Contacts of the strand formed by residues 66 - 73 (chain B) 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 LEU 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.8 25.6 - - + -
96A ALA* 3.5 29.6 - - + +
97A GLU* 3.8 10.1 - - - -
98A VAL* 4.1 17.6 - - + +
129A TYR* 3.7 9.4 - - + -
151A ILE 3.7 21.5 - - - +
152A TYR* 4.5 0.4 - - - -
153A PRO* 4.0 10.5 - - + -
57B VAL 4.8 0.2 - - - +
59B GLN* 3.3 20.4 + - - +
64B GLY 4.5 2.2 - - - +
65B ASP* 1.3 91.6 + - - +
67B ASN* 1.3 66.6 + - - +
68B PHE* 5.1 0.9 - - - -
151B ILE* 4.3 9.9 - - + -
152B TYR 3.5 18.8 - - - +
153B PRO* 3.9 2.9 - - + -
154B ALA 3.9 0.7 - - - +
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Residues in contact with ASN 67 (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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57B VAL 3.5 7.6 - - - +
58B GLU* 3.6 19.7 + - - +
59B GLN* 2.6 36.1 + - - +
66B LEU* 1.3 77.9 - - - +
68B PHE* 1.3 66.9 + - - +
151B ILE* 3.3 6.5 - - - +
152B TYR* 2.9 65.1 + - + +
154B ALA* 3.6 25.5 + - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 4.0 21.1 - - + -
127A VAL* 3.6 30.5 - - + -
129A TYR* 4.4 20.2 - + + -
6B PHE* 4.5 5.4 - + - -
8B VAL* 4.1 17.3 - - + -
17B ILE* 4.2 9.6 - - + -
55B TYR 4.1 0.2 - - - +
56B ALA* 4.4 0.5 - - - +
57B VAL* 2.8 72.1 + - + +
66B LEU 5.1 2.0 - - - -
67B ASN* 1.3 79.0 - - - +
69B ALA* 1.3 63.3 + - - +
149B LEU* 4.2 14.8 - - + -
150B ALA 3.1 12.8 - - - +
151B ILE* 4.1 14.4 - - + -
152B TYR* 4.0 3.3 + - - -
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Residues in contact with ALA 69 (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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17B ILE* 4.7 1.1 - - - -
54B VAL* 3.9 14.6 - - + -
55B TYR 3.1 12.6 - - - +
56B ALA* 3.9 11.9 - - + -
68B PHE* 1.3 77.0 - - - +
70B THR* 1.3 59.2 + - - +
71B THR* 4.3 0.7 + - - -
148B PHE* 4.0 0.3 - - - +
149B LEU* 3.4 5.7 - - - +
150B ALA* 2.6 39.5 + - - +
152B TYR* 4.1 7.9 - - + +
301B 6PG 3.8 21.3 + - - +
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.9 24.0 - - + -
15B GLY* 2.5 35.3 + - - +
17B ILE* 3.7 10.9 - - + +
54B VAL* 3.2 7.1 - - - +
55B TYR* 2.8 49.0 + - - +
69B ALA* 1.3 76.3 - - - +
71B THR* 1.3 63.7 + - - +
102B LEU* 4.8 2.9 - - + -
147B ILE* 5.0 0.4 - - - -
148B PHE 3.1 12.8 - - - +
149B LEU* 3.9 13.5 - - + -
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Residues in contact with THR 71 (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 TYR* 3.9 22.7 - - + -
53B GLU 3.2 10.1 - - - +
54B VAL* 3.8 4.3 - - - +
69B ALA 4.3 0.5 + - - -
70B THR* 1.3 77.1 + - - +
72B VAL* 1.3 73.9 - - - +
73B LEU* 3.8 2.5 - - + +
85B THR* 4.3 4.9 - - + -
146B PHE 3.6 0.7 - - - +
147B ILE* 3.2 8.5 - - - +
148B PHE* 3.1 60.6 + - + -
301B 6PG 2.7 31.4 + - - +
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Residues in contact with VAL 72 (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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14B THR 3.4 24.9 - - - +
15B GLY* 4.1 11.4 - - - +
52B TYR* 3.1 4.7 - - - -
53B GLU* 2.8 38.3 + - - +
55B TYR* 4.4 15.0 - - + -
71B THR* 1.3 76.7 - - - +
73B LEU* 1.3 59.7 + - - +
74B TYR* 3.6 32.2 + - + +
145B PRO* 4.0 23.1 - - + -
146B PHE 3.6 2.9 - - - -
147B ILE* 4.2 8.5 - - + -
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Residues in contact with LEU 73 (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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51B VAL* 3.7 14.4 - - + +
52B TYR* 3.7 7.9 - - + -
71B THR* 3.8 7.1 - - + -
72B VAL* 1.3 70.7 - - - +
74B TYR* 1.3 66.5 + - - +
83B PHE* 3.8 6.1 - - + +
84B PHE* 3.8 30.1 - - - +
85B THR* 4.3 10.3 - - + -
138B THR* 3.5 21.1 - - - +
139B VAL 3.4 10.5 - - - +
140B ASN* 2.8 51.4 + - + +
145B PRO* 3.7 1.3 - - - +
146B PHE* 2.8 37.6 + - + +
148B PHE* 4.7 0.9 - - + -
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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