Contacts of the strand formed by residues 69 - 75 (chain B) in PDB entry 1IL5
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 SER 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLU* 3.4 26.3 + - - +
62B LEU 3.2 15.3 + - - -
63B SER* 3.7 8.4 + - - -
67B GLU 4.0 3.2 + - - -
68B LEU* 1.3 77.2 - - - +
70B VAL* 1.3 69.6 + - - +
71B THR* 5.2 0.6 + - - -
85B ARG 4.7 3.6 - - - +
86B ALA* 5.2 0.2 - - - -
87B GLY 5.1 2.6 + - - -
148B ILE* 4.8 0.9 - - - -
152B TYR* 3.5 19.7 - - - -
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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
----------------------------------------------------------
60B VAL 3.6 1.6 - - - +
61B GLU* 4.6 0.4 - - - -
62B LEU* 2.8 38.2 + - + +
69B SER* 1.3 82.1 + - - +
71B THR* 1.3 63.3 + - - +
72B LEU* 3.7 21.1 - - + +
84B TYR* 3.6 28.7 - - + -
85B ARG 4.2 5.4 - - - +
86B ALA* 5.6 0.9 - - - -
148B ILE* 3.5 38.6 - - + +
151B LEU* 3.8 12.1 - - + -
152B TYR* 4.0 17.5 - - + +
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Residues in contact with THR 71 (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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8B ILE* 5.5 2.9 - - + -
59B LEU* 4.0 25.4 - - + -
60B VAL 3.3 12.3 - - - +
61B GLU* 4.2 17.4 + - + +
69B SER* 5.2 0.9 + - - -
70B VAL* 1.3 75.5 + - - +
72B LEU* 1.3 60.6 + - - +
84B TYR* 3.1 5.6 - - - -
85B ARG* 2.9 53.6 + - - -
108B PHE* 3.7 18.4 - - + -
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Residues in contact with LEU 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 ILE 3.7 0.7 - - - +
59B LEU* 3.6 2.9 - - - +
60B VAL* 2.8 45.1 + - + +
62B LEU* 3.6 34.1 - - + -
70B VAL* 3.7 21.1 - - + +
71B THR* 1.3 73.2 - - - +
73B ALA* 1.3 61.4 + - - +
74B LEU* 3.8 3.0 + - + -
81B VAL* 3.7 32.3 - - + -
83B GLY 3.6 0.7 - - - -
84B TYR* 3.6 21.3 - - + -
151B LEU* 4.3 15.0 - - + -
168B PHE* 4.7 4.5 - - + -
171B CYS* 5.1 9.0 - - + -
175B ILE* 4.8 9.9 - - + -
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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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57B PHE* 5.2 1.6 - - + -
58B ILE 3.8 4.7 - - - -
59B LEU* 4.1 4.0 - - + -
71B THR 4.0 0.8 + - - -
72B LEU* 1.3 71.4 - - - +
74B LEU* 1.3 61.6 + - - +
81B VAL* 3.5 3.2 - - - -
82B VAL* 2.9 48.3 + - + +
83B GLY 2.9 14.3 + - - +
92B PHE* 5.5 0.2 - - + -
107B LEU* 3.9 25.4 - - + -
108B PHE* 3.9 15.5 - - + -
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Residues in contact with LEU 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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28B VAL* 4.0 23.3 - - + -
32B LEU* 4.8 11.2 - - + -
57B PHE* 3.3 8.2 - - - -
58B ILE* 2.9 43.2 + - + +
60B VAL* 3.6 31.0 - - + -
72B LEU* 4.8 4.0 - - + +
73B ALA* 1.3 73.2 - - - +
75B ASP* 1.3 63.6 + - - +
76B VAL 3.4 1.0 + - - -
79B ALA* 3.6 23.8 - - + +
80B TYR 3.4 2.5 - - - +
81B VAL* 3.6 31.9 - - + -
175B ILE* 4.3 14.6 - - + -
176B SER* 3.8 4.7 - - - +
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Residues in contact with ASP 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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56B ARG* 2.9 39.8 + - - +
57B PHE* 4.0 10.0 - - + -
73B ALA 4.0 1.2 + - - -
74B LEU* 1.3 70.0 - - - +
76B VAL* 1.3 57.9 + - - +
77B THR* 2.8 26.0 + - - -
78B ASN* 3.2 17.9 + - - +
79B ALA* 2.6 34.9 + - - -
80B TYR 2.9 8.6 + - - +
82B VAL* 3.8 23.4 - - + +
100B ASP* 4.5 6.6 - - - +
104B ILE* 5.4 1.0 - - - +
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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