Contacts of the helix formed by residues 53 - 63 (chain A) in PDB entry 5WZF
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU 3.0 8.7 + - - +
49A ASN* 3.2 18.2 + - - -
51A ARG 3.9 0.2 - - - -
52A CYS* 1.3 79.2 - - - +
54A HIS* 1.3 65.5 + - - -
55A ARG 3.4 2.5 - - - -
56A ALA 3.3 3.2 + - - -
57A ALA* 3.1 19.8 + - - +
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Residues in contact with HIS 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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45A TRP* 3.8 16.3 - + - -
49A ASN* 3.3 15.2 + - - +
53A GLY* 1.3 70.6 - - - -
55A ARG* 1.3 59.9 + - - +
57A ALA* 3.1 3.1 + - - +
58A VAL* 2.9 52.0 + - + +
86B LEU 2.9 27.0 + - - -
87B VAL 3.1 21.1 + - - -
89B HIS 4.1 2.7 - - - -
90B ASP* 3.6 41.5 - - + +
92B ARG 5.7 1.1 - - - -
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Residues in contact with ARG 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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53A GLY 3.4 0.6 - - - -
54A HIS* 1.3 82.2 + - - +
56A ALA* 1.3 61.8 + - - +
58A VAL* 3.4 15.6 + - + +
59A ALA* 3.6 9.7 + - - +
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Residues in contact with ALA 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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13A GLY* 4.9 11.0 - - - +
48A LEU* 4.0 13.9 - - + +
52A CYS* 3.5 36.7 + - + +
53A GLY 3.3 4.5 + - - +
54A HIS 3.2 0.4 - - - -
55A ARG* 1.3 78.8 - - - +
57A ALA* 1.3 61.3 + - - +
59A ALA* 3.2 22.5 - - - +
60A ALA 3.7 2.6 + - - -
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Residues in contact with ALA 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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45A TRP* 3.1 34.4 - - + +
48A LEU* 4.1 9.3 - - - +
49A ASN* 3.7 28.0 - - + +
53A GLY 3.1 13.5 + - - +
54A HIS 3.1 6.0 + - - +
56A ALA* 1.3 76.0 - - - +
58A VAL* 1.3 65.9 + - - +
60A ALA* 2.9 15.7 + - - +
61A ALA 3.0 9.4 + - - -
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Residues in contact with VAL 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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45A TRP* 3.8 10.5 - - + -
54A HIS* 2.9 47.2 + - + +
55A ARG* 3.6 11.9 - - + +
56A ALA 3.3 0.4 - - - -
57A ALA* 1.3 76.4 - - - +
59A ALA* 1.3 63.0 + - - +
61A ALA* 3.0 4.6 + - - +
62A ALA* 2.9 24.7 + - + +
87B VAL* 4.4 25.1 - - + -
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Residues in contact with ALA 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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13A GLY* 6.2 3.6 - - - +
48A LEU* 5.9 0.7 - - + -
55A ARG 3.6 5.9 + - - +
56A ALA* 3.2 16.9 + - - +
58A VAL* 1.3 79.6 - - - +
60A ALA* 1.3 60.9 + - - +
62A ALA* 3.3 18.0 + - - +
63A ILE* 3.6 11.2 + - - +
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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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41A LEU* 4.1 10.9 - - - +
44A THR* 3.7 30.3 - - + -
45A TRP* 4.2 12.8 - - - +
48A LEU* 3.9 14.9 - - + +
56A ALA 3.7 0.8 + - - -
57A ALA 2.9 10.8 + - - +
59A ALA* 1.3 77.9 - - - +
61A ALA* 1.3 65.2 + - - +
63A ILE* 3.2 29.7 + - + +
64A ARG 4.3 0.5 + - - -
83B TRP* 5.0 2.0 - - - -
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Residues in contact with ALA 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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45A TRP* 4.1 4.3 - - + -
57A ALA 3.0 11.2 + - - +
58A VAL* 3.0 14.8 + - - +
60A ALA* 1.3 76.6 - - - +
62A ALA* 1.3 61.0 + - - +
63A ILE 3.2 1.2 + - - -
64A ARG* 2.9 40.5 + - - +
83B TRP* 3.6 34.7 - - + -
87B VAL* 4.1 13.9 - - + -
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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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58A VAL* 2.9 14.4 + - + +
59A ALA* 3.6 12.3 - - - +
60A ALA 3.2 0.4 - - - -
61A ALA* 1.3 74.0 - - - +
63A ILE* 1.3 59.9 + - - +
64A ARG* 3.1 1.1 - - - +
65A LEU* 2.9 42.7 + - + +
66A SER* 3.6 3.3 + - - -
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Residues in contact with ILE 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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9A TRP* 3.6 45.3 - - + -
36A THR* 4.7 0.2 - - + -
41A LEU* 3.9 23.1 - - + -
59A ALA 3.6 8.5 + - - +
60A ALA* 3.4 26.5 - - + +
61A ALA 3.2 0.2 - - - -
62A ALA* 1.3 79.2 - - - +
64A ARG* 1.3 56.6 + - - +
66A SER* 2.9 27.5 + - - -
69A VAL* 4.1 27.8 - - + -
71A VAL* 4.0 5.5 - - - +
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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