Contacts of the helix formed by residues 55 - 65 (chain A) in PDB entry 3QU3
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 ALA 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.5 2.0 - - + -
51A ASP 3.4 0.6 + - - +
52A GLU* 3.0 9.3 + - - +
54A ASP* 1.3 78.5 - - - +
56A GLN* 1.3 58.2 + - - +
57A ILE 3.4 2.0 - - - -
58A PHE* 3.9 18.2 - - + -
59A LYS* 2.8 33.2 + - + +
88A ARG* 3.5 44.6 - - + +
91A TRP* 4.7 4.3 - - + -
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Residues in contact with GLN 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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25A TYR* 3.6 25.9 + - + -
26A GLU* 5.3 9.0 + - - +
52A GLU* 3.6 21.3 + - + +
53A GLU* 3.7 34.3 + - - +
54A ASP 3.6 2.8 - - - -
55A ALA* 1.3 76.1 - - - +
57A ILE* 1.3 61.9 + - - +
59A LYS* 3.6 12.0 + - - +
60A ALA* 3.2 21.1 + - - +
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Residues in contact with ILE 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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15A TRP* 3.9 17.5 - - + -
16A LEU* 4.5 0.4 - - + -
19A GLU* 4.3 3.1 - - + -
25A TYR* 3.8 31.9 - - + -
28A LEU* 3.7 32.5 - - + -
40A VAL* 5.8 1.1 - - + -
41A PRO* 5.7 13.2 - - + +
54A ASP 5.7 1.3 - - - +
55A ALA 5.5 0.2 - - - -
56A GLN* 1.3 77.4 - - - +
58A PHE* 1.3 93.2 + - + +
60A ALA* 3.2 2.8 + - + +
61A TRP* 3.1 21.3 + - - +
95A PHE* 3.8 28.6 - - + -
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Residues in contact with PHE 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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41A PRO 5.6 4.9 - - - -
45A PHE* 4.4 3.8 - + - -
50A LEU* 3.7 18.4 - - + -
54A ASP 3.6 16.8 - - - -
55A ALA* 3.3 16.1 + - + +
57A ILE* 1.3 89.8 - - + +
59A LYS* 1.3 63.1 + - - +
61A TRP* 3.3 5.4 + - - +
62A ALA* 3.2 20.3 + - - +
65A ARG* 5.1 0.5 + - - -
88A ARG 4.3 0.4 - - - -
91A TRP* 3.7 27.6 - - + +
92A LYS* 3.3 36.8 - - + -
95A PHE* 3.6 37.9 - + + -
96A ARG* 3.9 24.9 - - - -
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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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52A GLU* 4.7 14.6 + - + -
55A ALA* 2.8 22.4 + - + +
56A GLN* 3.8 10.5 - - - +
58A PHE* 1.3 74.4 - - - +
60A ALA* 1.3 57.9 + - - +
62A ALA* 3.2 2.4 + - - +
63A VAL* 2.9 35.0 + - + +
68A TRP* 4.3 12.7 - - + -
70A PRO 5.8 2.4 + - - -
84A GLU* 3.8 32.6 + - - +
91A TRP* 3.4 34.5 - - + -
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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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15A TRP* 3.7 18.1 + - + -
19A GLU* 4.8 1.1 - - - +
25A TYR* 3.2 31.4 - - + +
56A GLN 3.2 11.0 + - - +
57A ILE* 3.2 10.9 + - + +
59A LYS* 1.3 77.3 - - - +
61A TRP* 1.3 57.6 + - - +
63A VAL* 3.6 7.8 + - - +
64A ALA* 3.0 26.0 + - - +
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Residues in contact with TRP 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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10A VAL* 4.9 9.0 - - + -
12A PHE* 3.7 37.7 - + + -
15A TRP* 3.6 49.7 - + + -
57A ILE 3.1 9.4 + - - +
58A PHE* 3.6 7.6 - - - +
59A LYS 3.2 0.2 - - - -
60A ALA* 1.3 74.9 - - - +
62A ALA* 1.3 59.0 - - - +
64A ALA* 3.0 30.2 + - + +
65A ARG* 3.0 48.2 + - + +
91A TRP 5.3 0.4 - - - -
94A ASN* 3.2 22.3 + - - -
95A PHE* 3.9 25.8 - - + -
98A ALA* 4.0 13.0 - - + +
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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 PHE 3.2 4.9 + - - +
59A LYS 3.2 8.8 + - - +
61A TRP* 1.3 76.4 - - - +
63A VAL* 1.3 61.0 + - - +
65A ARG* 3.1 19.8 + - - +
66A GLY 3.1 4.2 + - - -
67A ARG* 2.7 35.7 + - + +
68A TRP* 4.2 3.6 - - + -
91A TRP* 3.4 44.4 - - + +
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Residues in contact with VAL 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 LYS* 2.9 27.9 + - + +
60A ALA* 3.8 8.3 - - - +
62A ALA* 1.3 75.7 - - - +
64A ALA* 1.3 63.5 + - - +
66A GLY* 3.2 11.6 + - - -
68A TRP* 3.6 32.7 - - + +
69A PRO 3.8 11.7 - - - +
70A PRO* 4.0 32.5 - - + +
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Residues in contact with ALA 64 (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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15A TRP* 3.8 17.0 - - + +
60A ALA 3.0 15.1 + - - +
61A TRP* 3.0 34.4 + - + +
63A VAL* 1.3 79.5 - - - +
65A ARG* 1.3 57.8 + - - +
66A GLY 3.2 0.9 + - - -
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Residues in contact with ARG 65 (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 PHE 5.1 0.4 + - - -
61A TRP* 3.0 56.9 + - + +
62A ALA* 3.1 30.5 + - - +
64A ALA* 1.3 76.0 - - - +
66A GLY* 1.3 62.7 + - - +
67A ARG* 3.2 48.1 - - + +
91A TRP* 4.3 10.5 - - - +
94A ASN* 3.4 39.5 + - - +
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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