Contacts of the strand formed by residues 55 - 60 (chain F) in PDB entry 1IBL
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 ASP 55 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F PRO* 3.2 13.9 - - - +
13F ASN* 2.9 31.1 + - - +
48F LEU* 4.0 2.9 - - - +
51F PRO* 4.4 1.3 - - - -
52F ILE* 2.9 27.0 + - - +
53F ALA 2.7 9.1 + - - +
54F LYS* 1.3 74.8 - - - +
56F PRO* 1.3 76.1 - - - +
57F GLN* 3.1 18.8 + - - +
86F ARG* 3.0 35.9 + - - +
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Residues in contact with PRO 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ARG* 4.4 2.8 - - - +
48F LEU* 3.9 19.9 + - + +
50F TYR 5.7 0.2 - - - -
51F PRO* 4.6 11.6 - - + -
54F LYS 3.7 7.0 - - - +
55F ASP* 1.3 91.7 - - - +
57F GLN* 1.3 71.7 + - + +
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PRO* 2.9 26.3 + - + +
13F ASN* 5.8 1.0 + - - -
45F LEU* 4.0 23.5 - - + +
46F ARG 3.5 11.9 - - - +
47F ARG* 2.7 39.4 + - - +
48F LEU* 3.7 14.2 - - - +
55F ASP* 3.1 11.4 + - - +
56F PRO* 1.3 93.7 - - + +
58F GLY* 1.3 58.8 + - - +
86F ARG* 3.9 6.1 + - - -
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Residues in contact with GLY 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.0 15.0 - - - -
10F LEU 4.2 0.4 - - - -
12F PRO* 3.9 9.9 - - - -
44F GLY 3.0 3.5 - - - +
45F LEU* 3.3 3.0 - - - -
46F ARG 2.9 31.0 + - - -
48F LEU* 4.0 4.5 - - - +
57F GLN* 1.3 78.1 - - - +
59F TYR* 1.3 61.1 + - - -
60F PHE* 3.5 11.8 - - - -
86F ARG* 6.1 1.1 - - - -
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Residues in contact with TYR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE 3.6 0.3 - - - +
9F VAL* 3.3 2.6 - - - +
10F LEU* 2.8 73.0 + - + +
11F ASN 4.6 1.6 - - - +
12F PRO* 4.2 10.0 - - + +
19F LEU* 3.4 35.6 - - + +
23F LYS* 5.4 0.9 - - + -
42F GLU* 3.0 35.5 + - + +
44F GLY* 3.2 31.2 - - - -
45F LEU* 3.3 22.7 - - + -
58F GLY* 1.3 69.9 - - - -
60F PHE* 1.3 64.1 + - - +
61F LEU* 4.7 4.5 - - + -
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASN* 5.5 4.3 - - + -
8F ILE 3.5 2.7 - - - -
9F VAL* 3.4 32.8 - - + -
42F GLU* 3.9 1.4 - - - +
43F LEU* 3.7 18.4 + - + -
44F GLY* 2.7 38.4 + - - +
46F ARG* 4.2 17.0 - - + -
48F LEU* 3.7 16.8 - - + -
58F GLY 3.5 13.2 - - - -
59F TYR* 1.3 73.2 - - - +
61F LEU* 1.3 73.9 + - - +
35R ARG* 5.9 6.1 - - - -
76R LEU* 3.5 29.4 - - + -
78R LEU* 3.4 38.8 - - + -
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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