Contacts of the strand formed by residues 252 - 262 (chain L) in PDB entry 5FHX
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 THR 252 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253H PHE* 5.7 1.1 - - + -
274H LYS* 4.5 19.5 + - + +
275H ASP* 5.4 2.0 - - - +
247L GLN* 3.3 47.7 + - + +
248L LEU* 3.9 7.6 - - - +
250L SER* 4.8 8.3 - - - -
251L GLY* 1.3 79.4 - - - +
253L ALA* 1.3 69.2 + - - +
303L THR* 4.3 13.2 - - - +
304L LEU 4.0 9.7 + - - -
305L SER* 4.8 1.3 - - - +
306L LYS* 4.4 3.9 - - - +
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Residues in contact with ALA 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L PRO* 3.9 13.7 - - + -
247L GLN* 4.0 2.0 - - - -
248L LEU* 4.0 7.0 - - + -
252L THR* 1.3 79.2 + - - +
254L SER* 1.3 61.3 + - - +
255L VAL* 4.3 0.4 - - - -
302L LEU 3.7 2.4 - - - +
303L THR* 3.7 3.1 - - - +
304L LEU* 3.0 43.3 + - + +
305L SER 4.3 2.2 - - - +
306L LYS* 4.6 0.9 - - - -
309L TYR* 3.8 33.7 - - + -
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Residues in contact with SER 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255H LEU* 5.9 1.4 - - - +
272H LEU* 3.8 18.0 - - - +
274H LYS* 3.9 9.0 - - - -
241L PHE 4.2 0.3 - - - +
242L PRO 4.1 1.7 - - - +
243L PRO* 3.4 22.5 - - - +
247L GLN* 3.3 28.0 + - - +
253L ALA* 1.3 69.8 - - - +
255L VAL* 1.3 61.0 + - - +
256L VAL* 4.1 3.9 + - - +
301L THR* 3.7 16.8 - - - +
302L LEU 3.4 2.9 - - - -
303L THR* 3.4 23.2 - - - +
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Residues in contact with VAL 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240L ILE* 4.3 2.7 - - + -
241L PHE 3.4 15.5 - - - +
242L PRO* 4.5 0.4 - - + -
243L PRO* 4.2 14.6 - - + -
253L ALA 5.2 1.3 - - - +
254L SER* 1.3 75.2 - - - +
256L VAL* 1.3 60.6 + - - +
271L TRP* 3.5 28.6 - - + -
300L SER 3.4 1.6 - - - +
301L THR* 3.4 4.0 - - - -
302L LEU* 2.8 56.4 + - + +
304L LEU* 5.2 3.6 - - + -
309L TYR* 4.8 6.1 - - + -
315L TYR* 4.6 13.7 - - + -
332L PHE* 3.5 25.6 - - + -
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Residues in contact with VAL 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H LEU* 3.8 33.2 - - + -
272H LEU* 4.4 10.3 - - + -
310H SER* 4.3 13.5 - - - +
312H VAL* 5.8 2.0 - - + -
240L ILE* 3.4 7.3 - - - +
241L PHE* 2.8 55.4 + - + -
254L SER 4.1 2.6 + - - +
255L VAL* 1.3 75.7 - - - +
257L CYS* 1.3 69.8 + - - +
258L LEU* 4.7 2.0 - - + +
271L TRP* 3.9 1.1 - - - -
299L SER* 4.8 9.6 - - - -
300L SER 3.4 4.7 - - - +
301L THR* 3.5 26.5 - - + +
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Residues in contact with CYS 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238L VAL* 4.2 15.7 - - - -
239L PHE 3.4 10.5 - - - -
240L ILE* 4.9 1.3 - - - -
256L VAL* 1.3 77.5 - - - +
258L LEU* 1.3 62.2 + - - +
259L LEU* 4.3 10.0 - - + +
269L VAL* 4.9 0.4 - - + -
271L TRP* 3.6 15.3 - - + -
298L LEU 3.6 0.9 - - - +
299L SER* 3.2 6.8 - - - -
300L SER* 2.9 33.8 + - - +
317L CYS* 2.0 50.0 - - - -
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Residues in contact with LEU 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268H ALA* 4.0 14.8 - - + -
297H PHE* 3.6 24.2 - - + -
312H VAL* 3.8 33.4 - - + -
314H THR* 4.8 0.7 - - + -
237L SER 3.5 0.3 - - - +
238L VAL* 3.1 7.6 - - - +
239L PHE* 2.8 62.4 + - + +
241L PHE* 4.2 13.5 - - + -
256L VAL* 4.2 3.1 - - + -
257L CYS* 1.3 73.4 - - - +
259L LEU* 1.3 67.1 + - - +
260L ASN* 4.1 19.5 - - + +
297L SER* 4.9 0.4 - - - -
298L LEU 3.5 14.6 - - - +
299L SER* 4.7 1.6 - - - +
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Residues in contact with LEU 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L PRO* 4.0 11.7 - - + -
237L SER 3.7 3.4 - - - -
238L VAL* 4.4 2.2 - - + -
257L CYS* 4.3 10.3 - - - +
258L LEU* 1.3 76.1 - - - +
260L ASN* 1.3 58.8 + - - +
262L PHE* 3.5 22.9 - - + -
267L ALA* 4.4 13.2 - - + -
269L VAL* 3.7 32.8 - - + -
297L SER* 3.3 6.6 - - - -
298L LEU* 2.9 45.3 + - + +
319L VAL* 3.6 47.1 - - + -
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Residues in contact with ASN 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295H HIS* 3.1 27.0 - - - -
312H VAL* 4.6 0.5 - - - +
314H THR* 3.9 31.0 + - - +
236L PRO* 3.4 1.5 - - - +
237L SER* 2.8 53.0 + - - +
239L PHE* 4.2 4.9 - - + -
258L LEU* 3.8 21.3 - - + +
259L LEU* 1.3 72.9 - - - +
261L ASN* 1.3 92.4 + - - +
262L PHE 3.8 0.4 - - - -
297L SER* 4.0 2.5 - - - -
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Residues in contact with ASN 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H GLY* 6.0 0.9 - - - -
295H HIS* 3.1 27.5 + - - -
314H THR* 5.3 0.7 + - - -
234L ALA* 4.1 8.7 - - - +
235L ALA 3.5 11.6 - - - +
237L SER* 5.0 2.1 + - - +
260L ASN* 1.3 99.0 + - - +
262L PHE* 1.3 58.7 + - - +
290L ASP* 5.0 3.8 - - - +
293L ASP* 3.1 20.5 + - - +
295L THR* 2.8 27.5 + - + +
296L TYR 3.3 6.8 + - - -
297L SER* 3.1 12.1 + - - -
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Residues in contact with PHE 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L ALA 3.2 12.6 - - - +
236L PRO* 3.6 29.6 - - + -
259L LEU* 3.5 36.1 - - + -
261L ASN* 1.3 74.1 - - - +
263L TYR* 1.3 61.0 + - - +
264L PRO 3.6 13.7 - - - -
265L ARG* 3.3 33.7 - - - -
267L ALA* 4.2 8.7 - - + -
286L VAL* 4.9 0.9 - - + -
295L THR* 3.3 5.0 - - - -
296L TYR* 2.9 60.5 + - + -
297L SER* 3.7 5.4 - - - -
298L LEU* 3.8 17.5 - - + -
321L HIS* 3.8 12.8 - + - +
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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