Contacts of the strand formed by residues 81 - 86 (chain T) in PDB entry 5IY8
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 HIS 81 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T LEU* 3.7 35.4 - - + +
55T SER* 3.2 2.3 - - - -
56T PHE* 2.7 69.6 + + + +
58T LEU* 4.5 18.2 - - + -
80T GLU* 1.3 80.4 - - - +
82T PRO* 1.3 68.2 - - - +
83T PHE* 3.6 2.9 - - - -
116T CYS* 3.4 25.1 - - - -
117T ARG 4.0 4.0 - - - +
118T PRO* 5.3 7.0 - - + -
119T ALA* 5.3 2.2 - - + -
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Residues in contact with PRO 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54T VAL 3.6 9.9 - - - +
55T SER* 4.2 3.8 - - - -
80T GLU* 3.4 18.2 - - + +
81T HIS* 1.3 84.6 - - - +
83T PHE* 1.3 66.8 + - - +
84T VAL* 5.9 0.9 - - + -
116T CYS* 3.6 0.2 - - - -
117T ARG* 3.0 56.7 + - + +
118T PRO 5.2 1.3 - - - -
119T ALA* 4.5 7.2 - - + +
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Residues in contact with PHE 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127S PHE* 5.0 11.0 - + - -
19T TRP* 6.0 5.6 - + - -
21T VAL* 3.5 38.4 - - + -
23T VAL* 4.9 4.0 - - + -
31T TRP* 6.1 1.8 - + - -
43T LEU* 3.8 22.7 - - + -
54T VAL* 3.0 44.9 + - + +
56T PHE* 3.8 25.6 - + + -
81T HIS 3.6 5.8 - - - -
82T PRO* 1.3 82.8 - - - +
84T VAL* 1.3 63.5 + - - +
85T LEU* 4.1 7.7 + - + +
114T ALA* 4.7 13.5 - - + -
115T GLU 3.6 3.6 - - - -
116T CYS* 4.0 21.5 - - + -
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Residues in contact with VAL 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LYS* 5.6 8.5 - - - +
82T PRO* 5.5 1.6 - - + -
83T PHE* 1.3 76.3 - - - +
85T LEU* 1.3 73.6 + - - +
86T GLN* 4.0 5.4 - - + +
114T ALA* 3.1 4.3 - - - -
115T GLU* 2.7 45.4 + - + +
117T ARG* 3.5 31.0 - - + -
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Residues in contact with LEU 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T TRP* 4.1 26.2 - - + -
52T THR* 6.2 3.6 - - + -
54T VAL* 5.5 13.0 - - + -
83T PHE* 4.2 10.1 + - + +
84T VAL* 1.3 84.9 - - - +
86T GLN* 1.3 61.2 + - - +
112T GLN* 4.1 22.7 - - + +
113T ARG 3.6 2.0 - - - -
114T ALA* 3.9 16.8 - - + -
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Residues in contact with GLN 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B SER 5.9 0.4 + - - -
551B GLU* 4.3 24.0 + - - +
555B GLU* 5.6 0.6 + - - -
124S TYR* 6.0 0.7 - - - -
22T LYS* 5.3 4.7 - - - +
84T VAL* 4.0 10.1 - - + +
85T LEU* 1.3 78.0 - - - +
87T SER* 1.3 63.0 + - - +
88T VAL* 3.8 1.1 + - - +
112T GLN* 2.6 28.8 + - - +
113T ARG* 2.8 53.3 + - + +
114T ALA* 3.4 27.6 + - - +
115T GLU* 4.2 20.3 + - + +
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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