Contacts of the strand formed by residues 86 - 91 (chain G) in PDB entry 1ILL
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 ALA 86 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G PRO* 4.3 16.4 - - + +
4G VAL* 3.6 25.1 - - + -
75G GLN* 4.7 0.2 - - - -
76G LEU* 3.1 30.6 + - + +
85G GLN* 1.3 77.6 - - - +
87G THR* 1.3 70.4 + - - +
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Residues in contact with THR 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 4.7 2.2 - - - -
73G VAL* 5.2 3.6 - - - +
74G VAL* 2.8 26.4 + - - -
75G GLN* 5.3 0.9 - - - -
86G ALA* 1.3 81.9 - - - +
88G GLN* 1.3 86.0 + - - +
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Residues in contact with GLN 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 3.5 42.3 - - + +
73G VAL* 4.4 0.5 - - - +
74G VAL* 3.2 38.2 + - + +
87G THR* 1.3 94.5 + - - +
89G MET* 1.3 72.0 + - - +
90G LEU* 5.6 7.5 - - + +
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Residues in contact with MET 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G LYS* 6.4 1.1 - - - -
71G THR* 3.6 24.7 - - + -
72G PHE* 3.3 20.6 - - - +
73G VAL* 5.0 9.2 - - - +
74G VAL* 4.8 0.4 - - - -
88G GLN* 1.3 83.9 + - - +
90G LEU* 1.3 76.2 - - - +
91G LYS* 5.5 5.8 - - + -
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Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL 6.1 0.4 - - - +
5G GLN* 5.7 1.6 - - - -
6G CYS* 4.7 11.7 - - + +
8G VAL* 4.6 6.5 - - + -
71G THR* 3.2 6.5 - - - +
72G PHE* 3.1 57.9 + - + +
88G GLN* 5.6 7.6 - - + +
89G MET* 1.3 83.7 - - - +
91G LYS* 1.4 69.9 + - - +
94G ASN* 3.4 20.4 - - + +
95G LEU* 4.3 30.3 - - + -
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Residues in contact with LYS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084 THR* 5.6 4.7 - - - +
1114 ASN* 2.6 27.7 + - - +
8G VAL* 5.1 2.8 - - - +
70G GLN 3.7 6.5 - - - +
71G THR* 3.7 21.8 - - + +
72G PHE* 4.3 4.3 - - - -
89G MET* 5.5 5.2 - - + -
90G LEU* 1.4 83.4 - - - +
92G LEU* 1.3 67.6 + - - +
93G GLN* 2.5 51.4 + - - +
94G ASN* 3.4 27.8 + - + +
95G LEU* 4.1 2.9 + - - +
179G GLN* 6.0 0.9 - - - -
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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