Contacts of the helix formed by residues 309 - 321 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 4.5 9.4 - - + +
268A ALA* 3.9 31.2 - - + +
269A ASP* 5.9 0.2 - - - -
272A THR* 4.3 9.0 - - + -
305A ALA 4.3 5.4 - - - +
306A PHE 2.9 19.7 + - - +
307A CYS 3.6 3.4 - - - +
308A SER* 1.3 85.8 + - - +
310A THR* 1.3 66.4 + - - +
311A GLN* 3.8 15.3 - - - +
312A LEU* 3.2 28.5 + - + -
313A ARG 3.0 10.4 + - - -
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A CYS 4.8 1.6 - - - -
308A SER 3.9 4.2 + - - -
309A VAL* 1.3 71.8 - - - +
311A GLN* 1.3 77.9 + - + +
313A ARG* 3.2 16.8 + - - +
314A HIS* 3.2 47.7 + - + +
372A ASP* 4.4 0.6 - - - +
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 6.1 1.1 - - - -
272A THR* 3.7 24.4 - - + +
309A VAL* 3.4 15.1 - - - +
310A THR* 1.3 87.6 + - + +
312A LEU* 1.3 64.9 + - - +
314A HIS* 3.5 14.4 + - + +
315A MET* 3.3 31.3 + - + +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 4.1 4.9 - - + -
268A ALA 4.6 2.5 - - - +
271A LEU* 4.0 16.4 - - + +
272A THR* 3.5 39.0 - - + +
277A PHE* 3.6 30.2 - - + -
281A LEU* 5.0 0.2 - - - +
306A PHE* 3.4 45.4 - - + +
309A VAL* 3.2 26.8 + - + +
311A GLN* 1.3 74.9 - - - +
313A ARG* 1.3 60.5 + - - +
315A MET* 3.4 7.4 + - - +
316A LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE 3.7 2.8 + - - -
307A CYS* 3.5 39.3 + - + +
309A VAL 3.0 12.5 + - - +
310A THR* 3.2 17.1 + - - +
312A LEU* 1.3 73.8 - - - +
314A HIS* 1.3 58.5 + - - +
316A LEU* 3.5 5.6 + - - +
317A THR* 2.7 44.3 + - - +
368A GLU* 3.3 31.2 + - - +
369A ILE* 5.6 0.4 - - + -
371A GLU* 3.2 35.2 + - - +
372A ASP* 3.1 40.6 + - + +
375A ASP* 4.9 9.3 + - - +
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 3.2 40.9 + - + +
311A GLN* 3.6 14.6 - - + +
313A ARG* 1.3 78.6 - - - +
315A MET* 1.3 58.3 + - + +
317A THR* 3.4 1.2 + - - -
318A GLN* 2.9 35.9 + - - +
372A ASP* 2.9 35.5 + - - +
375A ASP* 5.8 2.9 - - + -
376A ALA* 4.7 18.3 - - + +
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Residues in contact with MET 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 3.5 32.8 - - - +
277A PHE* 3.6 35.7 - - + -
278A SER* 5.6 6.7 - - - -
281A LEU* 4.0 4.6 - - + +
311A GLN* 3.3 18.7 + - + +
312A LEU* 3.4 10.1 + - - +
313A ARG 3.4 0.2 - - - -
314A HIS* 1.3 76.9 - - + +
316A LEU* 1.3 58.0 + - - +
318A GLN* 4.0 4.0 - - - +
319A MET* 3.1 34.4 + - + +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LEU* 3.7 19.4 - - + +
285A LEU* 4.0 20.4 - - + -
303A LEU* 3.8 29.2 - - + +
306A PHE* 4.8 6.7 - - + -
307A CYS* 3.7 28.7 - - - -
312A LEU 3.0 17.7 + - - +
313A ARG 3.8 3.4 - - - +
315A MET* 1.3 74.3 - - - +
317A THR* 1.3 60.6 + - - +
319A MET* 3.2 4.1 + - - +
320A MET* 2.9 56.0 + - + +
365A LEU* 4.0 12.8 - - + -
369A ILE* 4.5 4.0 - - + -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ARG* 2.7 23.6 + - - +
314A HIS 3.7 1.3 - - - -
316A LEU* 1.3 76.7 - - - +
318A GLN* 1.3 60.9 + - - +
320A MET* 3.2 13.4 + - - +
321A PHE* 3.3 18.1 + - + -
369A ILE* 3.4 30.4 - - - +
372A ASP* 3.2 29.9 + - - +
373A VAL* 3.3 33.2 - - + +
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A HIS* 2.9 19.2 + - - +
315A MET* 4.2 4.7 - - - +
317A THR* 1.3 75.1 - - - +
319A MET* 1.3 60.7 + - - +
321A PHE* 3.1 26.1 - - - +
322A GLU* 3.7 10.6 - - + +
378A ASN* 5.1 8.0 + - - -
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Residues in contact with MET 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A SER* 3.1 40.2 - - - +
281A LEU* 3.8 20.6 - - + -
282A HIS* 3.6 49.5 + - + +
285A LEU* 3.7 17.7 - - + -
315A MET* 3.1 22.4 + - + +
316A LEU* 3.2 6.0 + - - +
318A GLN* 1.3 75.2 - - - +
320A MET* 1.3 63.1 + - - +
322A GLU* 4.6 9.1 + - - +
340A PRO* 4.6 8.1 - - - +
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Residues in contact with MET 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.1 13.0 - - + +
303A LEU* 5.9 0.2 - - + -
316A LEU* 2.9 42.9 + - + +
317A THR* 3.2 12.7 + - - +
319A MET* 1.3 79.9 - - - +
321A PHE* 1.3 67.4 + - + +
322A GLU 3.9 1.6 + - - -
337A CYS 5.6 1.6 - - - +
338A LEU* 6.2 0.3 - - - -
340A PRO* 3.5 38.4 - - - +
341A THR* 3.9 22.3 + - + +
344A LEU* 4.3 17.3 - - + -
365A LEU* 5.3 5.6 - - + -
369A ILE* 3.9 31.4 - - + -
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.3 22.9 + - + +
318A GLN* 3.1 16.6 - - - +
320A MET* 1.3 83.3 - - + +
322A GLU* 1.3 59.9 + - - +
341A THR* 4.1 10.5 - - + -
369A ILE* 3.5 32.5 - - + -
370A PHE* 4.1 11.2 - + - -
373A VAL* 3.5 31.9 - - + -
381A SER* 3.8 31.5 + - - +
382A ALA* 4.0 14.4 - - + -
385A PHE* 3.4 43.1 - + + -
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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