Contacts of the strand formed by residues 59 - 64 (chain B) in PDB entry 1QNB
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 ALA 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.3 0.9 - - - -
51B GLU 3.9 2.9 - - - +
52B TYR* 3.3 19.5 - - - -
53B ASN 4.6 1.0 + - - -
57B PHE* 3.1 25.0 + - + +
58B ALA* 1.3 80.3 - - - +
60B VAL* 1.3 64.8 + - - +
61B ILE* 3.8 9.0 + - + +
72B LEU* 4.1 5.6 - - + -
73B ILE 3.3 15.7 - - - +
74B PHE* 3.4 27.1 - - + -
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Residues in contact with VAL 60 (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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40B LEU* 3.6 49.1 - - + +
43B ILE* 4.1 15.3 - - + -
44B ALA* 4.2 3.8 - - + +
50B ALA* 3.9 27.1 - - + -
51B GLU 3.3 5.6 - - - +
52B TYR* 3.9 14.1 - - + -
59B ALA* 1.3 71.4 - - - +
61B ILE* 1.3 64.6 + - - +
62B MET* 3.8 8.6 + - + +
71B ALA 3.6 0.9 - - - +
72B LEU* 3.5 2.6 - - - -
73B ILE* 2.9 41.6 + - + +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN 4.2 0.9 - - - +
50B ALA* 3.3 4.5 - - - -
51B GLU* 2.8 58.1 + - + +
52B TYR* 6.2 0.2 - - - -
53B ASN* 6.3 1.3 - - - +
56B ARG* 5.6 2.9 - - - +
57B PHE* 5.5 7.2 - - + -
59B ALA* 4.2 10.8 - - + +
60B VAL* 1.3 73.0 - - - +
62B MET* 1.3 60.4 - - - +
63B ARG* 3.9 19.2 + - - +
70B THR* 3.7 25.6 - - + -
71B ALA 3.5 4.0 - - - +
72B LEU* 4.1 12.6 - - + -
220F A 4.1 7.6 - - - +
221F T 3.7 36.6 - - - +
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.7 22.7 - - + -
47B ALA* 3.6 29.4 - - + -
49B ASN 4.3 7.0 - - - +
50B ALA* 4.3 12.1 - - + -
60B VAL* 3.8 2.9 + - + -
61B ILE* 1.3 73.9 - - - +
63B ARG* 1.3 68.6 + - - +
70B THR* 3.4 2.6 - - - +
71B ALA* 2.8 33.3 + - + +
73B ILE* 4.0 26.5 - - + -
97B TYR* 3.7 17.2 + - + -
100B ILE* 3.6 41.1 - - + -
101B VAL* 4.9 2.5 - - + -
104B LEU* 4.6 1.6 - - + -
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Residues in contact with ARG 63 (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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49B ASN* 3.4 32.1 + - - +
51B GLU* 3.8 27.9 + - - +
61B ILE* 3.9 21.1 + - - +
62B MET* 1.3 80.0 - - - +
64B ILE* 1.3 69.8 + - - +
69B THR 3.5 7.9 - - - +
70B THR* 3.1 17.4 + - - +
97B TYR* 3.7 0.4 - - - -
221F T 3.8 14.8 + - - -
222F T 3.0 32.3 + - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 5.8 0.2 - - + -
63B ARG* 1.3 78.7 - - - +
65B ARG* 1.3 59.9 + - - +
66B GLU 3.7 20.0 - - - +
67B PRO 3.6 6.7 - - - +
68B LYS* 3.6 4.5 - - - +
69B THR* 3.3 44.8 + - - +
93B ALA* 4.1 15.5 - - - +
96B LYS* 4.0 25.1 - - + -
97B TYR* 3.2 24.6 + - + +
100B ILE* 3.9 20.2 - - + -
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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
------------------------------------------------------------
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