Contacts of the helix formed by residues 43 - 58 (chain A) in PDB entry 5HNK
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 PHE 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY 4.9 1.1 - - - -
34A PHE* 3.8 49.6 - + + +
35A LYS* 5.6 0.2 - - - -
38A ASN* 5.8 4.3 - - - +
41A LYS* 3.2 17.4 - - + +
42A PRO* 1.3 83.3 - - - +
44A ALA* 1.3 53.2 + - - +
45A SER 3.5 1.8 - - - -
46A SER* 3.8 15.3 - - - -
47A TYR* 2.8 43.1 + + + +
104A PHE* 3.8 33.9 - + - -
107A TYR* 3.4 39.7 - + + -
108A LEU* 3.8 14.1 - - + -
111A ALA* 4.1 10.8 - - + -
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Residues in contact with ALA 44 (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 PRO* 3.0 12.9 + - + +
43A PHE* 1.3 75.5 - - - +
45A SER* 1.3 64.4 + - - +
47A TYR* 3.3 3.3 + - - +
48A VAL* 3.2 19.8 + - - +
110A ASP* 4.2 12.1 - - + +
111A ALA* 4.0 31.0 - - - +
114A LEU* 3.6 20.0 - - + +
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Residues in contact with SER 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 PHE 3.5 0.2 - - - -
44A ALA* 1.3 78.8 - - - +
46A SER* 1.3 57.7 + - - +
48A VAL* 3.4 2.2 + - - +
49A SER* 2.9 31.7 + - - -
114A LEU* 3.8 14.7 - - - +
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Residues in contact with SER 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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34A PHE* 3.9 16.6 - - - -
41A LYS* 3.7 27.1 + - - -
43A PHE* 3.4 14.9 + - - -
44A ALA 3.3 0.6 - - - -
45A SER* 1.3 75.7 - - - +
47A TYR* 1.3 59.1 + - - +
49A SER* 3.3 8.2 + - - -
50A THR* 2.7 34.5 + - - -
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Residues in contact with TYR 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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27A GLY* 2.6 43.9 + - - -
30A LEU* 4.0 8.9 - - + +
31A GLY* 3.7 15.7 - - - -
34A PHE* 3.8 26.9 - + + -
43A PHE* 2.8 31.1 + + + +
44A ALA 3.4 4.5 - - - +
46A SER* 1.3 72.3 - - - +
48A VAL* 1.3 66.4 + - + +
50A THR* 3.4 4.2 + - - -
51A ILE* 3.3 45.5 + - + +
65A VAL* 4.2 2.9 - - + +
108A LEU* 4.4 4.7 - - + -
111A ALA* 3.8 30.7 - - + -
112A PHE* 3.4 14.4 - + - -
115A CYS* 4.5 13.2 - - + -
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Residues in contact with VAL 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 ALA 3.2 15.0 + - - +
45A SER 3.4 3.3 + - - +
47A TYR* 1.3 80.4 - - + +
49A SER* 1.3 58.3 + - - +
51A ILE* 3.1 9.7 + - - +
52A GLN* 2.9 42.0 + - - +
111A ALA 4.2 3.8 - - - +
114A LEU* 3.8 21.3 - - + -
115A CYS* 3.8 31.4 - - + +
118A THR* 4.1 18.6 - - - +
119A PHE* 4.3 10.9 - - + -
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Residues in contact with SER 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 SER 2.9 20.1 + - - -
46A SER* 3.3 14.0 + - - -
48A VAL* 1.3 74.5 - - - +
50A THR* 1.3 59.4 + - - +
52A GLN* 3.6 16.5 - - - +
53A SER* 2.9 30.8 + - - -
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Residues in contact with THR 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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30A LEU* 4.6 6.5 - - + -
33A ARG* 4.6 6.0 + - - +
34A PHE* 3.4 20.9 - - + -
46A SER 2.7 24.3 + - - -
47A TYR 3.6 5.6 - - - -
48A VAL 3.2 0.2 - - - -
49A SER* 1.3 76.9 + - - +
51A ILE* 1.3 57.8 + - - +
53A SER* 3.5 6.0 + - - -
54A LEU* 3.1 36.7 + - + +
169A PHE* 3.6 34.1 - - + -
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Residues in contact with ILE 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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23A MET* 3.6 10.6 - - + +
25A VAL* 4.2 11.2 - - + -
30A LEU* 3.7 21.5 - - + -
47A TYR* 3.3 45.0 + - + +
48A VAL* 3.1 9.4 + - - +
50A THR* 1.3 73.9 - - - +
52A GLN* 1.3 59.4 + - - +
54A LEU* 3.3 7.2 + - + +
55A ALA* 3.0 25.3 + - - +
63A THR* 3.7 22.0 - - + -
65A VAL* 4.2 15.9 - - + -
115A CYS* 4.3 6.1 - - - -
119A PHE* 3.6 22.0 - - + -
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 2.9 24.4 + - - +
49A SER* 3.6 22.7 - - - +
50A THR 3.4 0.2 - - - -
51A ILE* 1.3 74.2 - - - +
53A SER* 1.3 62.9 + - - +
55A ALA* 3.4 5.3 + - - +
56A LYS* 3.2 48.0 + - - +
118A THR* 3.9 16.8 - - - +
119A PHE* 3.6 23.3 - - + -
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Residues in contact with SER 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 SER 2.9 18.4 + - - -
50A THR* 3.6 7.6 - - - -
52A GLN* 1.3 77.6 - - - +
54A LEU* 1.3 59.7 + - - +
56A LYS* 3.5 13.0 + - - +
57A SER* 3.0 28.2 + - - -
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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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23A MET* 3.7 14.4 - - + -
25A VAL* 6.0 0.4 - - + -
30A LEU* 5.1 4.3 - - + -
50A THR* 3.1 28.6 + - + +
51A ILE* 3.6 10.1 - - + +
52A GLN 3.3 0.2 - - - -
53A SER* 1.3 73.5 - - - +
55A ALA* 1.3 60.3 + - - +
56A LYS 3.1 2.0 - - - -
57A SER* 3.1 7.4 + - - +
58A TYR* 3.0 45.6 + - + +
150A ILE* 4.1 17.5 - - + -
167A PHE* 4.1 22.2 - - + -
169A PHE* 3.6 40.8 - - + -
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Residues in contact with ALA 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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23A MET* 3.6 10.7 - - + -
51A ILE 3.0 16.7 + - - +
52A GLN* 3.4 8.3 + - - +
54A LEU* 1.3 76.2 - - - +
56A LYS* 1.3 58.3 + - + +
58A TYR* 5.3 0.2 - - - -
59A SER* 3.0 6.4 + - - -
60A ALA* 2.8 41.9 + - + +
63A THR* 3.4 25.8 - - + +
119A PHE* 5.2 4.0 - - + -
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Residues in contact with LYS 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 GLN* 3.2 38.3 + - - +
53A SER* 3.7 10.0 - - - +
54A LEU 3.1 0.6 - - - -
55A ALA* 1.3 78.1 - - + +
57A SER* 1.3 64.3 + - - +
59A SER* 3.4 13.5 + - - +
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Residues in contact with SER 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 SER* 3.0 19.0 + - - -
54A LEU* 3.1 12.3 + - - +
56A LYS* 1.3 76.6 - - - +
58A TYR* 1.3 74.2 + - - +
59A SER* 3.4 6.6 + - - -
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Residues in contact with TYR 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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21A ASN* 3.0 24.1 + - - +
23A MET* 4.6 7.2 - - + -
54A LEU* 3.0 40.4 + - + +
55A ALA 3.7 0.4 - - - +
57A SER* 1.3 84.6 - - - +
59A SER* 1.3 67.3 + - - +
60A ALA* 3.2 5.6 + - + +
148A TRP* 3.3 50.5 - + + +
150A ILE* 4.4 13.5 - - + -
167A PHE* 3.1 45.5 - + + +
174A GLU* 2.9 28.8 + - - -
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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