Contacts of the helix formed by residues 35 - 57 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ASN* 3.6 41.2 - - + +
31F ILE* 2.9 34.1 + - + +
34F GLN* 1.3 87.9 - - + +
36F HIS* 1.3 62.7 + - + +
38F GLN* 3.6 3.2 - - - +
39F ALA* 3.0 26.2 + - - +
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Residues in contact with HIS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E GLU* 3.9 7.4 - - - -
173E TYR* 2.8 29.9 + + - -
178E ASN* 3.6 26.3 - - + +
31F ILE 3.8 12.1 - - - -
32F HIS* 3.4 19.1 + - + +
35F LYS* 1.3 75.9 - - + +
37F HIS* 1.3 60.3 + - - +
38F GLN 3.0 1.1 - - - -
39F ALA* 2.7 32.9 + - - +
40F TYR* 3.2 18.0 + - + +
170F HIS* 3.2 54.4 + + + +
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Residues in contact with HIS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 3.6 12.0 - - + +
11F PRO* 3.5 34.1 - - + +
32F HIS 3.0 12.6 + - - +
33F HIS* 3.2 18.2 - - - +
35F LYS 3.6 0.2 - - - -
36F HIS* 1.3 74.7 - - - +
38F GLN* 1.3 62.7 + - - +
40F TYR* 3.2 18.6 + + - +
41F VAL* 3.2 9.5 + - + +
76F GLY 4.6 0.4 - - - -
77F TYR* 3.5 35.1 + + - -
80F HIS* 3.6 27.3 + + + -
81F LEU* 4.0 5.2 - - - -
84F TRP* 2.8 31.2 + + - +
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Residues in contact with GLN 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 3.4 34.4 - - - +
33F HIS 3.4 4.7 + - - +
34F GLN* 3.1 28.2 - - - +
35F LYS 3.6 2.9 - - - +
37F HIS* 1.3 80.0 - - - +
39F ALA* 1.3 61.4 + - - +
41F VAL* 3.2 15.9 + - - +
42F ASP* 2.9 60.9 + - - +
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Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LYS 3.0 14.3 + - - +
36F HIS* 2.7 23.1 + - - +
38F GLN* 1.3 71.4 - - - +
40F TYR* 1.3 58.5 + - + +
42F ASP* 3.4 8.1 + - - +
43F GLY* 2.7 31.0 + - - -
73F HIS* 4.0 4.4 + - - +
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F HIS* 3.3 27.5 + - + +
37F HIS* 3.2 10.6 + + - +
39F ALA* 1.3 78.6 - - + +
41F VAL* 1.3 60.2 + - - +
44F ALA* 2.9 33.4 + - - +
72F PHE* 3.9 18.1 - + - -
73F HIS* 3.5 37.7 - + - +
76F GLY* 3.9 9.2 - - - -
77F TYR* 3.7 9.9 - - - +
80F HIS* 3.3 37.2 - + - -
151F HIS* 3.1 24.7 + + - -
168F TRP* 3.7 10.4 - - - -
170F HIS* 3.3 20.8 - + - -
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.4 33.0 - - - +
9F GLU* 3.9 6.1 - - - -
10F LEU* 3.8 22.7 - - + +
37F HIS* 3.2 15.7 + - + +
38F GLN* 3.2 25.3 + - - +
40F TYR* 1.3 77.0 - - - +
42F ASP* 1.3 60.8 + - - +
44F ALA* 3.9 1.8 - - - +
45F ASN* 3.0 39.1 + - - +
77F TYR* 3.8 25.7 - - + +
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLN* 2.9 47.7 + - - +
39F ALA* 3.9 6.1 - - - +
41F VAL* 1.3 76.5 - - - +
43F GLY* 1.3 61.2 + - - +
45F ASN* 3.9 6.5 + - - +
46F ALA* 2.9 33.3 + - - +
49F ARG* 4.9 1.2 + - - -
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Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA 2.7 22.4 + - - -
42F ASP* 1.3 74.1 - - - +
44F ALA* 1.3 61.9 + - - +
46F ALA* 3.4 5.5 + - - +
47F LEU* 3.2 21.3 + - - +
69F GLU* 4.8 2.4 - - - +
73F HIS* 3.6 30.5 + - - -
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Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.6 29.8 - - + -
40F TYR 2.9 17.8 + - - +
41F VAL 3.9 1.3 - - - +
43F GLY* 1.3 75.0 - - - +
45F ASN* 1.3 59.2 + - - +
47F LEU* 3.4 7.1 + - - +
48F LEU* 3.0 32.7 + - - +
70F LEU* 4.4 5.0 - - - +
73F HIS* 3.6 15.9 - - + +
74F VAL* 4.0 14.1 - - + +
77F TYR* 5.6 1.3 - - + -
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Residues in contact with ASN 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PHE* 3.3 19.8 - - + +
8F TYR* 2.8 53.4 + - - +
41F VAL* 3.0 28.9 + - - +
42F ASP* 3.9 6.0 + - - +
44F ALA* 1.3 73.0 - - - +
46F ALA* 1.3 66.9 + - - +
47F LEU 3.1 1.6 - - - -
48F LEU* 3.1 6.4 + - - +
49F ARG* 3.0 43.9 + - - +
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASP 2.9 21.9 + - - +
43F GLY* 3.7 6.1 - - - +
45F ASN* 1.3 73.4 - - - +
47F LEU* 1.3 57.2 + - - +
49F ARG* 3.4 23.1 + - - +
50F LYS* 3.0 27.3 + - - +
69F GLU* 6.1 0.4 - - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLY 3.2 13.5 + - - +
44F ALA* 3.6 5.8 - - - +
45F ASN 3.1 0.4 - - - -
46F ALA* 1.3 77.4 - - - +
48F LEU* 1.3 67.0 + - - +
50F LYS* 3.2 25.8 + - + +
51F LEU* 3.0 30.0 + - + +
66F ALA* 3.1 43.7 - - + +
69F GLU* 3.9 22.0 - - + +
70F LEU* 3.2 39.3 - - + +
73F HIS* 5.6 0.7 - - - +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D THR* 4.7 1.3 - - + -
142D ARG* 3.8 38.4 + - - +
144D PHE* 3.7 28.5 - - + -
6F LYS 4.3 2.0 - - - +
7F PHE* 4.1 11.4 - - + -
8F TYR* 3.9 28.7 - - + -
44F ALA 3.0 18.0 + - - +
45F ASN* 3.1 15.7 + - - +
47F LEU* 1.3 76.7 - - - +
49F ARG* 1.3 57.2 + - - +
51F LEU* 3.2 12.1 + - + +
52F ASP* 2.9 33.9 + - - +
70F LEU* 4.4 11.4 - - + -
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Residues in contact with ARG 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.7 27.2 - - + -
42F ASP 4.9 1.0 + - - -
45F ASN* 3.0 36.0 + - - +
46F ALA* 3.4 27.9 - - - +
48F LEU* 1.3 76.7 - - - +
50F LYS* 1.3 58.0 + - - +
52F ASP* 3.2 9.4 + - - +
53F GLU* 2.8 40.5 + - - +
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Residues in contact with LYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ASP* 6.1 0.4 - - - -
46F ALA 3.0 15.4 + - - +
47F LEU* 3.4 30.3 - - + +
49F ARG* 1.3 77.0 - - - +
51F LEU* 1.3 65.9 + - + +
53F GLU* 3.4 10.6 + - - +
54F ALA* 3.1 22.0 + - - +
61F VAL* 5.1 17.2 - - + +
62F ASP* 5.8 3.8 - - - +
66F ALA* 5.5 6.5 - - - +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLU* 5.2 4.0 - - - +
47F LEU* 3.0 33.5 + - + +
48F LEU* 3.8 10.8 - - + +
50F LYS* 1.3 76.2 - - + +
52F ASP* 1.3 65.7 + - - +
54F ALA* 3.3 5.3 + - + +
55F ARG* 3.1 58.9 + - - +
61F VAL* 4.0 24.9 - - + -
63F ILE* 5.5 2.0 - - + -
66F ALA* 4.0 21.8 - - + -
67F LEU* 4.8 19.1 - - + -
70F LEU* 5.1 10.3 - - + -
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Residues in contact with ASP 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP 4.8 0.3 - - - +
142D ARG* 2.7 36.3 + - - -
5F LYS* 3.5 31.0 + - + +
7F PHE* 4.4 6.4 - - - -
48F LEU 2.9 16.7 + - - +
49F ARG* 3.2 10.9 + - - +
51F LEU* 1.3 74.7 - - - +
53F GLU* 1.3 66.9 + - - +
55F ARG* 3.1 16.6 + - - +
56F GLU* 2.9 39.9 + - - +
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ARG* 2.8 28.4 + - - +
50F LYS* 3.5 9.4 + - - +
51F LEU 3.3 0.2 - - - -
52F ASP* 1.3 73.2 - - - +
54F ALA* 1.3 63.0 + - - +
56F GLU* 3.2 15.6 + - - +
57F SER* 3.0 27.6 + - - -
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ARG* 3.5 12.0 + - - +
50F LYS 3.1 14.4 + - - +
51F LEU* 3.7 5.4 - - - +
52F ASP 3.2 0.2 - - - -
53F GLU* 1.3 76.3 - - - +
55F ARG* 1.3 57.6 + - - +
58F ASP* 2.9 6.1 + - - -
59F THR* 2.7 44.9 + - - +
61F VAL* 3.1 35.7 - - + -
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Residues in contact with ARG 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ASP* 2.8 31.3 + - - +
109D PHE* 3.4 39.1 - - - +
110D GLY* 5.7 2.7 - - - -
114D ARG* 3.6 25.7 - - - +
118D GLU* 2.9 31.8 + - - +
142D ARG* 5.3 3.0 - - - +
143D LEU 5.6 3.8 + - - -
145D ILE* 6.0 0.2 - - - +
51F LEU* 3.1 45.3 + - - +
52F ASP* 3.1 19.7 + - - +
54F ALA* 1.3 77.3 - - - +
56F GLU* 1.3 64.7 + - + +
58F ASP* 3.2 12.6 + - - +
67F LEU* 6.3 0.4 - - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 5.3 8.2 - - - +
52F ASP* 2.9 27.9 + - + +
53F GLU* 3.8 16.2 + - - +
55F ARG* 1.3 79.3 - - + +
57F SER* 1.3 60.2 + - - +
58F ASP* 3.2 1.4 + - - +
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Residues in contact with SER 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU 3.0 17.9 + - - -
54F ALA* 3.9 0.3 - - - -
56F GLU* 1.3 75.5 - - - +
58F ASP* 1.3 67.7 + - - +
59F THR* 2.7 43.0 + - - +
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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
------------------------------------------------------------
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