Contacts of the helix formed by residues 52 - 63 (chain A) in PDB entry 1XGW
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 SER 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLY 3.6 2.9 + - - -
51A PRO* 1.3 75.4 - - - +
53A GLY* 1.3 63.2 + - - +
54A GLN* 3.0 13.9 + - - +
55A LEU* 3.2 24.6 + - - +
56A MET* 3.1 23.7 + - - +
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Residues in contact with GLY 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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51A PRO 3.8 0.8 + - - -
52A SER* 1.3 72.5 - - - +
54A GLN* 1.3 56.0 + - - +
56A MET* 3.8 16.1 - - - +
57A GLY* 3.0 23.5 + - - -
100A TYR* 3.9 10.6 + - - -
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Residues in contact with GLN 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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52A SER* 3.0 10.1 + - - +
53A GLY* 1.3 77.4 - - - +
55A LEU* 1.3 69.5 + - - +
57A GLY* 3.3 2.0 + - - -
58A GLU* 3.1 38.6 + - - +
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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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39A LYS* 4.2 17.3 - - + +
42A GLU* 3.3 35.4 - - + +
43A ALA* 3.6 34.5 - - + +
51A PRO* 4.8 5.2 - - + -
52A SER* 3.2 19.5 + - - +
54A GLN* 1.3 81.6 + - - +
56A MET* 1.3 66.7 + - - +
58A GLU* 3.2 22.2 + - - +
59A ILE* 3.0 38.6 + - + +
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Residues in contact with MET 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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51A PRO* 3.4 46.7 - - + +
52A SER 3.1 13.5 + - - +
53A GLY* 3.8 13.2 - - - +
55A LEU* 1.3 76.7 - - - +
57A GLY* 1.3 55.7 + - - +
59A ILE* 3.4 1.8 + - - +
60A ALA* 2.9 30.7 + - - +
96A LEU* 4.2 12.1 - - - +
97A LEU* 3.9 20.4 - - + -
100A TYR* 3.3 50.5 - - + -
101A LEU* 4.2 0.7 - - - +
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Residues in contact with GLY 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 GLY 3.0 21.4 + - - -
54A GLN* 3.6 3.1 - - - -
55A LEU 3.2 1.0 - - - -
56A MET* 1.3 77.0 - - - +
58A GLU* 1.3 55.6 + - - +
60A ALA* 3.4 4.8 - - - +
61A LYS* 3.2 24.4 + - - +
100A TYR* 3.5 15.7 - - - -
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Residues in contact with GLU 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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39A LYS* 2.9 45.5 + - + +
54A GLN* 3.1 30.2 + - - +
55A LEU* 3.2 14.9 + - - +
57A GLY* 1.3 73.7 - - - +
59A ILE* 1.3 65.4 + - - +
61A LYS* 2.8 48.0 + - - +
62A ALA* 3.4 3.5 + - - +
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Residues in contact with ILE 59 (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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36A ILE* 4.5 5.4 - - + -
39A LYS* 3.6 42.2 - - + +
40A VAL* 4.1 6.5 - - + +
43A ALA* 3.9 19.1 - - + -
55A LEU* 3.0 26.0 + - + +
56A MET 3.9 3.4 - - - +
58A GLU* 1.3 75.2 - - - +
60A ALA* 1.3 66.3 + - - +
62A ALA* 3.2 7.7 + - - +
63A THR* 3.1 21.5 + - - +
72A LEU* 3.6 31.6 - - + +
97A LEU* 4.0 13.7 - - + -
101A LEU* 3.9 17.7 - - + -
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Residues in contact with ALA 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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56A MET 2.9 18.8 + - - +
57A GLY* 3.4 7.9 - - - +
58A GLU 3.3 0.2 - - - -
59A ILE* 1.3 78.8 - - - +
61A LYS* 1.3 57.0 + - - +
63A THR* 2.6 23.1 + - - -
64A PHE* 3.3 13.0 - - - -
100A TYR* 3.8 17.5 - - + +
101A LEU* 3.5 16.2 - - + +
104A ASN* 4.1 20.9 - - + +
105A GLY* 3.7 0.7 - - - -
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Residues in contact with LYS 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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39A LYS* 3.2 24.7 - - - +
57A GLY 3.2 7.8 + - - +
58A GLU* 2.8 44.4 + - + +
60A ALA* 1.3 76.5 - - - +
62A ALA* 1.3 76.9 + - - +
64A PHE* 3.1 33.9 + - - +
65A MET* 3.9 14.2 + - + +
68A GLN* 5.6 0.6 - - - +
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Residues in contact with ALA 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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36A ILE* 3.6 28.5 - - + -
58A GLU 3.4 8.0 + - - +
59A ILE 3.2 9.2 + - - +
61A LYS* 1.3 86.5 - - - +
63A THR* 1.3 57.9 + - - +
64A PHE 3.1 2.5 - - - -
65A MET* 3.0 37.6 + - + +
68A GLN* 3.7 18.4 - - - +
69A PHE 4.7 0.5 + - - -
72A LEU* 3.8 5.1 - - + +
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Residues in contact with THR 63 (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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59A ILE 3.1 13.9 + - - +
60A ALA 2.6 19.0 + - - +
62A ALA* 1.3 77.5 - - - +
64A PHE* 1.3 58.3 + - - +
65A MET 3.2 1.2 + - - -
66A TYR* 3.7 8.0 - - - -
69A PHE* 3.6 24.6 - - - +
72A LEU* 3.7 26.0 - - + -
73A MET* 4.3 3.1 - - + -
101A LEU* 4.2 12.1 - - + -
105A GLY* 3.3 1.0 - - - -
106A SER* 2.8 38.4 + - - -
109A VAL* 3.8 18.8 - - + -
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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