Contacts of the helix formed by residues 55 - 65 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.4 1.8 - - + -
51B ASP 3.6 0.4 + - - +
52B GLU 3.2 7.7 + - - +
54B ASP* 1.3 80.3 - - - +
56B GLN* 1.3 53.9 + - - +
57B ILE 3.4 2.5 - - - -
58B PHE* 3.5 23.3 - - + -
59B LYS* 2.7 36.4 + - - +
88B ARG* 3.7 39.3 - - + +
91B TRP* 4.7 4.7 - - + -
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 4.0 21.6 - - + +
26B GLU* 4.5 27.4 + - - +
52B GLU* 3.7 14.9 + - + +
53B GLU* 3.7 31.7 + - - +
54B ASP 3.8 1.8 - - - -
55B ALA* 1.3 76.7 - - - +
57B ILE* 1.3 59.8 + - - +
59B LYS* 3.7 13.1 - - - +
60B ALA* 3.0 26.2 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.5 25.1 - - + -
16B LEU* 4.2 4.7 - - + -
19B GLU* 4.3 2.5 - - + -
25B TYR* 4.1 22.6 - - + -
28B LEU* 3.9 27.4 - - + -
40B VAL* 5.8 0.2 - - + -
41B PRO* 5.5 17.0 - - + +
54B ASP 5.9 0.9 - - - +
56B GLN* 1.3 76.8 - - - +
58B PHE* 1.3 87.5 + - + +
60B ALA* 4.0 7.9 - - + -
61B TRP* 3.1 22.3 + - - +
95B PHE* 3.7 29.0 - - + -
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO 5.3 7.0 - - - -
45B PHE* 4.2 4.9 - + - -
50B LEU* 3.8 11.0 - - + -
54B ASP 3.3 16.4 - - - -
55B ALA* 3.5 25.6 - - + +
57B ILE* 1.3 87.5 - - + +
59B LYS* 1.3 63.5 + - - +
61B TRP* 3.3 5.9 + - - +
62B ALA* 3.1 20.1 + - - +
65B ARG* 4.9 0.3 + - - -
88B ARG 4.5 0.4 - - - -
91B TRP* 3.7 28.1 - - + +
92B LYS* 3.6 30.1 - - + -
95B PHE* 3.6 40.2 - + + -
96B ARG* 3.9 30.5 - - - -
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 4.7 15.7 + - + +
55B ALA* 2.7 21.2 + - + +
56B GLN* 3.7 13.0 - - - +
58B PHE* 1.3 75.1 - - - +
60B ALA* 1.3 53.3 + - - +
62B ALA* 3.0 3.6 + - - +
63B VAL* 2.7 47.4 + - + +
68B TRP* 4.3 12.8 - - + +
70B PRO 5.8 2.0 + - - -
84B GLU* 4.2 21.6 + - - +
91B TRP* 3.9 29.5 - - + -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.7 15.6 - - + -
19B GLU* 4.6 0.7 - - - +
25B TYR* 3.3 29.4 - - + +
56B GLN 3.0 17.7 + - - +
57B ILE* 3.6 8.7 - - + +
58B PHE 3.2 0.2 - - - -
59B LYS* 1.3 79.0 - - - +
61B TRP* 1.3 57.1 + - - +
63B VAL* 3.5 9.5 + - - +
64B ALA* 2.9 28.6 + - - +
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 5.1 6.3 - - + -
12B PHE* 3.5 45.0 - + + -
15B TRP* 3.6 45.7 - + + -
57B ILE 3.1 13.1 + - - +
58B PHE 3.5 8.5 - - - +
60B ALA* 1.3 74.9 - - - +
62B ALA* 1.3 58.7 + - - +
64B ALA* 3.0 14.8 + - + +
65B ARG* 3.0 60.9 + - + +
91B TRP 5.1 0.2 - - - -
94B ASN* 2.7 29.6 + - - -
95B PHE* 3.9 25.1 - - + -
98B ALA* 4.1 10.0 - - + +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE 3.1 8.6 + - - +
59B LYS 3.0 7.3 + - - +
61B TRP* 1.3 74.1 - - - +
63B VAL* 1.3 64.8 + - - +
65B ARG* 3.0 22.3 + - - +
67B ARG* 2.9 28.5 + - + +
68B TRP* 3.9 9.2 - - + -
91B TRP* 3.3 43.1 - - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 2.7 31.0 + - + +
60B ALA* 3.7 8.1 - - - +
62B ALA* 1.3 72.0 - - - +
64B ALA* 1.3 64.5 + - - +
66B GLY* 3.0 14.0 + - - -
68B TRP* 3.2 32.8 - - + +
69B PRO 3.8 13.5 - - - +
70B PRO* 3.9 30.4 - - + +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.7 26.5 - - + +
60B ALA 2.9 15.4 + - - +
61B TRP* 3.0 26.4 + - + +
63B VAL* 1.3 79.2 - - - +
65B ARG* 1.3 58.1 + - - +
66B GLY 3.2 3.2 + - - -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE 4.9 1.2 + - - -
61B TRP* 3.0 56.9 + - + +
62B ALA* 3.0 29.0 + - - +
64B ALA* 1.3 77.1 - - - +
66B GLY* 1.3 62.2 + - - +
67B ARG* 3.1 40.4 + - + +
91B TRP* 4.5 7.7 - - - +
94B ASN* 2.9 46.4 + - - +
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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