Contacts of the strand formed by residues 67 - 74 (chain A) in PDB entry 1ITB
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A MET* 4.2 20.9 - - + -
23A PRO* 5.1 3.8 - - + -
24A TYR* 3.3 42.0 - - + +
61A GLY* 3.1 4.5 - - - -
62A LEU* 2.9 43.8 + - + -
65A LYS* 3.8 10.1 - - + +
66A ASN* 1.3 77.8 - - - +
68A TYR* 1.3 66.8 + - - +
82A LEU* 3.7 25.8 - - + -
83A GLU 3.5 8.3 - - - +
84A SER* 3.5 21.1 - - - +
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Residues in contact with TYR 68 (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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43A SER* 4.0 13.2 + - - -
45A SER* 3.8 7.1 + - - -
59A ALA* 3.9 21.1 - - + -
60A LEU 3.5 16.6 - - - -
61A GLY* 3.5 19.4 - - - -
62A LEU 5.7 1.3 - - - -
66A ASN* 5.6 3.1 - - - -
67A LEU* 1.3 87.4 - - - +
69A LEU* 1.3 65.7 + - - +
70A SER* 3.3 4.3 + - - -
82A LEU* 3.8 1.7 - - - -
83A GLU* 2.9 31.7 + - - +
85A VAL* 3.7 24.0 - - + -
90A TYR* 4.5 12.8 - + + -
91A PRO* 3.2 28.8 - - + +
95A MET* 3.9 17.7 - - + -
99A PHE* 3.6 26.4 - + + -
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Residues in contact with LEU 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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10A LEU* 6.4 0.7 - - + -
26A LEU* 4.4 6.5 - - + -
42A PHE* 4.3 17.3 - - + -
60A LEU* 2.8 40.8 + - + +
62A LEU* 3.8 27.4 - - + -
68A TYR* 1.3 72.1 - - - +
70A SER* 1.3 59.3 + - - +
80A LEU* 4.1 19.3 - - + -
81A GLN 3.6 5.6 - - - -
82A LEU* 4.2 16.8 - - + -
99A PHE* 3.4 21.1 - - - +
101A PHE* 3.4 16.5 - - + -
122A ILE* 4.2 22.7 - - + -
132A VAL* 6.1 1.6 - - + -
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Residues in contact with SER 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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68A TYR 3.3 0.6 + - - -
69A LEU* 1.3 73.7 - - - +
71A CYS* 1.3 64.0 + - - +
72A VAL* 4.2 2.0 - - - +
80A LEU* 3.3 6.6 - - - +
81A GLN* 3.0 44.7 + - - +
83A GLU* 2.8 26.6 + - - +
98A ARG* 3.3 19.5 - - - -
99A PHE* 3.5 23.1 - - - -
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Residues in contact with CYS 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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70A SER* 1.3 75.5 - - - +
72A VAL* 1.3 62.4 + - - +
79A THR 3.4 4.7 - - - -
98A ARG* 2.9 33.7 + - - +
101A PHE* 3.4 33.2 - - - -
114A SER* 3.1 28.9 - - - +
116A GLN* 4.2 3.2 - - + +
117A PHE* 3.7 21.8 - - + -
134A LEU* 3.7 23.6 - - + -
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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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70A SER* 4.2 8.9 - - - +
71A CYS* 1.3 80.8 - - - +
73A LEU* 1.3 70.8 + - - +
74A LYS* 4.6 5.6 - - + +
78A PRO* 3.7 1.7 - - - +
79A THR* 2.9 45.9 + - - +
81A GLN* 3.1 35.9 - - + +
83A GLU* 4.9 2.0 - - - +
98A ARG* 4.5 14.1 - - - -
117A PHE* 3.8 7.9 - - - -
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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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72A VAL* 1.3 79.0 - - - +
74A LYS* 1.3 59.8 + - - +
75A ASP 4.0 0.6 + - - -
76A ASP* 3.6 37.0 - - - +
77A LYS 3.7 20.0 - - - +
78A PRO* 4.0 4.3 - - + -
117A PHE* 3.7 31.1 - - + -
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Residues in contact with LYS 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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72A VAL* 3.5 8.2 + - + -
73A LEU* 1.3 72.3 - - - +
75A ASP* 1.3 94.7 + - - +
77A LYS* 3.1 21.9 + - - +
79A THR* 3.1 29.7 - - + +
81A GLN* 5.5 2.2 - - - +
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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