Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 1QLS
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.1 9.9 + - - -
55A PRO* 1.3 78.3 - - - +
57A VAL* 1.3 63.7 + - - +
58A LEU 3.4 0.2 - - - -
59A ASP* 3.2 13.4 + - - +
60A ARG* 3.0 45.3 + - - +
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Residues in contact with VAL 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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49A THR* 5.9 1.6 - - + +
52A GLN* 3.6 39.9 - - + +
54A ASP* 3.0 28.9 + - + +
55A PRO* 4.7 0.7 - - + -
56A GLY* 1.3 76.2 - - - +
58A LEU* 1.3 75.2 + - + +
60A ARG* 2.8 21.2 + - + +
61A MET* 2.7 39.9 + - + +
11D TRP* 3.9 29.8 - - + -
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Residues in contact with LEU 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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34A LYS* 6.0 0.9 - - - -
37A PHE* 3.6 12.8 - - + -
38A LEU* 4.8 18.6 - - + -
41A MET* 4.1 41.3 - - + -
42A ASN* 4.2 11.9 - - - +
48A PHE* 4.9 3.1 - - + -
49A THR* 4.1 26.0 - - + +
55A PRO* 3.9 9.0 + - + +
56A GLY 3.4 0.4 - - - -
57A VAL* 1.3 88.7 - - + +
59A ASP* 1.3 63.5 + - - +
61A MET* 4.1 13.2 - - - +
62A MET* 2.9 26.2 + - - +
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Residues in contact with ASP 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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34A LYS* 2.5 38.0 + - - +
55A PRO 3.0 25.1 - - - +
56A GLY* 3.5 11.7 - - - +
57A VAL 3.2 0.6 - - - -
58A LEU* 1.3 78.5 - - - +
60A ARG* 1.3 64.9 + - + +
62A MET* 3.8 3.2 - - - +
63A LYS* 3.2 26.0 + - - +
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Residues in contact with ARG 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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54A ASP* 2.8 27.1 + - - -
56A GLY* 3.0 30.9 + - - +
57A VAL* 2.8 21.5 + - + +
59A ASP* 1.3 79.4 - - + +
61A MET* 1.3 65.2 + - + +
63A LYS* 3.6 5.5 + - - +
64A LYS* 3.2 22.3 + - - +
11D TRP* 5.6 5.5 - - - -
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Residues in contact with MET 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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37A PHE* 4.3 11.0 - - + -
41A MET* 3.9 11.9 - - + -
48A PHE* 3.8 31.9 - - + -
57A VAL* 2.7 31.9 + - + +
58A LEU* 3.1 19.0 + - - +
60A ARG* 1.3 71.2 - - - +
62A MET* 1.3 58.1 + - - +
64A LYS* 3.1 7.3 + - - +
65A LEU* 2.8 39.1 + - + +
81A LEU* 3.4 33.0 - - + -
85A LEU* 5.9 1.1 - - + -
11D TRP* 4.9 8.5 - - + +
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Residues in contact with MET 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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32A ILE 4.1 1.8 - - - +
33A SER 4.2 0.2 - - - -
34A LYS* 3.9 33.4 - - + +
37A PHE* 3.6 38.7 - - + -
58A LEU 2.9 17.5 + - - +
59A ASP* 3.8 7.4 - - - +
61A MET* 1.3 78.1 - - - +
63A LYS* 1.3 68.3 + - - +
65A LEU* 3.1 5.3 + - - +
66A ASP* 2.9 33.5 + - + +
71A GLY 3.3 29.8 - - - +
72A GLN* 3.7 22.0 - - - +
73A LEU* 4.0 14.6 - - + +
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Residues in contact with LYS 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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34A LYS* 6.1 3.1 - - - +
59A ASP 3.2 15.4 + - - +
60A ARG* 4.1 5.6 - - - +
62A MET* 1.3 91.0 - - - +
64A LYS* 1.3 63.5 + - - +
66A ASP* 2.6 54.1 + - - +
69A SER* 4.5 9.7 + - - +
71A GLY* 4.0 10.6 - - - +
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Residues in contact with LYS 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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60A ARG 3.2 11.8 + - - +
61A MET* 3.1 12.0 + - - +
63A LYS* 1.3 79.3 - - - +
65A LEU* 1.3 62.2 + - + +
67A LEU* 3.9 15.9 - - - +
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Residues in contact with LEU 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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37A PHE* 4.1 20.6 - - + -
61A MET* 2.8 31.6 + - + +
62A MET* 3.8 0.7 - - - +
64A LYS* 1.3 76.4 - - + +
66A ASP* 1.3 60.5 + - - +
67A LEU* 2.8 16.0 + - - +
73A LEU* 3.7 20.4 - - + -
77A GLU* 3.3 26.7 - - - +
80A ASN* 4.4 8.8 + - + -
81A LEU* 4.0 52.9 - - + +
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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