Contacts of the helix formed by residues 339 - 349 (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 GLU 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B GLY* 5.6 3.6 - - - -
289B ASN* 3.6 32.4 + - - +
338B LEU* 1.3 76.3 - - - +
340B PRO* 1.4 73.5 - - + +
342B VAL* 4.0 2.8 - - - +
343B ALA* 3.0 26.6 + - - +
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Residues in contact with PRO 340 (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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282B HIS* 5.5 8.7 - - + -
285B LEU* 4.5 32.1 - - + +
288B LEU* 4.7 2.5 - - + +
319B MET 4.6 11.2 - - - +
320B MET* 3.5 33.3 - - + +
338B LEU* 3.5 7.0 - - - +
339B GLU* 1.4 97.5 - - + +
341B THR* 1.3 60.3 + - - +
343B ALA* 3.5 6.3 - - + +
344B LEU* 3.4 24.1 + - - +
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Residues in contact with THR 341 (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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320B MET* 3.9 30.1 + - + +
321B PHE* 4.1 8.5 - - + -
338B LEU* 3.5 24.4 + - + +
340B PRO* 1.3 76.4 - - - +
342B VAL* 1.3 63.3 + - - +
344B LEU* 3.2 10.1 + - - +
345B LEU* 2.9 31.3 + - - +
366B PHE* 4.3 4.0 - - + -
385B PHE* 3.4 47.0 - - + -
388B LEU* 5.5 1.4 - - - +
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Residues in contact with VAL 342 (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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338B LEU* 3.2 26.3 + - + +
339B GLU* 4.2 3.4 - - - +
341B THR* 1.3 76.7 + - - +
343B ALA* 1.3 64.8 + - - +
345B LEU* 3.4 17.5 + - + +
346B ARG* 3.2 21.3 + - - +
388B LEU* 4.8 10.8 - - + -
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Residues in contact with ALA 343 (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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288B LEU* 3.6 33.4 - - + +
289B ASN* 3.8 15.0 - - - +
339B GLU 3.0 18.9 + - - +
340B PRO* 3.5 8.7 - - + +
342B VAL* 1.3 78.9 - - - +
344B LEU* 1.3 60.2 + - - +
346B ARG* 3.4 16.0 + - - +
347B TRP* 3.1 22.8 + - - -
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Residues in contact with LEU 344 (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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288B LEU* 3.9 16.6 - - + -
300B LEU* 3.4 33.4 - - + -
320B MET* 4.5 20.4 - - + -
340B PRO 3.4 13.4 + - - +
341B THR* 3.2 5.8 + - - +
343B ALA* 1.3 75.6 - - - +
345B LEU* 1.3 65.2 + - - +
347B TRP* 3.2 18.0 + - + +
348B LEU* 3.6 9.2 + - - +
362B ALA* 3.8 13.3 - - + +
365B LEU* 3.9 22.7 - - + -
366B PHE* 3.5 39.9 - - + -
369B ILE* 5.1 2.7 - - + -
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Residues in contact with LEU 345 (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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341B THR 2.9 19.6 + - - +
342B VAL* 3.7 16.8 - - + +
343B ALA 3.4 0.2 - - - -
344B LEU* 1.3 73.3 - - - +
346B ARG* 1.3 64.0 + - - +
348B LEU* 3.3 21.6 + - + +
349B SER* 3.4 16.3 + - - -
366B PHE* 4.6 3.8 - - + -
385B PHE* 4.3 16.8 - - + -
388B LEU* 4.4 23.3 - - + +
389B LEU* 3.4 24.2 - - + -
392B THR* 3.2 37.4 - - + +
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Residues in contact with ARG 346 (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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288B LEU 2.7 29.3 + - - -
289B ASN* 3.3 15.3 + - - +
290B GLY 3.1 13.5 + - - -
291B LYS* 4.0 32.6 + - - +
342B VAL* 3.2 12.6 + - + +
343B ALA* 3.4 13.6 + - - +
344B LEU 3.2 0.2 - - - -
345B LEU* 1.3 75.3 - - - +
347B TRP* 1.3 91.3 + - + +
349B SER* 3.4 15.1 + - - -
350B GLN* 3.4 26.8 + - - +
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Residues in contact with TRP 347 (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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288B LEU* 3.8 17.3 + - - +
290B GLY 3.8 1.6 - - - -
291B LYS 4.3 3.4 - - - -
292B ASP 3.8 12.8 - - - -
293B PRO* 3.9 16.2 - - + -
296B SER* 3.2 37.5 - - - -
300B LEU* 4.3 13.5 - - + -
343B ALA 3.1 28.1 + - - -
344B LEU* 3.2 13.9 + - + +
346B ARG* 1.3 107.2 - - - +
348B LEU* 1.3 57.4 + - - +
350B GLN* 3.6 30.5 + - + +
358B CYS* 3.5 44.2 - - + +
359B SER* 2.6 32.3 + - - -
362B ALA* 4.2 3.1 - - + -
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Residues in contact with LEU 348 (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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344B LEU 3.9 8.7 - - - +
345B LEU* 3.3 22.6 + - + +
347B TRP* 1.3 78.4 - - - +
349B SER* 1.3 56.8 + - - +
359B SER* 3.6 27.1 - - - +
362B ALA* 3.7 16.8 - - + -
363B LEU* 3.6 31.4 - - + +
366B PHE* 4.2 15.5 - - + -
389B LEU* 4.5 0.2 - - + -
392B THR* 4.6 13.0 - - - +
393B ILE* 4.3 14.4 - - + -
396B GLN* 2.9 23.8 + - + +
415B ARG* 2.8 27.0 + - - -
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Residues in contact with SER 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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345B LEU 3.4 11.9 + - - -
346B ARG* 3.4 11.3 + - - -
348B LEU* 1.3 73.1 - - - +
350B GLN* 1.3 66.3 + - - +
351B PRO* 3.7 2.1 - - - +
392B THR* 5.2 10.0 - - - +
396B GLN* 4.8 1.8 - - - +
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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