Contacts of the strand formed by residues 84 - 89 (chain X) in PDB entry 2FO6
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 ARG 84 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4X ASN* 3.4 30.3 - - + +
5X SER* 5.6 0.2 - - - +
16X LYS* 5.5 7.5 - - - +
52X HIS* 2.9 29.1 + - + -
53X MET 5.4 0.3 + - - +
54X LYS* 6.3 0.6 - - - +
82X GLU* 2.7 54.6 + - + +
83X TRP* 1.3 75.6 - - + +
85X TYR* 1.3 60.1 + - - +
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Residues in contact with TYR 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X SER* 4.5 3.1 - - - -
4X ASN 3.0 8.1 + - - -
5X SER* 3.2 33.4 - - - +
6X PHE* 3.8 4.6 + - - -
31X LEU* 3.9 33.4 - - + -
35X ARG* 5.3 0.2 - - - -
50X LEU* 4.0 16.8 - - + -
51X LYS 3.6 7.9 - - - +
52X HIS* 4.1 13.5 - + + +
61X LEU* 3.8 27.6 - - + -
67X VAL* 5.3 2.7 - - + +
70X VAL* 3.2 29.4 - - + +
71X GLN* 5.9 0.6 - - - -
81X ALA* 6.4 0.7 - - + -
82X GLU 3.5 21.1 + - - -
83X TRP* 3.7 37.6 - + + -
84X ARG* 1.3 78.3 - - - +
86X ASP* 1.3 60.6 + - - +
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Residues in contact with ASP 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X PHE* 3.4 30.0 - - + +
10X LYS* 2.7 34.2 + - - -
50X LEU* 3.3 6.3 - - - +
51X LYS* 2.9 44.5 + - + +
52X HIS* 5.1 0.4 - - - +
53X MET* 3.7 28.3 - - + +
85X TYR* 1.3 74.9 - - - +
87X LEU* 1.3 71.5 + - - +
88X GLN* 3.9 9.4 + - - +
120X GLN* 4.3 1.0 + - - -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X SER* 4.2 8.3 - - - +
6X PHE 3.4 26.5 - - - +
7X ASN 5.2 0.2 - - - -
8X PRO* 4.3 12.8 - - + -
10X LYS* 3.2 8.5 + - - -
32X LEU* 3.5 31.6 - - + -
35X ARG* 4.1 29.8 - - + -
36X ILE* 5.3 0.7 - - + -
48X LEU* 4.0 20.4 - - + -
49X ARG 3.5 6.1 - - - +
50X LEU* 4.1 11.9 - - + -
86X ASP* 1.3 79.8 + - - +
88X GLN* 1.3 61.2 + - - +
113X GLN* 2.7 34.9 + - - +
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Residues in contact with GLN 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X LEU* 3.5 7.2 - - - -
49X ARG 2.9 33.7 + - - +
51X LYS* 2.7 40.7 + - + +
53X MET* 4.7 1.6 - - - -
60X TRP* 3.5 21.5 - - + -
86X ASP* 3.9 5.9 + - - +
87X LEU* 1.3 83.6 - - - +
89X ILE* 1.3 63.6 + - - +
90X ARG 3.6 0.3 + - - -
113X GLN* 3.5 7.6 - - - +
117X ASP* 2.8 35.7 + - - +
120X GLN* 2.9 26.3 + - - +
122X TYR* 3.4 14.3 - - - -
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Residues in contact with ILE 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X GLY 3.7 2.5 - - - -
48X LEU* 4.0 24.2 - - + +
60X TRP* 3.5 12.6 - - - -
88X GLN* 1.3 74.1 - - - +
90X ARG* 1.3 58.0 + - - +
91X TYR 3.3 28.0 - - - +
92X LEU* 4.3 17.0 - - + -
110X PHE* 4.1 34.5 - - + +
113X GLN* 4.1 7.8 - - + +
114X LEU* 4.0 42.0 - - + +
117X ASP* 3.8 6.2 + - + +
207X PHE* 6.5 0.2 - - + -
216X ILE* 5.6 2.5 - - + -
217X ASP* 5.9 2.2 - - - +
218X GLN 5.1 2.9 - - - +
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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