A LEU* 3.8 21.4 - - - +
47A ALA* 1.4 71.9 - - - +
49A HIS* 1.3 67.9 + - - +
51A LYS* 3.5 10.2 + - - +
52A ALA* 2.9 29.7 + - + +
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 3.0 18.9 + - - +
46A LEU 3.6 3.6 - - - +
48A ARG* 1.3 77.2 - - - +
50A LEU* 1.3 69.2 + - + +
52A ALA* 3.3 6.1 + - - +
53A THR* 2.9 54.2 + - + -
152A GLU* 2.6 34.6 + - - -
154A VAL* 4.6 0.4 - - + -
174A PHE* 3.3 53.0 - + + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU 3.0 21.4 + - - +
47A ALA 3.8 3.4 - - - +
49A HIS* 1.3 79.9 - - + +
51A LYS* 1.3 58.4 + - - +
54A HIS* 2.8 45.2 + - + +
58A ILE* 4.0 13.2 - - + +
61A ILE* 4.5 1.6 - - + -
75A LEU* 4.1 18.4 - - + -
79A LEU* 4.0 24.0 - - + -
124A VAL* 3.9 27.6 - - + -
152A GLU* 4.0 17.5 - - - +
154A VAL* 3.9 26.5 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 3.0 32.3 + - - +
48A ARG* 4.0 7.0 - - - +
50A LEU* 1.3 78.8 - - - +
52A ALA* 1.3 57.6 + - - +
55A GLY* 2.9 39.6 + - - +
58A ILE* 5.6 0.9 - - + -
78A GLU* 4.7 16.9 + - - -
79A LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 2.9 23.2 + - + +
49A HIS* 3.6 7.2 - - - +
51A LYS* 1.3 76.3 - - - +
53A THR* 1.3 60.8 + - - +
55A GLY 4.7 0.6 + - - -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 2.9 39.0 + - + +
52A ALA* 1.3 80.0 - - - +
54A HIS* 1.3 75.6 + - + +
152A GLU* 3.5 20.9 - - - +
172A PRO* 6.3 0.7 - - + -
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 2.8 29.6 + - + +
53A THR* 1.3 91.3 + - + +
55A GLY* 1.3 65.2 + - - +
56A GLY 3.3 0.3 + - - -
57A ARG* 3.2 28.0 + - + +
58A ILE* 3.9 24.5 - - + -
124A VAL* 4.7 0.7 - - + -
151A LEU* 3.5 45.9 - - + +
152A GLU* 2.6 35.4 + - + +
172A PRO* 5.5 2.5 - - + -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 4.5 0.2 - - - +
51A LYS* 2.9 34.8 + - - +
52A ALA 4.7 0.6 - - - -
53A THR 3.8 0.4 - - - -
54A HIS* 1.3 79.5 - - - +
56A GLY* 1.3 59.3 + - - -
57A ARG 3.6 0.2 + - - -
58A ILE* 4.7 6.8 + - - +
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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
------------------------------------------------------------
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