Contacts of the strand formed by residues 60 - 66 (chain B) in PDB entry 1I72
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 GLN 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 4.1 3.5 - - - -
72A VAL 3.4 14.4 - - - +
73A SER* 4.0 6.1 - - - -
76A ARG* 2.7 31.6 + - - -
233A MET* 3.2 31.6 - - + +
234A LYS 5.0 0.8 + - - +
237A GLY* 3.2 28.7 + - - -
238A THR 3.4 17.2 + - - -
239A TYR* 3.4 15.1 - - - +
33B ARG* 4.3 1.5 - - - +
57B THR* 2.8 36.8 + - - +
59B LYS* 1.3 85.0 - - + +
61B GLU* 1.3 68.1 + - - +
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Residues in contact with GLU 61 (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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71A PHE* 3.5 3.1 - - - -
72A VAL* 2.8 35.7 + - + +
233A MET* 3.7 2.4 - - - +
33B ARG* 3.7 44.0 + - - +
54B VAL* 5.3 0.2 - - + -
55B THR 3.7 4.5 - - - -
56B LYS* 3.6 45.7 + - + +
57B THR 4.7 4.4 - - - +
60B GLN* 1.3 81.2 - - - +
62B ALA* 1.3 58.9 + - - +
63B TYR* 3.8 27.2 + - + +
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Residues in contact with ALA 62 (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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70A MET 3.6 3.6 - - - -
71A PHE* 3.5 17.3 - - + -
219A ASP* 4.8 1.8 - - + +
231A ASN* 3.8 18.4 - - + +
233A MET* 3.3 24.4 - - + +
54B VAL* 3.3 4.2 - - - +
55B THR* 2.8 46.9 + - - +
61B GLU* 1.3 71.6 - - - +
63B TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 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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69A SER* 3.4 3.5 - - - -
70A MET* 2.9 60.4 + - + +
72A VAL* 3.8 17.1 - - + +
231A ASN* 3.0 12.8 - - - +
35B ILE 5.5 0.2 + - - -
37B ARG* 4.7 7.1 - - - +
40B TRP* 3.8 19.4 + + - -
51B ILE* 3.4 30.1 - - + -
53B SER 3.3 5.4 - - - +
54B VAL* 3.5 34.5 - - + +
56B LYS* 5.0 3.3 + - - -
61B GLU* 3.8 36.3 + - + -
62B ALA* 1.3 76.9 - - - +
64B VAL* 1.3 59.4 + - - +
65B LEU* 4.3 10.1 - - + -
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Residues in contact with VAL 64 (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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68A PYR 3.9 3.8 - - - +
69A SER* 4.7 1.3 - - - +
219A ASP* 4.0 34.8 - - - +
221A THR* 3.8 20.2 - - - +
223A PHE* 4.6 0.7 - - + -
229A SER* 4.3 19.1 - - - -
230A MET* 5.4 3.4 - - - -
231A ASN* 3.5 18.2 - - - +
51B ILE* 3.7 4.3 - - - -
52B ILE* 3.0 42.8 + - + +
53B SER* 2.9 20.2 + - - +
63B TYR* 1.3 72.4 - - - +
65B LEU* 1.3 66.5 + - - +
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Residues in contact with LEU 65 (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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68A PYR 2.8 20.1 + - + +
69A SER* 3.9 17.7 - - - +
70A MET* 4.3 4.0 - - + -
79A LEU* 3.7 30.1 - - + -
80A LYS 4.3 0.2 - - - +
81A THR* 4.1 7.0 - - + -
223A PHE* 3.9 7.4 - - - -
368A MAO 3.2 24.2 - - - +
44B LEU* 4.1 9.4 - - + -
49B CYS* 3.9 22.9 - - + -
50B SER 3.3 9.2 - - - +
51B ILE* 3.7 28.3 - - + -
52B ILE* 4.3 1.1 - - - -
63B TYR* 4.3 9.0 - - + -
64B VAL* 1.3 81.4 - - - +
66B SER* 1.3 61.6 + - - +
67B GLU 5.6 0.4 - - - -
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Residues in contact with SER 66 (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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223A PHE* 4.1 3.8 - - - -
368A MAO 3.2 23.1 + - - -
49B CYS* 3.3 4.8 - - - -
50B SER* 2.8 34.4 + - - -
52B ILE* 3.4 34.6 - - - +
65B LEU* 1.3 75.4 - - - +
67B GLU* 1.3 77.5 + - - +
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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