Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 1QY4
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 PHE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A THR 3.6 1.9 - - - +
72A VAL* 3.7 0.2 - - - -
73A LEU* 2.8 45.2 + - + +
101A ALA* 4.4 11.2 - - + -
103A LYS 3.3 15.7 - - - -
104A GLY* 4.4 3.4 - - - -
105A LYS 3.8 5.6 - - - +
106A GLY* 3.7 26.2 - - - -
107A GLY 4.1 9.6 - - - -
122A MET* 3.6 42.2 - - + -
138A THR* 4.1 12.6 - - + -
139A VAL 4.0 9.9 - - - -
140A ASN* 3.4 23.1 - - + +
145A PRO* 1.3 71.4 - - - +
147A ILE* 1.3 61.6 + - - +
148A PHE* 3.6 28.7 + + - -
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Residues in contact with ILE 147 (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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12A PHE 4.7 2.0 - - - +
13A GLU 3.3 28.9 - - - +
14A THR* 3.8 14.6 - - - +
15A GLY* 3.7 23.8 - - - +
71A THR 3.3 8.1 - - - +
72A VAL* 3.7 23.1 - - + -
101A ALA* 3.8 1.6 - - - +
102A LEU* 2.7 45.9 + - + -
103A LYS* 2.8 36.3 + - + +
145A PRO* 4.3 10.5 - - + -
146A PHE* 1.3 80.2 - - - +
148A PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 148 (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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69A ALA 5.5 0.2 - - - -
70A THR* 3.1 6.4 - - - -
71A THR* 3.0 68.9 + - + -
73A LEU* 4.8 2.9 - - + -
99A TYR* 3.1 37.5 - + + -
100A VAL 3.2 15.3 - - - +
101A ALA* 3.9 8.3 - - + -
102A LEU* 4.1 7.9 - - - +
122A MET* 4.6 4.0 - - + -
138A THR* 3.3 34.1 - - + -
146A PHE* 3.6 30.3 - + + -
147A ILE* 1.3 76.2 - - - +
149A LEU* 1.3 64.9 + - - +
150A ALA* 4.6 4.5 - - + -
300A 6PG 3.4 10.5 - - - -
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Residues in contact with LEU 149 (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* 5.5 2.9 - - + -
12A PHE* 6.1 1.1 - - + -
17A ILE* 4.7 1.3 - - + -
68A PHE* 4.0 16.8 - - + -
69A ALA 3.4 31.6 - - - +
70A THR* 3.9 15.5 - - + +
98A VAL 3.9 0.5 - - - +
99A TYR* 3.3 3.3 - - - +
100A VAL* 2.7 52.5 + - + +
102A LEU* 4.3 12.5 - - + +
148A PHE* 1.3 75.5 - - - +
150A ALA* 1.3 62.7 + - - +
151A ILE* 3.9 16.6 - - + -
100B VAL* 3.7 33.4 - - + -
127B VAL* 4.5 13.7 - - + -
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Residues in contact with ALA 150 (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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68A PHE* 3.2 5.9 - - - +
69A ALA 2.7 36.6 + - - +
97A GLU* 4.4 2.0 - - - +
98A VAL 3.4 6.1 - - - +
99A TYR* 4.1 20.2 - - + +
148A PHE* 4.7 2.2 - - + -
149A LEU* 1.3 74.9 - - - +
151A ILE* 1.3 62.8 + - - +
152A TYR* 4.0 2.8 - - + -
300A 6PG 3.9 37.2 - - - +
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Residues in contact with ILE 151 (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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66A LEU* 4.5 13.9 - - + -
67A ASN 3.5 10.8 - - - +
68A PHE* 3.9 12.3 - - + -
97A GLU* 3.5 4.6 - - - +
98A VAL 2.9 35.8 + - - +
100A VAL* 4.5 9.0 - - + -
149A LEU* 3.9 22.7 - - + -
150A ALA* 1.3 79.7 - - - +
152A TYR* 1.3 63.3 + - - +
66B LEU* 3.7 4.8 - - + +
98B VAL* 4.1 22.7 - - + -
151B ILE* 3.4 55.9 - - + -
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Residues in contact with TYR 152 (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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56A ALA* 4.3 1.7 - - - +
58A GLU* 3.2 27.3 + - - +
66A LEU* 3.6 6.1 - - - -
67A ASN* 2.9 62.7 + - + +
68A PHE* 4.0 16.3 + - - -
69A ALA* 4.0 11.3 - - + +
97A GLU* 3.4 25.4 - - + +
150A ALA 4.0 7.9 - - - -
151A ILE* 1.3 77.1 - - - +
153A PRO* 1.3 82.9 - - + +
156A ALA* 4.8 8.3 - - + -
157A GLY 5.6 1.3 - - - -
158A HIS* 4.0 16.8 - + - -
300A 6PG 3.1 42.3 + - - -
66B LEU* 4.5 0.2 - - - -
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Residues in contact with PRO 153 (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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64A GLY 6.0 2.0 - - - +
65A ASP 3.6 9.6 - - - +
66A LEU* 4.1 4.2 - - + -
95A ARG* 3.6 21.8 - - + +
96A ALA 2.9 28.9 - - - +
152A TYR* 1.3 88.1 - - + +
154A ALA* 1.3 58.3 + - - +
155A ASP* 2.9 16.4 + - - +
156A ALA* 2.9 24.2 + - + +
64B GLY* 3.7 24.5 - - - +
66B LEU* 4.0 14.8 - - + -
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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