Contacts of the strand formed by residues 348 - 353 (chain B) in PDB entry 6FY5
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 ASN 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LYS* 3.3 34.2 - - - +
198B SER* 4.9 1.2 + - - -
307B LYS 3.3 4.2 + - - -
308B SER* 3.1 12.6 - - - -
309B VAL* 3.0 24.3 + - - +
346B LEU* 3.7 1.1 - - - +
347B LYS* 1.3 90.8 + - - +
349B VAL* 1.3 65.1 + - - +
350B TYR* 3.6 32.8 + - + -
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Residues in contact with VAL 349 (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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196B LYS 2.9 8.5 + - - +
197B LEU* 3.5 12.6 - - + -
198B SER* 2.9 25.6 + - - -
298B LEU* 4.6 2.2 - - + -
309B VAL* 3.2 22.0 - - + +
311B PHE* 3.9 29.6 - - + -
334B ILE* 4.1 5.6 - - + -
338B PHE* 3.3 38.8 - - + -
346B LEU* 5.0 1.1 - - + -
348B ASN* 1.3 77.4 - - - +
350B TYR* 1.3 65.6 + - - +
351B PHE* 3.9 19.8 - - + -
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Residues in contact with TYR 350 (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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185B ILE* 3.6 22.4 - - + -
198B SER* 3.3 19.1 - - - -
200B THR* 3.4 23.3 - - + +
210B MET* 5.4 2.0 - - - -
211B ARG 4.8 9.3 + - - -
212B VAL* 3.7 31.0 - - + -
308B SER* 4.2 4.0 - - - -
309B VAL 2.8 7.6 + - - +
310B ALA* 3.2 14.4 - - + -
311B PHE* 2.8 31.9 + - - +
348B ASN* 3.6 36.8 + - + -
349B VAL* 1.3 76.4 - - - +
351B PHE* 1.3 59.7 + - - +
352B LEU* 3.8 6.5 - - + -
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Residues in contact with PHE 351 (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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197B LEU* 4.1 26.5 - - + -
198B SER 2.9 18.0 + - - -
199B LEU* 3.5 26.9 - - + -
200B THR 2.9 27.0 + - - +
311B PHE* 3.6 8.1 - + + -
330B THR* 3.9 14.4 - - + -
331B LEU* 3.8 26.0 - - + -
334B ILE* 3.5 32.8 - - + -
349B VAL* 3.9 15.0 - - + -
350B TYR* 1.3 74.7 - - - +
352B LEU* 1.3 64.6 + - - +
353B LEU* 3.5 6.2 + - + +
362B TYR* 4.5 9.4 - + + -
366B MET* 5.3 0.4 - - - -
1001B EDO 3.7 26.5 - - - -
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Residues in contact with LEU 352 (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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183B PHE* 4.7 0.2 - - + -
200B THR* 3.7 12.8 - - - -
202B SER* 3.4 25.8 - - - +
207B ILE* 3.9 17.5 - - + -
210B MET* 3.1 48.0 - - + -
215B ILE* 5.0 2.7 - - + -
310B ALA* 4.0 17.3 - - + -
311B PHE 2.9 13.3 + - - +
312B PRO* 3.8 21.1 - - + -
313B PRO* 3.3 13.0 - - + +
350B TYR* 4.4 4.9 - - + -
351B PHE* 1.3 70.1 - - - +
353B LEU* 1.3 56.9 + - - +
354B PHE* 4.9 2.9 - - + -
1001B EDO 2.7 24.6 + - - -
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Residues in contact with LEU 353 (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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199B LEU* 4.0 20.6 - - + -
200B THR 3.0 12.3 + - - +
201B GLN* 3.6 6.1 + - - -
202B SER* 3.1 22.4 + - - -
313B PRO* 4.6 1.6 - - - -
351B PHE* 3.9 8.1 - - + +
352B LEU* 1.3 74.3 - - - +
354B PHE* 1.3 64.5 + - - +
358B SER* 4.0 7.6 - - - -
359B ILE* 3.8 32.2 - - + +
362B TYR* 3.7 40.4 - - + -
1001B EDO 3.3 22.7 - - - +
1002B EDO 3.5 22.0 - - - -
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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