Contacts of the helix formed by residues 49 - 62 (chain A) in PDB entry 1X5W
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 GLN 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.8 8.8 - - - -
47A THR* 2.9 25.5 + - - +
48A LYS* 1.3 88.3 - - + +
50A PRO* 1.3 73.9 - - + +
51A SER* 3.3 17.6 + - - -
52A ASN* 3.4 33.9 + - + +
53A LEU* 3.5 2.4 + - - +
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Residues in contact with PRO 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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38A PHE* 3.6 39.2 - - + -
48A LYS 4.7 0.7 - - - +
49A GLN* 1.3 88.5 - - + +
51A SER* 1.3 69.2 + - - +
53A LEU* 3.7 4.7 + - - +
54A SER* 3.0 25.7 + - - -
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Residues in contact with SER 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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49A GLN* 3.4 20.4 + - - -
50A PRO* 1.3 81.7 - - - +
52A ASN* 1.3 70.3 + - - +
53A LEU 3.0 2.2 - - - -
54A SER* 3.0 7.6 + - - -
55A LYS* 3.0 34.3 + - - +
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Residues in contact with ASN 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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45A PHE* 4.0 6.5 - - + -
47A THR* 2.9 34.3 + - + +
48A LYS 5.2 0.2 - - - +
49A GLN* 3.4 33.7 + - + +
50A PRO 3.5 0.4 - - - -
51A SER* 1.3 83.6 + - - +
53A LEU* 1.3 57.3 + - - +
55A LYS* 3.4 17.1 - - - +
56A HIS* 3.0 25.8 + - - +
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Residues in contact with LEU 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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38A PHE* 4.0 24.0 - - + -
39A LYS* 3.8 16.8 - - - +
40A CYS* 3.9 34.5 - - + +
45A PHE* 4.2 12.1 - - + +
47A THR* 3.4 17.7 - - + +
49A GLN 3.5 2.6 + - - +
50A PRO 3.9 7.4 - - - +
51A SER 3.0 0.4 - - - -
52A ASN* 1.3 78.2 - - - +
54A SER* 1.3 67.1 + - - +
56A HIS* 3.0 9.6 + - + +
57A MET* 2.8 38.4 + - + +
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Residues in contact with SER 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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50A PRO 3.0 14.7 + - - -
51A SER* 3.0 11.2 + - - -
53A LEU* 1.3 78.1 - - - +
55A LYS* 1.3 65.0 + - - +
57A MET* 2.9 26.4 + - - +
58A LYS* 3.6 5.5 + - - +
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Residues in contact with LYS 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 SER* 3.0 23.9 + - - +
52A ASN* 3.4 23.8 - - - +
54A SER* 1.3 78.8 - - - +
56A HIS* 1.3 54.1 + - - +
58A LYS* 3.4 5.8 + - - +
59A LYS* 2.7 53.0 + - + +
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Residues in contact with HIS 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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40A CYS* 4.0 5.8 - - - -
43A CYS* 3.7 3.6 - - - -
45A PHE* 3.0 54.9 - + + -
52A ASN 3.0 18.6 - - - +
53A LEU* 3.0 9.1 + - + +
55A LYS* 1.3 82.1 - - + +
57A MET* 1.3 73.4 + - + +
59A LYS* 3.7 12.3 - - - +
60A PHE* 3.0 52.1 + + + +
61A HIS* 4.0 1.2 + - - -
401A ZN 2.3 32.7 - - - -
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Residues in contact with MET 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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40A CYS* 3.3 34.1 - - - -
41A ASN* 4.8 11.4 - - - +
42A TYR* 3.7 21.1 - - + -
53A LEU* 2.8 31.7 + - + +
54A SER* 2.9 11.9 + - - +
56A HIS* 1.3 76.8 - - + +
58A LYS* 1.3 53.6 + - + +
61A HIS* 2.6 59.8 + - + +
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Residues in contact with LYS 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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54A SER 3.6 4.4 + - - +
55A LYS* 3.4 7.2 + - - +
56A HIS 3.2 0.2 - - - -
57A MET* 1.3 78.9 - - + +
59A LYS* 1.3 68.2 + - - +
60A PHE 3.1 2.4 - - - -
61A HIS 5.0 1.3 - - - +
62A GLY* 3.0 36.2 + - - -
63A ASP* 4.7 1.9 + - - +
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Residues in contact with LYS 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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45A PHE* 6.2 2.6 - - - -
55A LYS* 2.7 39.1 + - + +
56A HIS* 3.6 13.2 - - - +
58A LYS* 1.3 74.4 - - - +
60A PHE* 1.3 92.6 + - + +
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Residues in contact with PHE 60 (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 PHE* 5.4 3.6 - + - -
56A HIS* 3.0 43.4 + + - +
59A LYS* 1.3 115.4 - - + +
61A HIS* 1.3 77.3 + - + +
62A GLY 3.3 7.8 + - - -
63A ASP* 4.7 1.9 + - - -
64A MET* 4.6 6.2 - - - +
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Residues in contact with HIS 61 (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 TYR* 3.1 41.3 - + + +
43A CYS* 4.0 10.0 - - + -
56A HIS* 4.0 4.7 + + - -
57A MET* 2.6 40.0 + - + +
58A LYS* 3.9 1.2 - - - +
60A PHE* 1.3 80.1 - - + +
62A GLY* 1.3 58.0 + - - +
63A ASP 3.9 0.4 - - - -
64A MET* 3.6 39.1 - - + +
401A ZN 2.4 35.9 - - - -
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Residues in contact with GLY 62 (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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58A LYS* 3.0 40.7 + - - -
60A PHE 3.3 3.2 + - - -
61A HIS* 1.3 77.5 - - - +
63A ASP* 1.3 66.5 + - - +
64A MET 3.1 13.4 + - - +
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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