Contacts of the helix formed by residues 35 - 57 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 2.9 34.4 + - + +
34C GLN* 1.3 88.6 + - + +
36C HIS* 1.3 61.5 + - + +
37C HIS 3.7 0.2 - - - -
38C GLN* 3.6 3.4 - - - +
39C ALA* 3.0 26.7 + - - +
178D ASN* 3.7 39.2 - - + +
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Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE 3.8 12.1 - - - -
32C HIS* 3.4 17.6 + - + +
35C LYS* 1.3 76.0 - - + +
37C HIS* 1.3 68.6 + - - +
38C GLN 3.0 1.1 - - - -
39C ALA* 2.7 19.4 + - - +
40C TYR* 3.1 24.4 + - + -
170C HIS* 3.3 53.6 + + + +
169D GLU* 4.0 6.7 - - - -
173D TYR* 2.8 31.1 + + - -
178D ASN* 3.6 27.0 - - + +
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Residues in contact with HIS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.6 13.6 - - + +
11C PRO* 3.4 29.1 - - + +
32C HIS 3.1 9.3 + - - +
33C HIS* 3.2 17.6 + - - +
36C HIS* 1.3 76.9 - - - +
38C GLN* 1.3 62.4 + - - +
40C TYR* 3.1 18.8 + + - +
41C VAL* 3.2 10.5 + - + +
76C GLY 4.5 0.4 - - - -
77C TYR* 3.4 41.9 + + - -
80C HIS* 3.6 26.4 - + + -
81C LEU* 4.1 4.7 - - - -
84C TRP* 2.9 30.0 + + - +
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.4 34.1 - - + +
33C HIS 3.5 4.9 + - - +
34C GLN* 3.1 28.6 - - - +
35C LYS 3.6 3.4 - - - +
37C HIS* 1.3 78.9 - - - +
39C ALA* 1.3 62.5 + - - +
41C VAL* 3.1 18.2 + - - +
42C ASP* 2.9 58.5 + - - +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LYS 3.0 14.6 + - - +
36C HIS* 2.7 22.2 + - - +
38C GLN* 1.3 72.1 - - - +
40C TYR* 1.3 62.8 + - + +
42C ASP* 3.8 8.3 - - - +
43C GLY* 2.8 26.3 + - - -
73C HIS* 4.0 3.9 + - - +
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Residues in contact with TYR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C HIS* 3.1 29.9 + - + +
37C HIS* 3.1 8.0 + - - +
39C ALA* 1.3 77.8 - - + +
41C VAL* 1.3 67.6 + - - +
44C ALA* 2.9 27.5 + - - +
72C PHE* 4.0 17.0 - + - -
73C HIS* 3.4 41.2 - + - +
76C GLY* 3.9 8.1 - - - -
77C TYR* 3.7 8.7 - - - +
80C HIS* 3.3 37.9 - + - -
151C HIS* 3.2 23.4 + + - -
168C TRP* 3.7 10.0 - - - -
170C HIS* 3.4 20.3 - - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 3.4 21.7 - - - +
9C GLU* 3.9 5.8 - - - -
10C LEU* 3.7 27.8 - - + +
37C HIS* 3.2 14.7 + - + +
38C GLN* 3.1 16.8 + - - +
40C TYR* 1.3 77.2 - - - +
42C ASP* 1.3 64.9 + - - +
44C ALA* 3.9 2.1 - - - +
45C ASN* 3.0 51.2 + - - +
77C TYR* 3.9 23.7 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 2.9 50.1 + - - +
39C ALA* 3.9 6.5 - - - +
41C VAL* 1.3 75.8 - - - +
43C GLY* 1.3 60.6 + - - +
45C ASN* 3.8 6.4 + - - +
46C ALA* 2.8 32.6 + - - +
49C ARG* 5.0 1.4 + - - -
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA 2.8 18.2 + - - -
41C VAL 3.3 0.2 - - - -
42C ASP* 1.3 77.8 - - - +
44C ALA* 1.3 61.9 + - - +
46C ALA* 3.4 5.6 + - - +
47C LEU* 3.2 22.0 + - - +
69C GLU* 4.8 2.3 - - - +
73C HIS* 3.6 30.3 + - - -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 3.7 28.3 - - + -
40C TYR 2.9 19.6 + - - +
41C VAL* 3.9 0.9 - - - +
43C GLY* 1.3 73.8 - - - +
45C ASN* 1.3 58.3 + - - +
47C LEU* 3.4 6.9 + - - +
48C LEU* 3.0 33.3 + - - +
70C LEU* 4.4 4.9 - - - +
73C HIS* 3.6 11.6 - - + +
74C VAL* 3.9 19.3 - - + +
77C TYR* 5.6 1.1 - - + -
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Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.3 19.5 - - + +
8C TYR* 2.9 52.4 + - - +
41C VAL* 3.0 30.6 + - - +
42C ASP* 3.8 6.9 + - - +
44C ALA* 1.3 74.7 - - - +
46C ALA* 1.3 64.7 + - - +
47C LEU 3.2 0.2 + - - -
48C LEU* 3.2 6.3 + - - +
49C ARG* 3.0 45.4 + - - +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASP 2.8 21.8 + - - +
43C GLY* 3.7 6.1 - - - +
45C ASN* 1.3 72.1 - - - +
47C LEU* 1.3 57.2 + - - +
49C ARG* 3.4 23.2 + - - +
50C LYS* 3.0 26.2 + - - +
69C GLU* 6.2 0.2 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLY 3.2 13.4 + - - +
44C ALA* 3.6 5.2 - - - +
45C ASN 3.1 0.6 - - - -
46C ALA* 1.3 78.1 - - - +
48C LEU* 1.3 65.1 + - - +
50C LYS* 3.2 26.0 + - + +
51C LEU* 3.0 30.2 + - + +
66C ALA* 3.1 42.0 - - + +
69C GLU* 3.9 21.1 - - + +
70C LEU* 3.2 38.8 - - + +
73C HIS* 5.6 0.4 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS 4.4 2.0 - - - +
7C PHE* 4.1 11.4 - - + -
8C TYR* 3.9 27.1 - - + -
44C ALA 3.0 20.2 + - - +
45C ASN* 3.2 14.8 + - - +
47C LEU* 1.3 76.6 - - - +
49C ARG* 1.3 56.6 + - - +
51C LEU* 3.3 11.4 + - + +
52C ASP* 2.9 33.9 + - - +
70C LEU* 4.3 13.9 - - + -
140E THR* 4.8 1.1 - - + -
142E ARG* 3.9 37.0 + - - +
144E PHE* 3.8 29.2 - - + -
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.7 27.8 - - + -
42C ASP* 5.0 1.6 + - - +
45C ASN* 3.0 33.0 + - - +
46C ALA* 3.5 30.0 - - - +
48C LEU* 1.3 77.5 - - - +
50C LYS* 1.3 58.3 - - - +
52C ASP* 3.2 8.3 + - - +
53C GLU* 2.8 40.0 + - - +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA 3.0 14.7 + - - +
47C LEU* 3.3 28.9 - - + +
49C ARG* 1.3 76.3 - - - +
51C LEU* 1.3 64.8 + - + +
53C GLU* 3.4 10.1 + - - +
54C ALA* 3.1 22.0 + - - +
61C VAL* 4.8 19.0 - - + +
62C ASP* 5.8 4.5 - - - +
66C ALA* 5.4 7.2 - - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.0 30.6 + - + +
48C LEU* 3.8 10.1 - - + +
50C LYS* 1.3 76.3 - - + +
52C ASP* 1.3 66.2 + - - +
54C ALA* 3.4 4.7 + - + +
55C ARG* 3.1 59.4 + - - +
61C VAL* 4.0 29.4 - - + -
63C ILE* 5.4 2.5 - - + -
66C ALA* 4.0 19.5 - - + -
67C LEU* 4.8 18.2 - - + -
70C LEU* 5.1 9.6 - - + -
114E ARG* 5.2 0.2 + - - -
118E GLU* 5.2 3.8 - - - +
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Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS* 3.6 31.1 + - + +
7C PHE* 4.4 5.9 - - - -
48C LEU 2.9 20.9 + - - +
49C ARG* 3.5 8.0 - - - +
51C LEU* 1.3 76.1 - - - +
53C GLU* 1.3 57.7 + - - +
55C ARG* 3.1 17.4 + - - +
56C GLU* 2.9 45.7 + - + +
108E ASP 4.8 0.7 - - - +
142E ARG* 2.8 33.1 + - - -
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 2.8 28.6 + - - +
50C LYS* 3.6 8.2 - - - +
52C ASP* 1.3 73.2 - - - +
54C ALA* 1.3 64.2 + - - +
56C GLU* 3.3 16.1 + - - +
57C SER* 3.0 27.0 + - - -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS 3.1 12.9 + - - +
51C LEU* 3.8 5.4 - - + +
52C ASP 3.3 0.2 - - - -
53C GLU* 1.3 75.7 - - - +
55C ARG* 1.3 58.7 + - - +
57C SER* 3.8 0.2 - - - -
58C ASP* 2.9 5.7 + - - -
59C THR* 2.7 50.2 + - - +
60C ASP 4.8 0.2 - - - +
61C VAL* 3.1 36.6 - - + -
114E ARG* 3.6 6.6 + - - +
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.1 48.0 + - - +
52C ASP* 3.1 19.4 + - - +
54C ALA* 1.3 76.3 - - - +
56C GLU* 1.3 65.2 + - + +
58C ASP* 3.1 13.7 + - - +
108E ASP* 2.9 30.8 + - - +
109E PHE* 3.5 37.8 - - - +
110E GLY* 5.7 1.9 - - - -
114E ARG* 3.5 16.0 - - - +
118E GLU* 2.8 42.9 + - - +
142E ARG* 5.3 3.6 - - - +
143E LEU 5.7 2.8 + - - -
145E ILE* 5.8 0.4 - - - +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 5.3 8.6 - - - +
52C ASP* 2.9 28.1 + - + +
53C GLU* 3.8 17.7 - - - +
55C ARG* 1.3 78.2 - - + +
57C SER* 1.3 58.9 + - - +
58C ASP* 3.5 1.7 + - - +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU 3.0 16.1 + - - -
54C ALA* 3.8 0.3 - - - -
56C GLU* 1.3 75.0 - - - +
58C ASP* 1.3 68.4 + - - +
59C THR* 2.7 42.4 + - - +
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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