Contacts of the strand formed by residues 87 - 92 (chain B) in PDB entry 2XFN
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 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 1.3 79.4 - - - +
88B LEU* 1.3 67.3 + - - +
89B ILE* 4.7 0.2 - - - +
98B PRO* 3.6 33.3 - - + +
99B PHE 3.6 9.4 - - - +
100B ARG* 3.5 36.3 - - + +
309B LYS 2.9 26.7 + - - -
310B ASP* 2.9 27.2 + - - +
311B TYR* 3.3 24.6 + - + +
312B CYS* 2.9 21.8 + - - -
313B GLY 4.6 0.5 + - - -
314B THR 4.8 0.2 - - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.7 28.9 - - + +
86B GLU 4.1 5.6 - - - +
87B ARG* 1.3 79.4 - - - +
89B ILE* 1.3 61.2 + - - +
98B PRO* 3.2 5.7 - - - +
99B PHE* 2.8 71.0 + - + +
100B ARG* 4.5 5.8 - - + -
101B GLY 3.8 13.0 - - - +
312B CYS* 4.1 2.7 - - - -
314B THR* 3.8 27.1 - - + +
316B ILE* 5.3 0.2 - - + -
1501B XCG 3.6 31.2 - - + +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG 4.7 0.7 - - - +
88B LEU* 1.3 80.4 - - - +
90B HIS* 1.3 68.9 + - - +
91B HIS 4.0 0.7 - - - +
96B SER* 3.6 30.3 - - - +
97B TYR 3.8 4.3 - - - +
98B PRO* 4.6 4.3 - - + -
99B PHE* 3.6 6.3 - - - -
311B TYR* 3.7 47.8 - - + -
313B GLY 6.3 0.4 - - - +
314B THR 3.0 13.7 + - - +
315B MET* 3.5 8.8 - - + -
316B ILE* 2.8 28.9 + - - +
371B VAL* 3.7 28.5 - - + +
372B LEU* 3.9 14.1 - - + -
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 1.3 74.0 - - - +
91B HIS* 1.3 65.1 + - - +
92B VAL* 4.1 25.3 - - + +
97B TYR* 2.8 48.1 + - + +
99B PHE* 3.6 5.8 - - + -
104B PRO* 3.5 38.1 - - + +
105B PRO 5.5 1.4 + - - -
115B HIS* 6.1 2.7 - + - -
164B LEU* 4.0 23.0 - - + +
167B LEU* 5.7 0.2 - - - +
316B ILE* 3.3 30.6 - - + +
318B ASP* 4.7 11.6 + - - +
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.0 0.8 - - - +
90B HIS* 1.3 73.5 - - - +
92B VAL* 1.3 62.9 + - - +
94B GLY* 3.4 23.8 - - - -
95B LYS* 3.3 24.2 - - - -
96B SER* 2.8 25.5 + - - +
316B ILE 2.8 14.3 + - - +
317B ILE* 4.2 15.0 - - + -
318B ASP* 3.0 28.7 + - - +
367B LEU* 5.6 2.1 - - + +
370B LYS* 4.3 13.0 - - + +
371B VAL* 3.7 43.5 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 4.1 28.7 - - + +
91B HIS* 1.3 76.9 - - - +
93B LYS* 1.3 89.3 - - + +
94B GLY 3.1 2.0 + - - -
95B LYS* 2.9 14.9 + - - +
97B TYR* 3.5 33.5 + - + -
163B GLN* 5.2 8.5 - - - +
318B ASP* 4.6 11.7 - - + +
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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