Contacts of the helix formed by residues 326 - 340 (chain A) in PDB entry 5ULM
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 ASP 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ALA* 5.9 1.4 - - - +
321A TYR* 2.9 36.3 + - + +
322A ARG* 4.8 0.2 - - - +
324A ILE* 3.1 16.3 + - + +
325A GLN* 1.3 69.1 - - - +
327A TYR* 1.3 63.6 + - - +
328A ASP* 3.7 8.1 + - - +
329A SER* 2.6 35.1 + - - -
330A ILE* 3.3 20.8 + - - +
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Residues in contact with TYR 327 (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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322A ARG* 3.8 14.1 - - + +
325A GLN* 3.3 43.5 + - + +
326A ASP* 1.3 71.1 + - - +
328A ASP* 1.3 59.9 + - - +
330A ILE* 3.1 14.3 + - + +
331A VAL* 2.9 33.9 + - - +
357A PHE* 3.8 24.1 - + - -
358A ALA* 3.7 36.3 - - + +
361A ARG* 3.5 30.9 - - + +
362A ARG* 4.3 11.0 - - + +
509A TRP* 3.3 30.3 - - - +
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 3.3 6.9 - - - +
327A TYR* 1.3 78.0 - - - +
329A SER* 1.3 56.3 + - - +
331A VAL* 3.3 1.4 + - - +
332A LYS* 3.0 63.4 + - - +
362A ARG* 2.9 42.2 + - + +
364A LEU* 5.1 2.6 - - - +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 4.7 5.3 + - - +
321A TYR* 3.8 27.2 + - - -
326A ASP* 2.6 37.6 + - - -
328A ASP* 1.3 71.5 + - - +
330A ILE* 1.3 67.2 + - - +
332A LYS* 3.9 4.6 - - - +
333A LEU* 3.0 26.2 + - - +
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Residues in contact with ILE 330 (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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318A LEU* 3.7 49.8 - - + +
321A TYR* 3.6 20.4 - - + -
322A ARG* 4.0 11.2 - - + +
326A ASP 3.3 11.1 + - - +
327A TYR* 3.1 34.4 + - + +
329A SER* 1.3 76.0 - - - +
331A VAL* 1.3 63.5 + - - +
333A LEU* 3.8 0.9 - - - +
334A VAL* 3.0 28.3 + - + +
354A HIS* 4.0 13.2 - - + +
355A TYR* 4.6 1.1 - - - -
357A PHE* 6.3 0.2 - - + -
358A ALA* 3.6 16.8 - - + -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR 2.9 20.3 + - - +
328A ASP 3.3 3.8 + - - +
330A ILE* 1.3 76.2 - - - +
332A LYS* 1.3 57.7 + - - +
334A VAL* 3.3 2.1 + - - +
335A GLU* 2.9 45.5 + - - +
355A TYR* 4.1 12.4 - - + +
358A ALA* 4.0 6.7 - - + +
359A LEU* 3.8 44.2 - - + +
362A ARG* 3.6 40.8 - - - +
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 5.7 0.4 - - - -
328A ASP* 3.0 50.0 + - - +
329A SER* 4.1 4.5 - - - +
331A VAL* 1.3 76.7 - - - +
333A LEU* 1.3 61.2 + - - +
335A GLU* 3.8 16.2 - - - +
336A THR* 3.1 31.1 + - + +
362A ARG* 4.5 7.6 - - - +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 4.1 30.9 - - - +
303A VAL* 5.5 0.9 - - + -
304A ASP* 5.6 0.9 - - - +
309A LEU* 4.8 12.3 - - + -
314A VAL* 4.8 7.4 - - + +
317A LEU* 3.7 31.2 - - + -
318A LEU* 3.6 25.6 - - + -
321A TYR* 4.6 3.1 - - + -
329A SER 3.0 18.9 + - - +
330A ILE 3.8 2.9 - - - +
332A LYS* 1.3 75.7 - - - +
334A VAL* 1.3 63.8 + - + +
336A THR* 2.6 29.3 + - - +
337A LEU* 3.1 27.0 + - + +
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Residues in contact with VAL 334 (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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318A LEU* 3.9 30.5 - - + -
330A ILE* 3.0 20.5 + - + +
333A LEU* 1.3 76.0 - - + +
335A GLU* 1.3 62.3 + - - +
337A LEU* 3.2 10.3 + - + +
338A GLU* 3.1 20.4 + - - +
345A LEU* 3.9 25.0 - - + +
351A VAL* 4.2 7.6 - - + -
355A TYR* 3.4 48.9 - - + -
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Residues in contact with GLU 335 (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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331A VAL* 2.9 37.1 + - + +
332A LYS* 3.8 19.5 - - - +
333A LEU 3.3 0.2 - - - -
334A VAL* 1.3 75.7 - - - +
336A THR* 1.3 61.8 + - + +
338A GLU* 3.3 18.2 + - - +
339A LYS* 3.4 13.6 + - - +
355A TYR* 3.6 22.3 + - - +
359A LEU* 5.6 1.0 - - - +
362A ARG* 4.6 6.6 + - - -
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Residues in contact with THR 336 (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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300A ARG* 5.4 2.4 + - - +
332A LYS* 3.1 16.2 + - + +
333A LEU* 2.6 30.5 + - - +
335A GLU* 1.3 77.6 - - + +
337A LEU* 1.3 59.0 + - - +
339A LYS* 3.4 28.7 - - - +
340A LEU* 3.1 36.1 + - - +
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Residues in contact with LEU 337 (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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309A LEU* 4.0 23.3 - - + -
314A VAL* 3.5 37.2 - - + -
333A LEU* 3.1 21.2 + - + +
334A VAL* 3.2 14.5 + - + +
336A THR* 1.3 74.2 - - - +
338A GLU* 1.3 66.6 + - - +
340A LEU* 3.1 41.7 - - + +
343A PHE* 3.8 47.9 - - + +
345A LEU* 5.3 2.9 - - + -
351A VAL* 4.8 4.5 - - + -
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Residues in contact with GLU 338 (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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334A VAL 3.1 12.7 + - - +
335A GLU* 3.3 13.9 + - - +
337A LEU* 1.3 78.0 - - - +
339A LYS* 1.3 57.2 + - - +
340A LEU 4.3 2.6 - - - +
341A PRO* 5.5 0.7 - - - +
343A PHE 5.2 2.1 - - - +
345A LEU* 3.0 41.4 - - + +
346A ALA 5.1 0.5 + - - -
355A TYR* 6.0 2.5 - - + +
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Residues in contact with LYS 339 (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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335A GLU 3.4 6.6 + - - +
336A THR* 3.4 41.6 - - - +
337A LEU 3.2 0.8 - - - -
338A GLU* 1.3 75.3 - - - +
340A LEU* 1.3 72.8 + - + +
341A PRO* 2.9 19.1 - - - +
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Residues in contact with LEU 340 (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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309A LEU* 5.2 12.6 - - + -
336A THR* 3.1 28.0 + - - +
337A LEU* 3.1 40.9 + - + +
338A GLU 4.3 2.1 - - - +
339A LYS* 1.3 88.7 - - + +
341A PRO* 1.4 72.6 - - + +
342A THR* 3.1 5.5 + - - +
343A PHE* 3.3 17.6 + - + +
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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