Contacts of the helix formed by residues 40 - 62 (chain A) in PDB entry 2ZI0
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG* 4.3 1.6 - - - -
39A LYS* 1.3 75.1 - - - +
41A PRO* 1.3 67.3 - - - +
42A SER* 3.2 2.9 + - - -
43A GLU* 2.6 36.5 + - - +
44A GLN* 2.8 29.5 + - - +
14C C 3.4 28.9 + - - -
15C U 2.9 26.3 + - - -
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Residues in contact with PRO 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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39A LYS 4.6 0.7 - - - +
40A SER* 1.3 87.3 - - - +
42A SER* 1.3 55.8 + - - +
44A GLN* 3.6 11.9 - - + +
45A ARG* 3.0 36.7 + - - +
14C C 3.7 21.3 - - - +
15C U 3.6 19.3 - - - +
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Residues in contact with SER 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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40A SER* 3.2 5.5 + - - -
41A PRO* 1.3 74.7 - - - +
43A GLU* 1.3 65.2 + - - +
44A GLN 3.1 1.1 - - - -
45A ARG* 3.7 18.0 + - - +
46A ARG* 2.9 33.7 + - - +
15C U 2.4 44.2 + - - -
16C G 3.3 28.9 + - - -
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Residues in contact with GLU 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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30A LYS* 5.8 4.7 - - - +
33A ARG* 2.8 30.2 + - - -
39A LYS* 3.4 16.9 - - + +
40A SER* 2.6 44.2 + - - +
42A SER* 1.3 78.0 + - - +
44A GLN* 1.3 56.1 + - - +
46A ARG* 3.3 27.9 + - - +
47A SER* 3.0 30.8 + - - -
14C C 6.2 0.4 - - - -
15C U 5.1 9.9 - - - +
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Residues in contact with GLN 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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39A LYS* 4.3 17.7 - - + +
40A SER 2.8 21.0 + - - +
41A PRO* 3.6 10.2 - - - +
43A GLU* 1.3 70.2 - - - +
45A ARG* 1.3 67.2 + - - +
47A SER* 3.0 9.8 + - - +
48A GLU* 3.0 50.1 + - + +
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Residues in contact with ARG 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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41A PRO* 3.0 32.8 + - - +
42A SER* 3.7 19.1 + - - +
44A GLN* 1.3 75.5 - - - +
46A ARG* 1.3 64.0 + - - +
48A GLU* 3.3 7.6 + - - +
49A LEU* 3.0 39.5 + - + +
15C U 4.1 9.5 + - - -
16C G 3.5 26.5 + - - -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 2.9 20.7 + - - +
43A GLU* 3.6 37.2 + - - +
44A GLN 3.1 0.2 - - - -
45A ARG* 1.3 77.0 - - - +
47A SER* 1.3 63.3 + - - +
49A LEU* 3.3 10.7 + - - +
50A TRP* 3.2 18.9 + - - +
15C U 5.2 2.8 + - - -
16C G 3.7 23.4 + - - -
17C U 3.3 14.7 + - - -
18C C 3.3 26.0 - - - +
19C U 4.6 2.2 - - - +
1D A 4.0 13.2 + - - +
2D G 3.3 22.6 + - - -
3D A 3.3 11.1 - - - +
4D C 5.2 0.8 - - - +
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Residues in contact with SER 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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39A LYS* 4.1 16.0 + - - +
43A GLU 3.0 13.9 + - - -
44A GLN* 3.0 17.7 + - - +
46A ARG* 1.3 75.4 - - - +
48A GLU* 1.3 57.2 + - - +
50A TRP* 3.1 2.4 + - - +
51A HIS* 2.9 45.5 + - - -
1D A 3.9 34.5 - - - -
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Residues in contact with GLU 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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44A GLN* 3.0 49.0 + - + +
45A ARG* 3.6 6.6 - - - +
47A SER* 1.3 77.3 - - - +
49A LEU* 1.3 63.6 + - - +
51A HIS* 3.5 7.0 + - + +
52A ALA* 3.1 24.9 + - - +
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Residues in contact with LEU 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 ARG* 3.0 36.6 + - + +
46A ARG* 3.3 9.4 + - - +
48A GLU* 1.3 74.6 - - - +
50A TRP* 1.3 61.0 + - - +
52A ALA* 3.5 7.9 + - + +
53A ARG* 3.1 24.6 + - - +
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Residues in contact with TRP 50 (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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46A ARG 3.2 12.0 + - - +
47A SER 3.1 9.3 + - - +
49A LEU* 1.3 74.5 - - - +
51A HIS* 1.3 80.2 + + - +
53A ARG* 3.1 11.5 + - + +
54A GLN* 2.9 76.5 + - + +
19C U 4.5 10.0 + + - +
1D A 3.1 89.3 - + + +
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Residues in contact with HIS 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 SER* 2.9 36.7 + - - +
48A GLU* 4.0 7.2 - - + +
50A TRP* 1.3 99.3 - + - +
52A ALA* 1.3 61.6 + - - +
54A GLN* 3.5 5.7 + - - +
55A VAL* 3.2 29.1 + - + +
1D A 2.5 42.2 + - - -
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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 GLU 3.1 19.0 + - - +
49A LEU* 3.6 9.4 - - + +
51A HIS* 1.3 75.7 - - - +
53A ARG* 1.3 57.5 + - - +
55A VAL* 3.4 9.1 + - - +
56A GLU* 3.2 25.2 + - - +
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Residues in contact with ARG 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 LEU 3.1 17.1 + - - +
50A TRP* 3.1 14.1 + - - +
52A ALA* 1.3 75.8 - - - +
54A GLN* 1.3 65.5 + - - +
56A GLU* 3.3 13.7 + - + +
57A LEU* 2.9 56.7 + - + +
19C U 5.2 18.0 - - - +
20C U 4.5 18.7 + - - -
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Residues in contact with GLN 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 TRP* 2.9 82.8 + - + +
51A HIS* 3.7 8.1 - - - +
53A ARG* 1.3 81.5 - - - +
55A VAL* 1.3 64.2 + - + +
57A LEU* 3.5 16.8 + - - +
58A SER* 3.0 30.0 + - - -
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Residues in contact with VAL 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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51A HIS 3.2 14.9 + - - +
52A ALA* 3.5 10.1 - - - +
53A ARG 3.3 0.2 - - - -
54A GLN* 1.3 78.7 - - + +
56A GLU* 1.3 63.7 + - - +
58A SER* 3.4 6.6 + - - -
59A ALA* 3.2 20.2 + - + +
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Residues in contact with GLU 56 (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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52A ALA 3.2 11.6 + - - +
53A ARG* 3.3 16.7 + - + +
55A VAL* 1.3 81.3 - - - +
57A LEU* 1.3 59.3 + - + +
59A ALA* 3.0 24.4 + - + +
60A ILE* 3.2 24.6 + - + +
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Residues in contact with LEU 57 (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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53A ARG* 2.9 44.3 + - + +
54A GLN* 4.0 19.7 - - - +
55A VAL 3.4 0.2 - - - -
56A GLU* 1.3 76.8 - - + +
58A SER* 1.3 58.8 + - - +
60A ILE* 3.3 24.3 + - + +
61A ASN* 3.0 33.3 + - - +
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Residues in contact with SER 58 (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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54A GLN 3.0 19.4 + - - -
55A VAL* 3.9 5.8 - - - -
56A GLU 3.3 0.2 - - - -
57A LEU* 1.3 74.8 - - - +
59A ALA* 1.3 57.1 + - - +
60A ILE 3.3 1.1 - - - -
61A ASN* 3.5 16.7 + - - +
62A SER* 3.1 25.3 + - - -
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Residues in contact with ALA 59 (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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55A VAL* 3.2 12.6 + - + +
56A GLU* 3.0 16.3 + - + +
58A SER* 1.3 74.2 - - - +
60A ILE* 1.3 61.4 + - + +
62A SER* 3.2 19.4 + - - -
63A ASP* 3.9 8.0 + - - +
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Residues in contact with ILE 60 (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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56A GLU* 3.3 23.8 - - + +
57A LEU* 3.3 30.5 + - + +
59A ALA* 1.3 78.5 - - - +
61A ASN* 1.3 61.1 + - - +
62A SER 3.4 0.7 - - - -
63A ASP* 3.3 30.7 + - + +
64A ASN* 4.2 4.5 + - - +
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Residues in contact with ASN 61 (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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57A LEU* 3.0 19.5 + - - +
58A SER* 3.4 19.7 + - - +
60A ILE* 1.3 79.5 - - - +
62A SER* 1.3 59.7 + - - +
63A ASP 3.3 0.4 - - - -
64A ASN* 2.9 34.5 + - - +
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Residues in contact with SER 62 (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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58A SER 3.1 12.1 + - - -
59A ALA* 3.2 21.2 + - - -
61A ASN* 1.3 73.4 - - - +
63A ASP* 1.3 55.9 + - - +
64A ASN* 2.9 15.5 + - - -
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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
------------------------------------------------------------
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