Contacts of the helix formed by residues 44 - 59 (chain A) in PDB entry 5H1P
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 5.1 - - - +
43A VAL* 1.3 75.2 - - - +
45A PRO* 1.3 77.6 - - + +
46A ALA* 3.2 9.7 + - - +
47A GLN* 2.9 46.8 + - - +
48A TRP 2.9 18.2 + - - -
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Residues in contact with PRO 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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1A MET* 3.5 19.5 - - + -
44A ASP* 1.3 90.7 - - + +
46A ALA* 1.3 57.9 + - - +
48A TRP* 3.3 4.6 + - + +
49A THR* 2.9 30.6 + - - -
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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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44A ASP* 3.2 8.3 + - - +
45A PRO* 1.3 75.7 - - - +
47A GLN* 1.3 66.5 + - + +
49A THR* 3.2 8.2 + - - -
50A ALA* 3.0 23.9 + - - +
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.9 24.8 - - + +
42A GLU 4.4 1.2 - - - +
43A VAL* 3.5 18.6 - - + +
44A ASP* 2.9 46.8 + - - +
46A ALA* 1.3 76.5 - - + +
48A TRP* 1.3 63.1 + - - +
50A ALA* 3.4 6.4 + - - +
51A LEU* 3.0 25.3 + - - +
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Residues in contact with TRP 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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1A MET* 3.6 21.8 - - + -
3A VAL* 3.7 31.9 - - + -
5A VAL* 4.0 9.6 - - + -
41A ILE* 4.7 1.6 - - + -
43A VAL* 3.9 10.5 - - + +
44A ASP 2.9 7.4 + - - +
45A PRO* 3.5 8.7 - - + +
47A GLN* 1.3 74.5 - - - +
49A THR* 1.3 71.1 + - - +
51A LEU* 3.2 30.0 + - + -
52A ARG* 2.8 50.9 + - + +
55A LEU* 4.4 0.9 - - + -
68A PHE* 3.6 48.0 - + + -
70A HIS* 3.4 32.2 + + - -
80B GLU* 5.4 1.0 + - - -
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Residues in contact with THR 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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45A PRO 2.9 15.9 + - - -
46A ALA* 3.2 11.2 + - - -
48A TRP* 1.3 83.5 - - - +
50A ALA* 1.3 64.0 + - - +
52A ARG* 3.7 8.6 + - - +
53A GLN* 3.2 21.7 + - + +
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Residues in contact with ALA 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 15.9 + - - +
47A GLN* 3.7 6.7 - - - +
48A TRP 3.2 0.2 - - - -
49A THR* 1.3 80.7 - - - +
51A LEU* 1.3 62.1 + - - +
53A GLN* 3.4 5.8 + - - +
54A ARG* 3.3 25.4 + - - +
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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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26A ALA* 3.6 33.7 - - + +
27A CYS* 4.4 3.1 - - - -
30A LEU* 4.3 17.5 - - + -
41A ILE* 3.6 41.7 - - + -
43A VAL* 5.1 0.4 - - + -
47A GLN 3.0 17.9 + - - +
48A TRP* 3.9 15.3 - - + +
50A ALA* 1.3 73.3 - - - +
52A ARG* 1.3 67.7 + - - +
54A ARG* 3.0 11.1 + - + +
55A LEU* 2.9 43.4 + - + +
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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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48A TRP* 2.8 53.2 + - + +
49A THR* 3.7 7.9 + - - +
51A LEU* 1.3 73.7 - - - +
53A GLN* 1.3 79.8 + - - +
55A LEU* 3.3 5.7 + - - +
56A CYS* 3.0 45.6 + - - -
68A PHE* 3.7 18.3 - - + -
80B GLU* 2.7 43.4 + - - -
82B VAL* 4.8 1.2 - - - +
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Residues in contact with GLN 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 THR* 3.2 11.4 + - + +
50A ALA* 3.6 10.3 - - - +
51A LEU 3.3 0.2 - - - -
52A ARG* 1.3 92.4 + - - +
54A ARG* 1.3 64.9 + - + +
56A CYS* 3.4 9.6 + - - +
57A ASP* 3.0 53.9 + - - +
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Residues in contact with ARG 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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22A LYS 5.6 0.6 + - - -
26A ALA* 3.6 32.0 + - + +
50A ALA 3.3 13.6 + - - +
51A LEU* 3.0 16.6 + - + +
53A GLN* 1.3 81.5 - - + +
55A LEU* 1.3 58.2 + - - +
57A ASP* 3.1 7.8 + - - +
58A LEU* 2.9 56.8 + - + +
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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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5A VAL* 4.1 23.3 - - + -
23A VAL* 4.0 22.0 - - + -
26A ALA* 4.1 13.0 - - + -
27A CYS* 3.9 20.9 - - - -
48A TRP* 4.4 4.9 - - + -
51A LEU* 2.9 41.7 + - + +
52A ARG 3.7 5.6 - - - +
54A ARG* 1.3 77.0 - - - +
56A CYS* 1.3 62.3 + - - +
58A LEU* 3.3 11.9 + - + +
59A ILE* 3.3 21.5 + - - +
66A LEU* 3.8 15.3 - - + -
68A PHE* 4.1 22.0 - - + -
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Residues in contact with CYS 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 ARG* 3.0 42.0 + - - +
53A GLN* 3.7 14.1 - - - +
55A LEU* 1.3 76.5 - - - +
57A ASP* 1.3 62.9 + - - +
59A ILE* 3.5 18.2 + - - +
61A PRO* 5.2 4.2 - - - +
66A LEU* 4.2 5.2 - - - -
68A PHE* 4.2 9.4 - - - -
82B VAL* 3.9 36.5 - - + +
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Residues in contact with ASP 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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53A GLN* 3.0 48.2 + - - +
54A ARG* 3.1 7.6 + - - +
56A CYS* 1.3 79.5 - - - +
58A LEU* 1.3 62.6 + - + +
59A ILE 3.7 5.0 + - - +
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Residues in contact with LEU 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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19A ARG* 3.8 21.7 - - - +
22A LYS* 3.8 59.2 - - + +
23A VAL* 4.2 16.4 - - + +
26A ALA* 4.0 17.3 - - + -
54A ARG* 2.9 40.6 + - + +
55A LEU* 3.3 4.7 + - - +
57A ASP* 1.3 79.7 - - + +
59A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 59 (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 TYR* 3.4 30.3 - - + -
19A ARG* 4.2 2.0 - - - +
23A VAL* 4.2 6.3 - - + -
55A LEU 3.4 12.8 - - - +
56A CYS 3.5 15.5 - - - +
57A ASP 3.8 7.1 - - - +
58A LEU* 1.3 81.8 - - - +
60A ASP* 1.3 58.1 + - - +
61A PRO* 3.5 29.8 - - + +
64A ASP* 3.7 19.5 - - + +
66A LEU* 3.6 32.1 - - + +
82B VAL* 4.2 23.8 - - + +
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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