Contacts of the helix formed by residues 35 - 57 (chain D) in PDB entry 1MA1
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 LYS 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C ASN* 3.7 39.7 - - + +
31D ILE* 2.9 36.7 + - + +
34D GLN* 1.3 88.8 + - + +
36D HIS* 1.3 61.0 + - + +
38D GLN* 3.6 3.4 - - - +
39D ALA* 3.0 26.9 + - - +
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Residues in contact with HIS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU* 3.9 7.0 - - - -
173C TYR* 2.8 32.4 + + - -
178C ASN* 3.7 25.1 - - + +
31D ILE 3.8 13.0 - - - -
32D HIS* 3.4 17.6 + - + +
35D LYS* 1.3 76.5 - - + +
37D HIS* 1.3 68.3 + - - +
38D GLN 3.0 1.1 - - - -
39D ALA* 2.8 21.4 + - - +
40D TYR* 3.1 24.0 + - + -
170D HIS* 3.2 51.5 + + + +
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Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 3.6 13.0 - - + +
11D PRO* 3.5 28.4 - - + +
32D HIS 3.1 9.4 + - - +
33D HIS* 3.2 18.0 + - - +
36D HIS* 1.3 78.0 - - - +
38D GLN* 1.3 62.7 + - - +
40D TYR* 3.1 18.1 + + - +
41D VAL* 3.2 9.8 + - + +
76D GLY 4.6 0.7 - - - -
77D TYR* 3.4 40.9 + + - -
80D HIS* 3.6 25.5 - + + -
81D LEU* 4.0 4.9 - - - -
84D TRP* 2.8 32.1 + + - +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.3 34.5 - - + +
33D HIS 3.5 4.5 + - - +
34D GLN* 3.1 28.6 - - - +
35D LYS 3.6 3.6 - - - +
37D HIS* 1.3 80.3 - - - +
39D ALA* 1.3 62.9 + - - +
41D VAL* 3.2 17.0 + - - +
42D ASP* 2.9 59.3 + - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS 3.0 15.0 + - - +
36D HIS* 2.8 20.7 + - - +
38D GLN* 1.3 73.6 - - - +
40D TYR* 1.3 62.2 + - + +
42D ASP* 3.4 8.1 + - - +
43D GLY* 2.8 26.5 + - - -
73D HIS* 4.0 4.5 + - - +
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Residues in contact with TYR 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D HIS* 3.1 29.2 + - + +
37D HIS* 3.1 10.6 + - - +
39D ALA* 1.3 79.7 - - + +
41D VAL* 1.3 66.8 + - - +
44D ALA* 2.9 27.4 + - - +
72D PHE* 4.0 14.8 - + - -
73D HIS* 3.5 37.8 - + - +
76D GLY* 3.9 9.0 - - - -
77D TYR* 3.8 9.9 - - - +
80D HIS* 3.3 36.6 - + - -
151D HIS* 3.1 29.4 + + - -
168D TRP* 3.7 10.6 - - - -
170D HIS* 3.3 21.7 - - - -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.5 33.4 - - + +
9D GLU* 3.9 6.3 - - - -
10D LEU* 3.8 23.8 - - + +
37D HIS* 3.2 15.7 + - + +
38D GLN* 3.2 24.4 + - - +
40D TYR* 1.3 76.7 - - - +
42D ASP* 1.3 59.7 + - - +
44D ALA* 3.8 2.0 - - - +
45D ASN* 3.0 38.7 + - - +
77D TYR* 3.8 24.8 - - + -
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 2.9 50.2 + - - +
39D ALA* 3.9 7.1 - - - +
41D VAL* 1.3 76.5 - - - +
43D GLY* 1.3 60.3 + - - +
45D ASN* 3.9 6.5 + - - +
46D ALA* 2.9 33.1 + - - +
49D ARG* 4.9 1.0 + - - -
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA 2.8 17.8 + - - -
42D ASP* 1.3 76.7 - - - +
44D ALA* 1.3 61.6 + - - +
46D ALA* 3.4 5.7 + - - +
47D LEU* 3.2 22.7 + - - +
69D GLU* 4.8 2.4 - - - +
73D HIS* 3.5 31.2 + - - -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TYR* 3.6 30.1 - - + -
40D TYR 2.9 17.7 + - - +
41D VAL 3.8 0.7 - - - +
43D GLY* 1.3 75.9 - - - +
45D ASN* 1.3 58.3 + - - +
47D LEU* 3.4 6.9 + - - +
48D LEU* 3.0 33.4 + - - +
70D LEU* 4.4 4.7 - - + +
73D HIS* 3.6 14.6 - - + +
74D VAL* 4.0 14.1 - - + +
77D TYR* 5.6 1.3 - - + -
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.5 17.3 - - + +
8D TYR* 2.9 52.6 + - - +
41D VAL* 3.0 29.3 + - - +
42D ASP* 3.9 6.8 + - - +
44D ALA* 1.3 72.6 - - - +
46D ALA* 1.3 66.8 + - - +
47D LEU 3.0 2.0 + - - -
48D LEU* 3.1 6.9 + - - +
49D ARG* 3.0 45.1 + - - +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ASP 2.9 18.3 + - - +
43D GLY* 3.4 6.5 + - - +
45D ASN* 1.3 75.7 - - - +
47D LEU* 1.3 58.0 + - - +
49D ARG* 3.4 23.4 + - - +
50D LYS* 3.0 26.3 + - - +
69D GLU* 6.1 0.4 - - - +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY 3.2 13.9 + - - +
44D ALA* 3.6 5.6 - - - +
45D ASN 3.0 0.6 - - - -
46D ALA* 1.3 79.4 - - - +
48D LEU* 1.3 65.3 + - - +
50D LYS* 3.2 26.4 + - + +
51D LEU* 3.0 30.5 + - + +
66D ALA* 3.1 43.3 - - + +
69D GLU* 3.9 21.3 - - + +
70D LEU* 3.1 38.1 - - + +
73D HIS* 5.6 0.4 - - - +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS 4.4 2.5 - - - +
7D PHE* 4.1 12.3 - - + -
8D TYR* 4.0 23.3 - - + -
44D ALA 3.0 23.4 + - - +
45D ASN* 3.5 17.9 - - - +
47D LEU* 1.3 76.5 - - - +
49D ARG* 1.3 57.3 + - - +
51D LEU* 3.2 11.4 + - + +
52D ASP* 2.9 34.1 + - - +
70D LEU* 4.3 12.6 - - + -
140F THR* 4.8 1.1 - - + -
142F ARG* 3.9 36.4 + - - +
144F PHE* 3.8 28.3 - - + -
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.7 26.8 - - + -
42D ASP 4.9 1.6 + - - -
45D ASN* 3.0 36.4 + - - +
46D ALA* 3.4 27.9 - - - +
48D LEU* 1.3 78.0 - - - +
50D LYS* 1.3 56.5 + - - +
52D ASP* 3.2 9.6 + - - +
53D GLU* 2.8 40.5 + - - +
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA 3.0 13.6 + - - +
47D LEU* 3.4 29.2 - - + +
49D ARG* 1.3 77.4 - - - +
51D LEU* 1.3 64.0 + - + +
53D GLU* 3.4 10.3 + - - +
54D ALA* 3.1 22.0 + - - +
61D VAL* 5.1 19.5 - - + +
62D ASP* 5.8 4.0 - - - +
66D ALA* 5.3 7.2 - - - +
62E ASP* 6.1 1.1 - - - -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.0 31.8 + - + +
48D LEU* 3.8 11.0 - - + +
50D LYS* 1.3 77.6 - - + +
52D ASP* 1.3 66.6 + - - +
54D ALA* 3.4 5.6 + - + +
55D ARG* 3.1 58.0 + - - +
61D VAL* 4.0 29.2 - - + -
63D ILE* 5.4 2.0 - - + -
66D ALA* 4.0 17.9 - - + -
67D LEU* 4.8 17.9 - - + -
70D LEU* 5.1 9.9 - - + -
118F GLU* 5.2 4.9 - - - +
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Residues in contact with ASP 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 3.7 28.2 + - + +
7D PHE* 4.4 6.2 - - - -
48D LEU 2.9 16.8 + - - +
49D ARG* 3.5 11.5 - - - +
51D LEU* 1.3 73.0 - - - +
53D GLU* 1.3 66.7 + - - +
55D ARG* 3.1 17.9 + - - +
56D GLU* 2.9 39.1 + - - +
108F ASP 4.8 0.9 - - - +
142F ARG* 2.8 35.7 + - - -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 2.8 28.4 + - - +
50D LYS* 3.6 9.0 + - - +
52D ASP* 1.3 71.8 - - - +
54D ALA* 1.3 62.4 + - - +
56D GLU* 3.3 15.4 + - - +
57D SER* 3.0 27.8 + - - -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS 3.1 13.1 + - - +
51D LEU* 3.8 4.5 - - - +
52D ASP 3.2 0.4 - - - -
53D GLU* 1.3 77.2 - - - +
55D ARG* 1.3 57.8 + - - +
58D ASP* 2.9 6.6 + - - -
59D THR* 2.7 45.2 + - - +
61D VAL* 3.2 36.6 - - + -
114F ARG* 3.5 12.4 + - - +
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.1 44.5 + - - +
52D ASP* 3.1 19.3 + - - +
54D ALA* 1.3 76.7 - - - +
56D GLU* 1.3 65.6 + - + +
58D ASP* 3.2 13.3 + - - +
67D LEU* 6.3 0.2 - - - +
108F ASP* 3.0 31.7 + - - +
109F PHE* 3.4 39.0 - - - +
110F GLY* 5.7 2.5 - - - -
114F ARG* 3.5 25.7 - - - +
118F GLU* 2.8 33.8 + - - +
142F ARG* 5.3 3.6 - - - +
143F LEU 5.5 3.4 + - - -
145F ILE* 5.6 0.8 - - - +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 5.3 8.4 - - - +
52D ASP* 2.9 27.6 + - + +
53D GLU* 3.3 17.9 + - - +
55D ARG* 1.3 78.3 - - + +
57D SER* 1.3 59.3 + - - +
58D ASP* 3.2 2.0 + - - +
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU 3.0 15.5 + - - -
54D ALA* 3.5 0.3 + - - -
56D GLU* 1.3 75.8 - - - +
58D ASP* 1.3 67.2 + - - +
59D THR* 2.8 42.1 + - - +
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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
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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