Contacts of the helix formed by residues 309 - 321 (chain B) in PDB entry 5UFL
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 VAL 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 4.4 10.8 - - + +
268B ALA* 3.6 38.1 - - + +
269B ASP* 5.2 0.9 - - - +
272B THR* 4.4 5.2 - - + -
305B ALA 4.3 4.9 - - - +
306B PHE 2.9 19.5 + - - +
307B CYS 3.6 3.2 - - - +
308B SER* 1.3 85.6 - - - +
310B THR* 1.3 67.0 + - - +
311B GLN* 4.3 6.1 - - + +
312B LEU* 3.2 30.0 + - + +
313B ARG 3.0 10.2 + - - -
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B CYS 4.8 1.6 - - - -
308B SER 3.9 4.0 + - - -
309B VAL* 1.3 72.3 - - - +
311B GLN* 1.3 63.9 + - + +
313B ARG* 3.2 17.8 + - - +
314B HIS* 3.2 46.3 + - + +
372B ASP* 4.3 0.8 - - - +
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.7 26.9 - - + -
309B VAL* 3.4 3.2 - - + +
310B THR* 1.3 77.7 - - - +
312B LEU* 1.3 64.9 + - - +
314B HIS* 3.5 25.8 + - - +
315B MET* 3.3 43.6 + - + +
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Residues in contact with LEU 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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262B LEU* 4.0 9.9 - - + -
268B ALA 4.5 2.9 - - - +
271B LEU* 4.0 15.3 - - + +
272B THR* 3.5 40.1 - - + +
277B PHE* 3.6 31.0 - - + -
306B PHE* 3.4 43.8 - - + +
309B VAL* 3.2 22.7 + - + +
311B GLN* 1.3 75.1 - - - +
313B ARG* 1.3 59.4 + - - +
315B MET* 3.4 6.8 + - - +
316B LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 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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306B PHE 3.7 2.6 + - - -
307B CYS* 3.5 37.7 + - + +
309B VAL 3.0 12.6 + - - +
310B THR* 3.4 17.1 + - - +
312B LEU* 1.3 74.5 - - - +
314B HIS* 1.3 58.6 + - - +
316B LEU* 3.8 5.4 - - + +
317B THR* 2.7 44.2 + - - +
368B GLU* 3.3 32.8 + - - +
369B ILE* 5.2 0.7 - - + +
371B GLU* 3.2 35.0 + - - +
372B ASP* 3.1 39.9 + - + +
375B ASP* 4.9 9.1 + - - +
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B THR* 3.2 36.3 + - + +
311B GLN* 3.6 35.0 - - - +
312B LEU 3.3 0.4 - - - -
313B ARG* 1.3 76.9 - - - +
315B MET* 1.3 56.3 + - + +
317B THR* 3.4 1.4 + - - -
318B GLN* 2.9 35.6 + - - +
372B ASP* 2.9 35.8 + - - +
375B ASP* 5.7 3.6 - - + -
376B ALA* 4.5 19.8 - - + +
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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
----------------------------------------------------------
272B THR* 3.5 25.1 - - - +
277B PHE* 3.6 36.3 - - + -
278B SER* 6.1 3.1 - - - -
281B LEU* 4.0 4.7 - - + +
311B GLN* 3.3 40.4 + - + +
312B LEU* 3.7 11.4 - - - +
313B ARG 3.4 0.2 - - - -
314B HIS* 1.3 76.8 - - + +
316B LEU* 1.3 58.2 + - - +
318B GLN* 4.0 4.0 - - - +
319B MET* 3.1 33.8 + - + +
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Residues in contact with LEU 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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281B LEU* 3.7 19.9 - - + +
285B LEU* 4.0 19.5 - - + -
303B LEU* 3.8 29.4 - - + +
306B PHE* 4.8 6.1 - - + -
307B CYS* 3.7 29.4 - - - -
312B LEU 3.0 16.6 + - - +
313B ARG 3.8 3.8 - - - +
315B MET* 1.3 73.7 - - - +
317B THR* 1.3 59.8 + - - +
319B MET* 3.2 2.4 + - - +
320B MET* 2.9 55.2 + - + +
365B LEU* 4.0 13.2 - - + -
369B ILE* 4.5 4.3 - - + -
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG* 2.7 25.1 + - - +
314B HIS 3.7 1.6 - - - -
316B LEU* 1.3 77.3 - - - +
318B GLN* 1.3 60.5 + - - +
320B MET* 3.2 13.4 + - - +
321B PHE* 3.3 18.6 + - + -
369B ILE* 3.4 30.7 - - - +
372B ASP* 3.2 30.1 + - - +
373B VAL* 3.3 34.3 - - + -
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B HIS* 2.9 18.9 + - - +
315B MET* 4.2 4.3 - - - +
317B THR* 1.3 75.1 - - - +
319B MET* 1.3 61.3 + - - +
321B PHE* 3.1 26.2 - - - +
322B GLU* 3.7 9.9 - - + +
378B ASN* 4.8 11.9 + - - -
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Residues in contact with MET 319 (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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278B SER* 3.2 40.8 - - - +
281B LEU* 3.8 20.4 - - + -
282B HIS* 3.6 48.3 + - + +
285B LEU* 3.7 17.5 - - + -
315B MET* 3.1 23.3 + - + +
316B LEU* 3.5 5.6 - - - +
318B GLN* 1.3 75.5 - - - +
320B MET* 1.3 63.7 + - - +
322B GLU* 4.5 9.8 + - - +
340B PRO* 4.6 8.7 - - - +
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Residues in contact with MET 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 4.1 12.1 - - + -
288B LEU* 6.3 0.2 - - + -
316B LEU* 2.9 43.5 + - + +
317B THR* 3.2 12.3 + - - +
319B MET* 1.3 79.1 - - - +
321B PHE* 1.3 67.3 + - + +
322B GLU 3.8 2.3 + - - -
338B LEU* 5.7 6.1 - - - +
340B PRO* 3.5 39.5 - - - +
341B THR* 3.9 22.2 + - + +
344B LEU* 4.5 16.4 - - + -
365B LEU* 5.2 5.8 - - + -
369B ILE* 3.9 33.0 - - + -
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B THR* 3.3 23.8 + - + +
318B GLN* 3.1 17.0 - - - +
320B MET* 1.3 81.4 - - + +
322B GLU* 1.3 60.2 + - - +
341B THR* 4.1 10.3 - - + -
369B ILE* 3.5 32.1 - - + -
370B PHE* 4.1 11.2 - + - -
373B VAL* 3.5 32.5 - - + -
381B SER* 3.8 30.9 + - - +
382B ALA* 4.0 13.2 - - + -
385B PHE* 3.4 42.4 - + + -
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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