Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 1UB6
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.0 1.3 - - - -
50A VAL* 3.6 25.1 - - + +
61A TYR* 3.2 22.3 - - + -
65A VAL* 3.1 43.1 + - + +
66A ALA 4.6 4.0 - - - +
67A GLY 5.0 1.0 - - - -
68A ARG* 1.3 108.7 + - + +
70A THR* 1.3 66.4 + - - +
82A LEU* 4.4 10.1 - - + -
83A GLN 3.2 3.1 - - - +
84A MET* 3.7 42.2 - - + -
85A SER 4.2 2.7 - - - -
87A LEU* 4.1 4.7 - - + -
91A ASP* 3.8 25.1 - - - -
95A TYR* 4.0 12.8 - + - -
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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
----------------------------------------------------------
61A TYR* 3.3 8.7 + - - +
68A ARG 5.0 1.9 + - - -
69A PHE* 1.3 78.1 + - - +
71A ILE* 1.3 70.5 + - - +
72A SER* 3.9 9.4 + - - -
81A TYR 4.3 0.3 - - - -
82A LEU* 3.6 3.5 + - - -
83A GLN* 2.7 53.9 + - + +
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Residues in contact with ILE 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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36A MET 3.8 22.4 - - - +
37A SER* 4.5 1.1 - - - -
38A TRP* 3.5 24.7 - - + +
51A ALA* 3.9 12.6 - - + +
52A SER* 3.7 33.9 - - - +
53A ILE* 3.8 11.5 - - + +
59A THR* 3.8 19.0 - - + +
61A TYR* 2.9 31.5 + - + +
70A THR* 1.3 77.1 - - - +
72A SER* 1.3 64.7 + - - +
80A LEU* 4.0 10.3 - - + -
81A TYR 3.4 13.9 - - - +
82A LEU* 4.4 1.8 - - + +
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Residues in contact with SER 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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53A ILE* 4.3 8.1 - - - -
70A THR* 3.9 9.6 + - - -
71A ILE* 1.3 76.9 - - - +
73A ARG* 1.3 61.1 + - - +
80A LEU* 3.1 9.3 - - - +
81A TYR* 2.8 54.9 + - - +
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Residues in contact with ARG 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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29A PHE* 3.0 32.1 + - + -
30A SER* 3.6 20.2 - - - +
34A TYR 3.1 17.0 + - - -
36A MET* 3.9 5.3 - - - +
53A ILE* 3.8 30.3 + - + +
54A SER 2.4 27.3 + - - -
55A SER 3.3 15.2 + - - -
57A GLY* 3.8 7.3 - - - +
72A SER* 1.3 79.4 - - - +
74A ASP* 1.3 65.9 + - - +
75A ASN* 2.9 36.5 + - - +
79A ILE 3.4 10.3 - - - +
80A LEU* 4.2 7.9 - - + -
81A TYR* 4.8 2.5 - - - +
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Residues in contact with ASP 74 (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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73A ARG* 1.3 71.6 - - - +
75A ASN* 1.3 54.0 + - - +
76A VAL* 3.0 21.3 + - - +
77A ARG* 2.8 51.5 + - - +
78A ASN* 2.8 31.7 + - - -
79A ILE* 2.8 24.7 + - + +
81A TYR* 4.1 21.2 + - + -
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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
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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