Contacts of the strand formed by residues 65 - 72 (chain A) in PDB entry 1QZG
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 TRP 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A SER 4.9 0.7 - - - -
56A ARG* 3.6 26.7 - - - -
57A GLN* 3.6 45.6 - - + +
63A LYS 5.4 0.7 - - - -
64A ASP* 1.3 73.8 - - - +
66A VAL* 1.3 58.1 + - - +
88A PHE* 3.2 5.9 - - - -
89A SER* 2.9 38.4 + - - +
90A LYS 5.9 0.2 - - - -
92A GLY* 3.5 27.2 - - - +
93A ASN* 3.1 49.9 - - + +
95A LEU* 3.7 13.9 - - + -
65B TRP* 5.0 17.0 - + - -
93B ASN* 6.1 3.4 - - + -
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Residues in contact with VAL 66 (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 THR* 6.1 0.2 - - - +
54A PRO 4.1 2.1 - - - +
55A SER* 3.3 2.6 - - - -
56A ARG* 2.8 52.2 + - + +
58A SER* 3.4 22.0 - - - +
65A TRP* 1.3 76.5 - - - +
67A THR* 1.3 71.6 + - - +
68A THR* 4.6 4.9 - - - +
86A HIS* 4.6 6.1 - - + +
87A LEU 3.2 9.6 - - - +
88A PHE* 3.5 33.2 - - + -
95A LEU* 3.6 3.3 - - - +
5C A 4.1 23.3 - - - +
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 5.6 0.9 - - - +
53A THR* 2.8 23.5 + - - -
54A PRO* 4.6 0.5 - - - +
55A SER* 4.0 13.8 + - - -
66A VAL* 1.3 76.8 - - - +
68A THR* 1.3 63.1 + - - +
69A VAL* 4.7 6.4 - - + +
85A ILE 3.8 0.2 - - - +
86A HIS* 3.7 1.2 - - - -
87A LEU* 2.7 67.2 + - + +
95A LEU* 3.9 20.6 - - + -
96A PRO* 4.4 10.2 + - + +
98A ILE* 5.1 3.3 - - - +
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Residues in contact with THR 68 (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 PHE* 3.1 4.3 - - - +
53A THR* 2.8 47.1 + - - +
66A VAL* 4.6 1.4 - - - +
67A THR* 1.3 74.3 + - - +
69A VAL* 1.3 69.9 + - - +
70A TYR* 4.1 24.5 - - + -
84A GLN* 4.1 8.5 - - + +
85A ILE 3.3 11.0 - - - +
86A HIS* 2.8 36.4 + - + +
5C A 3.7 12.3 + - - -
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Residues in contact with VAL 69 (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 VAL* 4.9 5.2 - - + -
51A ASP 3.4 7.6 - - - +
52A PHE* 4.3 1.3 - - + -
67A THR* 4.7 4.5 - - - +
68A THR* 1.3 79.7 - - - +
70A TYR* 1.3 65.4 + - - +
71A LEU* 4.5 4.7 - - + -
83A LEU 3.5 1.0 - - - +
84A GLN* 3.7 1.2 - - - -
85A ILE* 2.8 59.8 + - + +
87A LEU* 4.3 20.9 - - + -
98A ILE* 3.3 33.0 - - + -
105A LEU* 4.3 18.6 - - + -
107A LEU* 4.6 0.7 - - + -
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Residues in contact with TYR 70 (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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48A ILE 3.6 0.2 - - - +
49A VAL* 3.6 2.6 - - - -
50A LYS* 2.7 31.9 + - - -
51A ASP* 2.8 35.2 + - + +
52A PHE* 4.9 1.6 - - - -
53A THR* 5.9 1.3 - - - -
68A THR* 4.1 18.2 - - + -
69A VAL* 1.3 76.4 - - - +
71A LEU* 1.3 61.1 + - - +
81A ILE* 3.6 53.4 - - + +
82A GLY 4.0 6.5 - - - -
83A LEU 3.4 4.0 - - - +
84A GLN* 3.0 45.5 + - + -
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Residues in contact with LEU 71 (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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30A ILE* 3.6 20.0 - - + +
45A LEU* 4.0 19.7 - - + -
47A GLY* 3.7 24.7 - - - +
48A ILE 3.5 22.4 - - - +
49A VAL* 4.0 6.3 - - + +
69A VAL* 3.9 6.5 - - + -
70A TYR* 1.3 73.0 - - - +
72A TRP* 1.3 60.2 + - - +
82A GLY* 3.2 4.3 - - - -
83A LEU 3.0 30.8 + - - +
85A ILE* 3.8 27.4 - - + -
105A LEU* 4.1 24.2 - - + +
107A LEU* 3.9 15.9 - - + -
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Residues in contact with TRP 72 (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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30A ILE* 3.9 4.3 - - - -
47A GLY* 3.2 5.4 - - - -
48A ILE* 2.7 51.6 + - + +
50A LYS* 3.2 50.6 - - + +
71A LEU* 1.3 76.0 - - - +
73A ASP* 1.3 86.3 + - - +
74A PRO* 3.7 25.6 - - + -
76A CYS* 3.9 16.4 - - + +
77A ASP 3.6 13.7 + - - -
78A THR* 5.2 2.0 - - - -
80A SER 3.9 9.6 - - - -
81A ILE 4.2 2.7 - - - +
82A GLY* 4.7 0.2 - - - -
165A LEU* 4.5 2.0 - - + -
168A ILE* 4.3 0.2 - - + -
169A TRP* 3.8 39.7 - + + -
172A GLN* 3.5 28.9 - - + -
173A THR* 6.3 0.7 - - + -
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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