Contacts of the strand formed by residues 69 - 75 (chain B) in PDB entry 1Q41
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 VAL 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 3.9 17.3 - - + -
63B GLY 3.4 13.0 - - - +
64B ASN* 3.5 16.4 - - - +
68B GLY* 1.3 78.0 - - - -
70B VAL* 1.3 73.1 + - - +
71B TYR* 3.4 38.2 - - + +
84B ILE 3.6 1.4 - - - +
85B LYS* 3.5 2.6 - - - +
86B LYS* 2.9 36.0 + - + +
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Residues in contact with VAL 70 (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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61B VAL* 3.8 2.6 - - - -
62B ILE* 3.0 43.9 + - + -
63B GLY* 3.0 20.5 + - - +
64B ASN 4.9 6.3 - - - +
68B GLY 5.6 0.4 - - - -
69B VAL* 1.3 79.9 - - - +
71B TYR* 1.3 67.2 + - - +
83B ALA* 4.2 6.5 - - + -
84B ILE 3.4 6.5 - - - +
85B LYS* 4.2 17.5 - - + +
452B IXM 3.8 46.0 - - + +
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.6 26.9 - - + -
60B LYS 3.3 9.0 - - - +
61B VAL* 3.8 25.6 - - + +
62B ILE* 4.1 3.8 - - - -
69B VAL* 3.4 38.2 - - + +
70B VAL* 1.3 75.7 - - - +
72B GLN* 1.3 66.2 + - - +
73B ALA* 5.7 0.2 - - + -
83B ALA* 3.0 9.0 - - - +
84B ILE* 2.7 56.2 + - + +
86B LYS* 4.2 28.5 + - + +
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Residues in contact with GLN 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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58B ASP* 3.5 5.0 + - - +
59B THR* 3.3 5.4 - - - -
60B LYS* 2.8 65.1 + - + +
62B ILE* 3.7 26.9 - - + +
71B TYR* 1.3 77.4 - - - +
73B ALA* 1.3 70.7 + - - +
81B LEU* 4.1 22.5 - - + +
82B VAL 3.4 9.0 - - - +
134B TYR* 3.3 36.4 + - + -
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Residues in contact with ALA 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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56B TYR* 3.9 24.2 - - + -
57B THR 3.5 11.4 - - - +
58B ASP 3.9 3.6 - - - -
59B THR* 4.2 5.6 - - + +
71B TYR* 5.7 0.4 - - + -
72B GLN* 1.3 77.4 - - - +
74B LYS* 1.3 61.6 + - - +
81B LEU* 3.3 9.9 - - - +
82B VAL* 2.8 39.0 + - + +
84B ILE* 4.1 17.5 - - + -
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Residues in contact with LYS 74 (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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56B TYR* 3.1 5.4 - - - -
57B THR* 2.7 54.0 + - + +
58B ASP* 3.8 23.5 - - + +
73B ALA* 1.3 75.0 - - - +
75B LEU* 1.3 67.5 + - - +
76B CYS* 3.5 1.7 + - - -
79B GLY* 3.0 44.0 + - - +
80B GLU 3.3 4.5 - - - +
81B LEU* 4.1 14.4 - - + -
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Residues in contact with LEU 75 (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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54B VAL* 4.0 27.4 - - + -
55B SER 3.7 4.7 - - - +
56B TYR* 4.2 8.7 - - + -
74B LYS* 1.3 72.5 - - - +
76B CYS* 1.3 59.8 + - - +
77B ASP* 3.8 18.4 - - - +
78B SER* 3.8 15.7 - - - +
79B GLY* 2.7 34.3 + - - -
80B GLU* 2.8 18.8 + - + +
82B VAL* 3.8 35.0 - - + -
113B ARG* 4.4 12.6 - - - +
114B TYR* 5.0 14.1 - - + +
131B VAL* 5.1 6.7 - - + -
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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