Contacts of the helix formed by residues 35 - 57 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 2.9 28.4 + - + +
34A GLN* 1.3 90.4 + - - +
36A HIS* 1.3 60.8 + - + +
38A GLN* 3.6 3.0 - - - +
39A ALA* 3.0 27.0 + - - +
178B ASN* 3.5 47.1 - - + +
104E TYR* 3.0 35.8 + - - -
141E ASP* 4.6 5.7 + - - -
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Residues in contact with HIS 36 (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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31A ILE 3.5 12.5 + - - -
32A HIS* 3.4 17.1 + - + +
35A LYS* 1.3 74.1 - - + +
37A HIS* 1.3 69.6 - - - +
38A GLN 3.0 1.1 - - - -
39A ALA* 2.7 18.7 + - - +
40A TYR* 3.1 22.9 + - + -
170A HIS* 3.1 52.1 + + + +
169B GLU* 3.8 7.9 - - - -
172B TYR* 6.1 0.7 - - - -
173B TYR* 2.8 31.6 + + - -
178B ASN* 3.6 25.3 - - + +
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Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.6 12.2 - - + +
11A PRO* 3.5 27.7 - - + +
32A HIS 3.1 8.7 + - - +
33A HIS* 3.2 18.4 - - - +
36A HIS* 1.3 77.4 - - - +
38A GLN* 1.3 62.9 + - - +
40A TYR* 3.1 18.7 + + - +
41A VAL* 3.2 9.2 + - + +
76A GLY 4.6 0.2 - - - -
77A TYR* 3.4 41.5 + + - -
80A HIS* 3.6 25.9 + + + +
81A LEU* 3.9 4.9 - - - -
84A TRP* 2.8 31.8 + + - +
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.4 32.9 - - - +
33A HIS 3.5 4.5 + - - +
34A GLN 3.1 24.6 - - - +
35A LYS 3.6 4.0 - - - +
36A HIS 3.0 0.2 - - - -
37A HIS* 1.3 79.7 - - - +
39A ALA* 1.3 62.3 + - - +
41A VAL* 3.2 16.7 + - - +
42A ASP* 2.9 53.5 + - - +
99E GLY* 6.0 1.0 - - - -
100E LYS* 3.3 41.4 + - + +
103E GLU* 4.7 1.2 - - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS 3.0 14.4 + - - +
36A HIS* 2.7 21.4 + - - +
38A GLN* 1.3 72.2 - - - +
40A TYR* 1.3 62.6 - - + +
42A ASP* 3.7 8.2 - - - +
43A GLY* 2.8 26.5 + - - -
73A HIS* 4.0 4.5 + - - +
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 3.1 29.1 + - + +
37A HIS* 3.1 9.9 + - - +
39A ALA* 1.3 80.9 - - + +
41A VAL* 1.3 65.0 + - - +
44A ALA* 2.9 27.5 + - - +
72A PHE* 4.0 14.6 - + - -
73A HIS* 3.4 39.2 - + - +
76A GLY* 3.9 9.0 - - - -
77A TYR* 3.7 9.4 - - - +
80A HIS* 3.3 36.1 - + - -
151A HIS* 3.1 28.0 + + - -
168A TRP* 3.6 10.6 - - - -
170A HIS* 3.4 20.8 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.4 33.5 - - - +
9A GLU* 4.0 5.6 - - - -
10A LEU* 3.8 26.9 - - + +
37A HIS* 3.2 13.3 + - + +
38A GLN* 3.2 24.2 + - - +
40A TYR* 1.3 75.5 - - - +
42A ASP* 1.3 59.0 + - - +
44A ALA* 3.8 2.2 - - - +
45A ASN* 3.0 35.6 + - - +
77A TYR* 3.9 24.1 - - + -
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 2.9 45.9 + - - +
39A ALA* 3.9 7.4 - - - +
41A VAL* 1.3 76.7 - - - +
43A GLY* 1.3 61.2 + - - +
45A ASN* 3.9 5.6 + - - +
46A ALA* 2.9 33.3 + - - +
49A ARG* 4.9 1.4 + - - -
100E LYS* 3.7 13.6 + - - -
201E GLU* 5.4 4.5 - - - +
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Residues in contact with GLY 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 ALA 2.8 21.6 + - - -
40A TYR 3.3 0.2 + - - -
41A VAL 3.3 0.2 - - - -
42A ASP* 1.3 76.3 - - - +
44A ALA* 1.3 61.3 + - - +
46A ALA* 3.3 5.6 + - - +
47A LEU* 3.2 21.0 + - - +
69A GLU* 4.8 2.4 - - - +
73A HIS* 3.5 30.9 + - - -
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Residues in contact with ALA 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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8A TYR* 3.6 30.5 - - + -
40A TYR 2.9 17.8 + - - +
41A VAL 3.8 0.7 - - - +
43A GLY* 1.3 75.2 - - - +
45A ASN* 1.3 58.3 + - - +
47A LEU* 3.3 7.7 + - - +
48A LEU* 3.0 33.4 + - - +
70A LEU* 4.4 4.2 - - - +
73A HIS* 3.6 15.5 - - + +
74A VAL* 4.0 13.2 - - + +
77A TYR* 5.6 1.1 - - + -
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Residues in contact with ASN 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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7A PHE* 3.3 19.7 - - + +
8A TYR* 2.8 52.3 + - - +
41A VAL* 3.0 28.2 + - - +
42A ASP* 3.9 6.7 + - - +
43A GLY 3.2 0.2 - - - -
44A ALA* 1.3 73.0 - - - +
46A ALA* 1.3 65.7 + - - +
47A LEU 3.0 1.8 - - - -
48A LEU* 3.1 7.1 + - - +
49A ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 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 ASP 2.9 18.0 + - - +
43A GLY* 3.7 6.1 - - - +
45A ASN* 1.3 77.3 - - - +
47A LEU* 1.3 56.7 + - - +
49A ARG* 3.4 23.0 + - - +
50A LYS* 3.0 26.0 + - - +
69A GLU* 6.1 0.4 - - - +
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Residues in contact with LEU 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 GLY 3.2 9.5 + - - +
44A ALA* 3.6 9.4 - - - +
45A ASN 3.0 0.4 - - - -
46A ALA* 1.3 78.8 - - - +
48A LEU* 1.3 65.5 + - - +
50A LYS* 3.1 27.2 + - + +
51A LEU* 2.9 30.5 + - + +
66A ALA* 3.2 41.7 - - + +
69A GLU* 3.9 23.1 - - + +
70A LEU* 3.2 38.4 - - + +
73A HIS* 5.5 0.4 - - - +
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Residues in contact with LEU 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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6A LYS 4.4 9.9 - - - +
7A PHE* 4.1 17.5 - - + -
8A TYR* 4.0 24.0 - - + -
44A ALA 3.0 19.7 + - - +
45A ASN* 3.1 18.8 + - - +
47A LEU* 1.3 77.9 - - - +
49A ARG* 1.3 57.2 + - - +
51A LEU* 3.3 11.0 + - + +
52A ASP* 2.9 36.0 + - - +
55A ARG* 5.8 0.2 + - - -
70A LEU* 4.4 20.9 - - + -
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Residues in contact with ARG 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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7A PHE* 3.7 27.7 - - + -
42A ASP 4.9 1.2 + - - -
45A ASN* 3.0 33.9 + - - +
46A ALA* 3.4 30.3 - - - +
48A LEU* 1.3 76.5 - - - +
50A LYS* 1.3 57.5 + - - +
52A ASP* 3.2 9.0 + - - +
53A GLU* 2.8 40.2 + - - +
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Residues in contact with LYS 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 ALA 3.0 14.5 + - - +
47A LEU* 3.3 29.6 - - + +
49A ARG* 1.3 77.4 - - - +
51A LEU* 1.3 64.6 + - + +
53A GLU* 3.4 10.7 + - - +
54A ALA* 3.1 22.2 + - - +
61A VAL* 5.2 18.3 - - + +
62A ASP* 5.9 3.8 - - - +
66A ALA* 5.4 6.5 - - - +
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Residues in contact with LEU 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 LEU* 2.9 29.9 + - + +
48A LEU* 3.8 11.7 - - + +
50A LYS* 1.3 76.8 - - + +
52A ASP* 1.3 65.8 + - - +
54A ALA* 3.4 5.2 + - + +
55A ARG* 3.1 60.6 + - - +
61A VAL* 4.1 24.7 - - + -
63A ILE* 5.4 2.2 - - + -
66A ALA* 4.0 24.2 - - + -
67A LEU* 4.8 17.7 - - + -
70A LEU* 5.0 10.1 - - + -
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Residues in contact with ASP 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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5A LYS* 3.6 41.4 + - + +
7A PHE* 4.4 11.1 - - - -
48A LEU* 2.9 27.6 + - - +
49A ARG* 3.5 8.8 - - - +
51A LEU* 1.3 74.3 - - - +
53A GLU* 1.3 66.3 + - - +
55A ARG* 3.1 20.2 + - - +
56A GLU* 2.9 39.0 + - + +
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Residues in contact with GLU 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 ARG* 2.8 29.7 + - - +
50A LYS* 3.6 8.2 - - - +
52A ASP* 1.3 74.0 - - - +
54A ALA* 1.3 63.0 + - - +
56A GLU* 3.2 15.5 + - - +
57A SER* 3.0 27.2 + - - -
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Residues in contact with ALA 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 LYS 3.1 12.9 + - - +
51A LEU* 3.8 5.6 - - - +
52A ASP 3.3 0.4 - - - -
53A GLU* 1.3 78.6 - - - +
55A ARG* 1.3 58.5 + - + +
58A ASP* 2.9 7.3 + - - -
59A THR* 2.7 50.8 + - - +
61A VAL* 3.1 36.6 - - + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 5.8 2.3 - - - +
51A LEU* 3.1 47.7 + - - +
52A ASP* 3.1 23.6 + - - +
54A ALA* 1.3 78.2 - - + +
56A GLU* 1.3 65.8 + - + +
58A ASP* 3.2 14.5 + - - +
67A LEU* 6.3 0.4 - - - +
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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
----------------------------------------------------------
5A LYS* 5.2 9.4 - - - +
52A ASP* 2.9 27.8 + - + +
53A GLU* 3.9 17.3 - - - +
55A ARG* 1.3 78.4 - - + +
57A SER* 1.3 59.5 + - - +
58A ASP* 3.2 1.8 + - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 3.0 15.6 + - - -
54A ALA* 3.6 0.5 + - - -
56A GLU* 1.3 75.8 - - - +
58A ASP* 1.3 67.8 + - - +
59A THR* 2.9 36.0 + - - +
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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