Contacts of the strand formed by residues 57 - 63 (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 PHE 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B TYR* 3.1 47.4 - + + +
7B PRO* 4.2 2.4 - - - +
53B ILE* 4.8 1.8 - - + -
55B GLN* 3.4 3.1 - - - -
56B ARG* 1.3 102.5 - - + +
58B ILE* 1.3 73.0 - - - +
59B LEU* 5.6 0.2 - - + -
73B ALA* 5.2 0.4 - - + -
74B LEU 3.3 15.9 - - - +
75B ASP* 4.0 21.3 - - - -
76B VAL* 3.9 0.9 - - - +
82B VAL* 4.4 11.9 - - + -
103B ALA* 3.7 26.2 - - + -
104B ILE* 3.7 26.7 - - + -
107B LEU* 3.4 45.3 - - + -
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Residues in contact with ILE 58 (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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6B TYR* 4.5 1.1 - - - -
7B PRO* 3.6 22.2 - - + +
9B ILE* 4.5 10.5 - - + -
28B VAL* 6.0 2.9 - - + +
31B ARG* 3.5 48.7 - - + +
32B LEU* 3.6 26.2 - - + -
57B PHE* 1.3 80.7 - - - +
59B LEU* 1.3 73.2 + - - +
60B VAL* 5.0 5.6 - - + -
72B LEU 3.7 0.5 - - - +
73B ALA* 3.8 1.2 - - - -
74B LEU* 2.9 42.3 + - + +
76B VAL* 3.7 13.5 - - + -
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Residues in contact with LEU 59 (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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5B GLN* 6.3 1.3 - - + -
6B TYR* 4.3 23.6 - - + +
7B PRO 2.9 13.1 + - - +
8B ILE* 3.1 29.4 - - + -
9B ILE* 2.8 24.8 + - - -
58B ILE* 1.3 77.6 - - - +
60B VAL* 1.3 62.5 + - - +
61B GLU 4.1 0.2 - - - -
71B THR* 4.0 12.1 - - + -
72B LEU 3.6 0.4 - - - -
73B ALA* 4.1 16.8 - - + -
107B LEU* 4.3 11.2 - - + -
108B PHE* 3.6 39.0 - - + -
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Residues in contact with VAL 60 (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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9B ILE* 3.4 12.6 - - + +
11B PHE* 5.5 0.2 - - + -
24B PHE* 3.6 31.6 - - + -
28B VAL* 4.9 7.2 - - + -
58B ILE* 4.5 6.1 - - + +
59B LEU* 1.3 78.0 - - - +
61B GLU* 1.3 60.6 + - - +
62B LEU* 3.5 24.1 + - + +
70B VAL 3.6 2.1 - - - +
71B THR* 3.3 4.2 - - - -
72B LEU* 2.8 43.9 + - + +
74B LEU* 3.6 35.4 - - + -
175B ILE* 4.8 5.8 - - + -
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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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8B ILE* 4.1 16.6 - - + +
9B ILE 2.8 10.0 + - - +
10B ASN* 3.1 30.6 + - - +
11B PHE 3.1 27.6 + - - +
59B LEU 4.1 1.0 + - - -
60B VAL* 1.3 70.4 - - - +
62B LEU* 1.3 61.0 + - - +
63B SER* 3.5 14.5 + - - +
69B SER* 3.4 20.8 + - - +
70B VAL 3.7 2.7 - - - -
71B THR* 4.2 17.0 + - + +
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Residues in contact with LEU 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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11B PHE* 3.7 17.7 - - + -
24B PHE* 5.0 1.6 - - + -
60B VAL* 3.5 29.6 - - + +
61B GLU* 1.3 69.8 - - - +
63B SER* 1.3 61.2 + - - +
64B ASN 4.1 0.2 + - - -
69B SER* 3.2 5.2 + - - -
70B VAL* 2.8 40.1 + - + +
72B LEU* 3.6 27.6 - - + -
144B LEU* 4.3 13.0 - - + -
148B ILE* 3.8 37.9 - - + +
171B CYS* 4.4 7.2 - - - -
175B ILE* 3.9 24.7 - - + -
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Residues in contact with SER 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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10B ASN* 5.0 2.8 + - - +
11B PHE* 2.7 18.6 + - - -
12B THR* 2.9 36.4 + - - -
13B THR* 3.0 8.3 + - - +
61B GLU* 3.5 23.2 + - - -
62B LEU* 1.3 73.3 - - - +
64B ASN* 1.3 61.9 + - - +
68B LEU 3.8 4.9 - - - -
69B SER* 3.7 6.0 + - - -
148B ILE* 4.8 3.3 - - - +
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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