Contacts of the strand formed by residues 311 - 317 (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 TYR 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.4 5.0 - - - +
87B ARG* 3.3 32.9 + - + +
89B ILE* 3.7 35.9 - - + -
96B SER* 5.3 5.0 - - - -
98B PRO* 3.8 23.4 - - + +
306B TRP* 3.1 35.2 + - + +
307B ARG* 3.4 7.1 - - - -
309B LYS* 3.8 27.1 - - + +
310B ASP* 1.3 83.5 - - - +
312B CYS* 1.3 64.2 + - - +
313B GLY 4.3 3.6 - - - +
371B VAL 5.3 1.4 + - - -
372B LEU* 3.5 35.1 + - + -
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Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASN* 3.1 31.6 + - - +
84B GLU* 3.9 9.2 - - - -
86B GLU* 3.3 38.7 - - - +
87B ARG 2.9 21.3 + - - -
88B LEU* 4.1 7.4 - - - -
306B TRP* 3.4 3.3 + - - -
311B TYR* 1.3 74.1 - - - +
313B GLY* 1.3 56.4 + - - +
314B THR* 3.4 32.5 - - - -
329B ASP* 3.1 18.7 - - - +
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Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG 4.6 0.2 + - - -
89B ILE* 6.5 0.2 - - - -
306B TRP* 3.5 18.5 - - - -
311B TYR* 3.3 5.7 - - - +
312B CYS* 1.3 78.8 - - - +
314B THR* 1.3 61.1 + - - +
315B MET* 3.9 7.2 - - - +
327B THR* 2.8 25.1 + - - +
328B LEU 3.9 4.2 - - - -
329B ASP* 4.1 8.3 - - - -
340B ILE* 4.0 11.9 - - - +
372B LEU* 5.0 6.3 - - - -
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Residues in contact with THR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASN 4.6 4.3 + - - -
84B GLU* 4.9 5.0 + - - +
87B ARG 4.8 0.2 - - - +
88B LEU* 3.8 27.7 - - + +
89B ILE* 3.0 24.1 + - - +
201B THR* 5.0 0.7 + - - +
312B CYS* 3.4 21.7 - - - -
313B GLY* 1.3 77.7 + - - +
315B MET* 1.3 67.9 + - - +
316B ILE* 4.9 3.1 - - + -
326B TYR* 3.9 26.5 - - + +
327B THR 3.2 13.7 - - - +
328B LEU* 3.4 17.0 - - + +
329B ASP 5.0 0.5 + - - -
1501B XCG 4.4 2.0 - - + +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.5 9.9 - - + -
313B GLY 3.9 8.5 - - - +
314B THR* 1.3 78.7 - - - +
316B ILE* 1.3 61.8 + - - +
317B ILE* 3.8 21.5 - - + +
325B ALA 3.8 0.2 - - - +
326B TYR* 3.2 10.3 - - - -
327B THR* 2.9 58.9 + - + +
340B ILE* 4.0 12.6 - - + -
368B TYR* 4.0 17.3 - - + -
371B VAL* 3.4 35.0 - - + -
372B LEU* 3.9 37.9 - - + -
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE 2.8 10.3 + - - +
90B HIS* 3.3 22.9 - - + +
91B HIS 2.8 25.1 + - - -
99B PHE* 3.7 28.9 - - + -
104B PRO* 4.2 7.4 - - + -
164B LEU* 4.2 4.3 - - + -
167B LEU* 3.8 20.9 - - + -
314B THR* 4.9 4.3 - - + -
315B MET* 1.3 74.5 - - - +
317B ILE* 1.3 61.2 + - - +
325B ALA 3.5 3.8 - - - -
326B TYR* 3.8 19.5 - - + -
1501B XCG 3.5 47.6 - - + +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B HIS* 3.8 20.4 - - + -
167B LEU* 3.5 7.6 - - - +
315B MET* 3.8 31.9 - - + +
316B ILE* 1.3 75.7 - - - +
318B ASP* 1.3 67.8 + - - +
319B GLY 4.1 1.0 + - - +
322B ALA* 3.5 26.6 - - + +
324B VAL 3.6 20.1 - - - +
325B ALA* 2.8 29.2 + - - +
327B THR* 4.7 9.4 - - + -
367B LEU* 3.9 24.5 - - + -
368B TYR* 4.8 1.1 - - + -
371B VAL* 4.0 17.3 - - + -
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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