Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 1QXR
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 LEU 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL 4.9 0.5 - - - +
59A GLN* 3.4 20.3 + - - +
64A GLY 4.4 1.6 - - - +
65A ASP* 1.3 89.5 + - - +
67A ASN* 1.3 65.4 + - - +
68A PHE* 5.0 0.9 - - - -
151A ILE* 4.5 7.4 - - + -
152A TYR 3.7 12.6 - - - +
153A PRO* 4.2 5.8 - - + -
154A ALA* 3.9 0.7 - - - +
66B LEU* 3.9 24.7 - - + -
96B ALA* 3.5 30.7 - - + +
97B GLU* 3.5 21.3 - - - -
98B VAL* 3.8 15.7 - - + +
129B TYR* 3.8 10.6 - - + -
151B ILE 3.6 14.8 - - - +
152B TYR* 4.4 0.7 - - - -
153B PRO* 4.1 11.0 - - + -
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Residues in contact with ASN 67 (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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57A VAL 3.6 7.4 - - - +
58A GLU* 3.7 23.1 + - - +
59A GLN 2.8 27.5 + - - +
66A LEU* 1.3 76.0 - - - +
68A PHE* 1.3 65.3 + - - +
151A ILE* 3.4 6.6 - - - +
152A TYR* 2.9 66.5 + - + +
154A ALA* 3.7 30.0 + - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.4 4.3 - + - -
8A VAL* 3.9 18.2 - - + -
17A ILE* 4.4 10.1 - - + -
56A ALA* 3.7 0.2 - - - -
57A VAL* 2.8 77.9 + - + +
59A GLN* 5.6 0.2 - - - -
66A LEU 5.0 1.8 - - - -
67A ASN* 1.3 78.7 - - - +
69A ALA* 1.3 59.5 + - - +
149A LEU* 4.1 13.9 - - + -
150A ALA 3.1 12.6 - - - +
151A ILE* 4.1 15.3 - - + -
152A TYR* 4.0 3.2 + - - -
98B VAL* 3.8 22.0 - - + -
127B VAL* 3.5 34.3 - - + -
129B TYR* 4.5 17.9 - + + -
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Residues in contact with ALA 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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17A ILE* 4.3 2.2 - - - -
54A VAL* 3.9 17.3 - - + -
55A TYR 3.1 14.8 - - - +
56A ALA* 3.7 12.8 - - + -
68A PHE* 1.3 76.9 - - - +
70A THR* 1.3 59.7 + - - +
71A THR* 5.1 0.2 + - - -
148A PHE* 3.9 0.5 - - - +
149A LEU* 3.7 6.2 - - - +
150A ALA* 2.8 38.9 + - - +
152A TYR* 4.0 11.9 - - + +
300A PA5 4.1 10.7 + - - +
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Residues in contact with THR 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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10A VAL* 4.0 15.0 - - + -
15A GLY* 2.7 35.3 + - - +
17A ILE* 3.5 18.1 - - + +
54A VAL* 3.2 6.4 - - - +
55A TYR* 2.9 44.1 + - - +
69A ALA* 1.3 75.9 - - - +
71A THR* 1.3 64.3 + - - +
102A LEU* 4.6 3.6 - - + -
147A ILE* 4.9 0.7 - - - -
148A PHE 3.0 13.2 - - - +
149A LEU* 3.9 17.0 - - + -
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Residues in contact with THR 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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52A TYR* 4.1 21.3 - - + -
53A GLU 3.3 9.9 - - - +
54A VAL* 3.9 3.2 - - + +
69A ALA 5.1 0.2 + - - -
70A THR* 1.3 78.6 + - - +
72A VAL* 1.3 73.7 + - - +
73A LEU* 3.8 2.2 - - + +
85A THR* 4.3 4.5 - - + -
146A PHE 3.6 1.6 - - - +
147A ILE* 3.2 8.4 - - - +
148A PHE* 2.9 58.6 + - + -
300A PA5 2.7 32.1 + - - +
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Residues in contact with VAL 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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14A THR 3.4 25.1 - - - +
15A GLY* 4.2 4.7 - - - -
52A TYR* 3.2 4.9 - - - -
53A GLU* 2.8 39.4 + - - +
55A TYR* 4.3 18.6 - - + -
71A THR* 1.3 77.0 - - - +
73A LEU* 1.3 59.3 + - - +
74A TYR* 3.5 35.2 + - + +
145A PRO* 4.0 16.8 - - + -
146A PHE 3.7 2.5 - - - -
147A ILE* 4.1 15.5 - - + -
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Residues in contact with LEU 73 (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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51A VAL* 3.5 18.8 - - + +
52A TYR* 3.9 9.6 - - + -
71A THR* 3.8 4.9 - - + -
72A VAL* 1.3 71.8 - - - +
74A TYR* 1.3 67.9 + - - +
83A PHE 4.1 1.8 - - - +
84A PHE* 4.0 25.4 - - - +
85A THR* 4.2 13.5 - - + +
138A THR* 3.6 20.6 - - - +
139A VAL* 3.6 7.4 - - - -
140A ASN* 2.8 40.1 + - + +
145A PRO* 3.5 0.8 - - - +
146A PHE* 2.7 57.4 + - + +
148A PHE* 4.8 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