Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 1H4R
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LYS 4.4 2.9 - - - +
41A TRP* 1.3 77.4 - - - +
43A GLY* 1.3 67.6 + - - +
44A LYS* 3.2 3.1 - - + +
45A ASP* 2.9 26.6 + - - +
46A LEU 3.4 8.3 + - - -
77A MET 3.5 11.0 - - - +
78A ASP* 3.6 28.8 + - - +
79A LYS 3.3 17.3 - - - +
80A LYS* 3.8 13.7 - - + +
81A VAL* 3.8 8.0 - - - +
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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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42A LYS* 1.3 72.4 - - - +
44A LYS* 1.3 56.5 + - - +
46A LEU* 3.2 3.5 + - - +
47A PHE* 2.8 30.7 + - - +
75A LEU* 4.1 20.2 - - - +
76A LYS 3.4 17.0 - - - -
77A MET* 3.4 12.1 + - - +
79A LYS 2.9 14.1 + - - -
81A VAL* 4.2 2.8 - - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 3.2 3.1 - - + -
43A GLY* 1.3 72.1 - - - +
45A ASP* 1.3 61.1 + - - +
48A ASP* 2.9 61.7 + - - +
77A MET* 2.9 46.4 + - + +
78A ASP* 6.1 0.2 - - - +
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Residues in contact with ASP 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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41A TRP* 3.4 44.1 + - + +
42A LYS* 2.9 34.8 + - - +
44A LYS* 1.3 78.8 - - - +
46A LEU* 1.3 66.0 - - - +
48A ASP* 3.9 5.3 - - - +
49A LEU* 3.1 23.4 + - - +
52A ARG* 5.1 1.0 + - - -
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Residues in contact with LEU 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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24A VAL* 4.1 20.2 - - + -
26A ILE* 4.5 3.4 - - + -
35A PHE* 4.8 7.9 - - + -
37A CYS* 4.4 20.0 - - + -
41A TRP* 4.5 4.9 - - + -
42A LYS 3.4 7.0 + - - +
43A GLY* 3.2 6.1 + - - +
45A ASP* 1.3 76.9 - - - +
47A PHE* 1.3 66.9 + - - +
49A LEU* 3.2 18.4 + - + +
50A VAL* 3.0 36.6 + - + +
64A LEU* 4.0 18.4 - - + -
75A LEU* 4.1 6.1 - - + -
81A VAL* 4.2 14.1 - - + -
94A PHE* 3.9 30.3 - - + -
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Residues in contact with PHE 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 2.8 18.0 + - - +
44A LYS 3.9 2.7 - - - +
46A LEU* 1.3 77.9 - - - +
48A ASP* 1.3 73.7 + - - +
50A VAL* 3.3 4.2 + - - +
51A CYS* 3.0 41.2 + - - -
59A THR* 3.5 26.9 - - - -
62A PHE* 3.5 31.0 - - + -
63A GLY* 3.8 6.7 - - - -
64A LEU* 3.9 26.0 - - + +
77A MET* 3.8 28.9 - - + -
96A PHE* 3.7 22.0 - + - -
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Residues in contact with ASP 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 LYS* 2.9 56.4 + - - +
45A ASP* 3.9 5.1 - - - +
46A LEU 3.3 0.2 - - - -
47A PHE* 1.3 88.3 - - - +
49A LEU* 1.3 58.4 + - - +
51A CYS* 3.4 6.1 + - - +
52A ARG* 2.9 48.6 + - + +
59A THR* 6.2 0.2 - - - +
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Residues in contact with LEU 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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35A PHE* 3.5 39.5 - - + -
36A ASN 4.8 1.6 - - - +
41A TRP* 3.8 30.7 - - + -
45A ASP 3.1 18.1 + - - +
46A LEU* 3.2 8.9 + - + +
48A ASP* 1.3 73.1 - - - +
50A VAL* 1.3 65.6 + - - +
52A ARG* 3.4 30.5 + - + +
53A THR* 2.8 39.5 + - - +
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Residues in contact with VAL 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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26A ILE* 3.9 30.5 - - + -
28A THR* 5.4 0.2 - - + -
33A MET* 5.4 2.2 - - - -
35A PHE* 3.9 28.7 - - + -
46A LEU* 3.0 19.9 + - + +
47A PHE* 3.6 7.6 - - - +
49A LEU* 1.3 76.6 - - - +
51A CYS* 1.3 62.5 + - - +
53A THR* 3.2 3.1 + - - -
54A LEU* 3.1 36.3 + - + +
64A LEU* 4.6 6.1 - - + -
96A PHE* 3.6 30.5 - - + -
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Residues in contact with CYS 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 PHE* 3.0 56.0 + - - +
48A ASP* 3.8 6.3 - - - +
50A VAL* 1.3 77.6 - - - +
52A ARG* 1.3 62.3 + - + +
54A LEU* 3.2 3.9 + - - -
55A GLY 3.0 3.8 + - - -
56A LEU* 2.9 49.1 + - + +
59A THR* 3.7 15.9 - - + -
96A PHE* 4.0 14.1 - - - -
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Residues in contact with ARG 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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41A TRP* 6.1 1.6 - - - -
45A ASP 5.1 1.0 + - - -
48A ASP* 2.9 43.1 + - + +
49A LEU* 3.4 33.9 - - + +
50A VAL 3.3 0.2 - - - -
51A CYS* 1.3 76.0 - - + +
53A THR* 1.3 63.9 + - - +
55A GLY* 3.0 15.0 + - - -
56A LEU 5.0 0.7 - - - +
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Residues in contact with THR 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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33A MET* 4.3 13.0 - - + -
35A PHE* 3.3 34.4 - - + -
49A LEU* 2.8 27.2 + - - +
50A VAL 3.2 4.7 + - - -
52A ARG* 1.3 76.4 - - - +
54A LEU* 1.3 61.7 + - + +
55A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 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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28A THR* 4.5 10.1 - - + +
30A ASP* 6.2 1.1 - - + +
33A MET* 4.2 24.9 - - + -
50A VAL* 3.1 30.3 + - + +
51A CYS* 3.7 4.9 - - - +
52A ARG 3.2 0.2 - - - -
53A THR* 1.3 78.8 - - + +
55A GLY* 1.3 62.8 + - - +
56A LEU* 3.5 9.8 + - + -
96A PHE* 3.7 34.8 - - + -
113A ILE* 3.8 32.5 - - + +
117A LEU* 4.4 9.6 - - + -
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Residues in contact with GLY 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 CYS 3.0 3.8 + - - -
52A ARG* 3.0 15.0 + - - -
53A THR 3.2 0.6 + - - -
54A LEU* 1.3 78.7 - - - +
56A LEU* 1.3 60.1 + - - +
57A ARG* 4.0 9.4 + - - -
111A GLN* 3.0 22.7 + - - -
113A ILE* 3.9 3.7 - - - +
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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