Contacts of the strand formed by residues 312 - 316 (chain B) in PDB entry 1FUU
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 ILE 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B LEU* 6.3 0.7 - - + -
254B TYR* 3.2 42.8 - - + +
262B ALA 3.5 2.7 - - - +
264B ILE* 3.9 19.3 - - + -
279B LEU* 4.4 17.3 - - + -
284B PHE* 4.0 24.9 - - + -
285B THR 4.4 4.6 + - - +
286B VAL* 3.6 27.3 - - + -
287B SER* 3.1 23.9 + - - -
305B PHE* 3.8 5.8 - - - -
310B SER* 3.4 0.9 - - - +
311B ARG* 1.3 80.5 - - + +
313B LEU* 1.3 65.3 + - - +
314B ILE* 3.8 14.8 - - + -
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Residues in contact with LEU 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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262B ALA 3.1 7.7 + - - +
263B VAL* 3.2 23.4 - - + +
264B ILE 2.9 23.5 + - - -
287B SER* 3.2 31.0 - - - +
289B ILE* 3.9 24.0 - - + -
302B MSE 4.0 21.8 - - + -
305B PHE* 3.4 44.0 - - + -
312B ILE* 1.3 75.2 - - - +
314B ILE* 1.3 63.3 + - - +
315B SER* 5.4 3.1 - - - -
323B ILE* 4.9 10.1 - - + -
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Residues in contact with ILE 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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264B ILE* 3.5 15.5 - - + +
266B CYS* 4.5 2.9 - - - -
272B VAL* 3.3 35.1 - - + +
275B LEU* 3.5 39.7 - - + -
276B THR* 3.8 14.1 - - - +
279B LEU* 3.5 12.6 - - + -
286B VAL* 3.4 26.2 - - + -
287B SER 2.9 8.0 + - - +
288B ALA* 3.4 3.3 - - - -
289B ILE* 3.1 24.8 + - - +
312B ILE* 3.8 8.1 - - + -
313B LEU* 1.3 75.9 - - - +
315B SER* 1.3 64.8 + - - +
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Residues in contact with SER 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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263B VAL* 5.7 1.6 - - - -
264B ILE 3.2 10.2 + - - +
265B PHE* 3.4 5.6 - - - -
266B CYS 3.3 20.4 + - - -
272B VAL* 3.8 10.4 - - - +
289B ILE* 3.3 15.8 + - - -
313B LEU* 4.1 6.8 + - - -
314B ILE* 1.3 76.7 - - - +
316B THR* 1.3 70.5 + - - +
319B LEU* 3.3 27.0 - - - +
323B ILE* 3.3 25.9 - - - +
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Residues in contact with THR 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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265B PHE* 3.5 13.5 - - - -
266B CYS 3.6 7.6 - - - -
267B ASN 5.4 2.2 - - - -
268B THR 3.8 3.1 - - - +
269B ARG* 3.6 31.6 - - + +
272B VAL* 3.5 21.3 - - + -
289B ILE 4.0 1.2 + - - +
290B TYR* 5.0 6.5 - - + -
291B SER* 3.7 24.7 + - - +
315B SER* 1.3 87.2 + - - +
317B ASP* 1.3 63.9 + - - +
318B LEU* 3.4 8.7 + - - +
319B LEU* 3.5 10.2 + - - +
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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