Contacts of the helix formed by residues 44 - 58 (chain A) in PDB entry 1ML0
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 VAL 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU* 1.3 73.3 - - + +
45A THR* 1.3 59.7 + - - +
46A GLU 3.2 0.5 + - - -
47A CYS* 3.2 3.5 + - - +
48A ALA* 2.5 40.4 + - + +
142A ASP 3.3 27.8 - - - +
143A ASN* 3.7 9.0 - - - +
144A VAL 3.4 27.4 - - - +
145A VAL* 3.7 15.3 - - + -
155A MET* 4.0 13.9 - - + +
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Residues in contact with THR 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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43A GLU* 3.1 27.1 + - - +
44A VAL* 1.3 80.8 - - - +
46A GLU* 1.3 66.8 + - - +
48A ALA* 3.4 4.9 - - - +
49A GLY* 2.8 29.5 + - - -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 4.3 13.5 - - + +
41A GLU* 3.4 43.9 - - + +
43A GLU* 3.0 39.3 - - - +
44A VAL 3.2 0.6 + - - -
45A THR* 1.3 83.6 - - - +
47A CYS* 1.3 61.0 - - - +
49A GLY* 3.3 1.6 + - - -
50A ILE* 2.8 29.1 + - + +
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 3.8 15.7 - - - +
36A CYS* 2.0 52.5 - - - -
43A GLU 5.0 1.0 + - - +
44A VAL 3.2 2.5 + - - +
46A GLU* 1.3 79.7 - - - +
48A ALA* 1.3 64.0 + - - +
50A ILE* 3.1 6.7 + - - +
51A LEU* 3.0 45.0 + - - +
108A LEU* 4.8 2.7 - - - -
145A VAL* 4.2 11.0 - - + -
155A MET* 3.9 16.4 - - + -
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Residues in contact with ALA 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 VAL* 2.5 33.6 + - + +
45A THR* 3.4 7.0 - - - +
47A CYS* 1.3 73.5 - - - +
49A GLY* 1.3 61.1 + - - +
52A LYS* 3.3 22.9 + - - +
144A VAL 4.8 0.7 - - - +
145A VAL* 3.4 33.0 - - - +
146A PHE* 5.6 0.2 - - - -
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Residues in contact with GLY 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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28A ARG* 4.1 4.6 + - - -
45A THR 2.8 19.5 + - - -
46A GLU 3.8 2.5 - - - -
48A ALA* 1.3 72.8 - - - +
50A ILE* 1.3 60.5 + - - +
52A LYS* 4.1 6.7 - - - +
53A ASP* 3.8 17.2 + - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.5 44.6 - - + +
31A GLU* 3.9 24.7 - - + +
32A ILE* 4.4 10.1 - - + -
35A HIS* 3.8 39.3 - - + -
36A CYS* 4.7 5.6 - - - -
46A GLU* 2.8 26.5 - - - +
47A CYS* 3.1 6.6 + - - +
49A GLY* 1.3 76.5 - - - +
51A LEU* 1.3 66.7 + - + +
53A ASP* 3.5 2.6 + - - +
54A VAL* 3.0 33.9 + - + +
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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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32A ILE* 4.9 8.5 - - + -
36A CYS* 4.1 9.6 - - - -
47A CYS* 3.0 30.4 + - - +
48A ALA 4.0 0.2 - - - +
50A ILE* 1.3 77.4 - - - +
52A LYS* 1.3 57.7 + - - +
54A VAL* 4.5 1.8 - - + +
55A LEU* 2.6 65.0 + - + +
62A LEU* 4.0 21.5 - - + -
108A LEU* 5.4 2.7 - - + -
145A VAL* 3.4 46.9 - - + +
146A PHE* 4.1 7.2 - - + -
153A VAL* 4.6 6.7 - - + -
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Residues in contact with LYS 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 ALA 3.3 15.1 + - - +
49A GLY* 4.1 8.1 - - - +
50A ILE 3.3 0.2 - - - -
51A LEU* 1.3 79.8 - - - +
53A ASP* 1.3 62.7 + - - +
56A SER* 2.7 45.1 + - - +
146A PHE* 4.2 18.1 - - + -
147A THR 5.8 3.6 - - - +
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Residues in contact with ASP 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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27A LYS* 5.6 0.9 + - - -
28A ARG* 2.8 46.8 + - - +
49A GLY 3.8 6.1 + - - +
50A ILE 3.5 2.5 + - - +
51A LEU 3.2 0.2 - - - -
52A LYS* 1.3 83.2 - - - +
54A VAL* 1.3 61.1 + - - +
56A SER* 4.1 1.8 - - - -
57A LYS* 2.9 57.7 + - - +
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Residues in contact with VAL 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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27A LYS* 3.8 9.4 - - + +
28A ARG* 3.9 35.9 - - + -
32A ILE* 4.6 9.4 - - + -
50A ILE* 3.0 23.1 + - + +
51A LEU* 4.1 2.5 - - + +
53A ASP* 1.3 73.3 - - - +
55A LEU* 1.3 61.8 + - + +
56A SER 3.1 4.7 - - - -
57A LYS* 3.1 10.7 + - - +
58A ASN* 2.8 26.9 + - - +
61A GLU* 2.7 47.1 - - + +
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Residues in contact with LEU 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 LEU* 2.6 52.5 + - + +
54A VAL* 1.3 77.6 - - + +
56A SER* 1.3 58.3 + - - +
57A LYS 3.4 0.2 - - - -
58A ASN 3.0 15.7 - - - +
59A LEU* 3.1 36.1 + - - +
61A GLU* 4.0 18.8 - - + +
62A LEU* 4.1 26.9 - - + -
146A PHE* 3.3 38.6 - - + -
151A MET* 4.3 11.0 - - + -
153A VAL* 4.5 1.1 - - + -
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Residues in contact with SER 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 LYS* 2.7 45.6 + - - +
53A ASP* 4.1 2.5 - - - -
54A VAL 3.1 0.6 - - - -
55A LEU* 1.3 78.4 - - - +
57A LYS* 1.3 66.2 + - - +
58A ASN 3.2 0.2 - - - -
59A LEU 5.1 0.7 + - - -
146A PHE* 4.4 4.6 - - - -
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Residues in contact with LYS 57 (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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27A LYS* 4.6 28.5 - - + +
53A ASP* 2.9 43.2 + - - +
54A VAL* 3.1 8.4 + - - +
56A SER* 1.3 79.8 - - - +
58A ASN* 1.3 62.9 + - + +
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Residues in contact with ASN 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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27A LYS* 6.2 0.9 - - + -
54A VAL 2.8 9.3 + - - +
55A LEU* 3.0 24.5 - - - +
57A LYS* 1.3 82.4 - - + +
59A LEU* 1.3 60.2 + - - +
60A HIS* 3.2 21.2 + - - +
61A GLU* 2.9 49.2 + - - +
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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
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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