Contacts of the helix formed by residues 319 - 333 (chain A) in PDB entry 5L0P
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 GLY 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A TYR* 4.2 2.5 - - - -
318A ILE* 1.3 78.6 - - - +
320A LEU* 1.3 65.1 + - - -
321A ALA 3.5 2.0 - - - -
322A THR* 3.1 26.3 + - - -
323A VAL* 3.2 8.5 + - - +
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Residues in contact with LEU 320 (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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304A ALA 4.5 2.2 - - - +
305A GLU* 4.1 31.6 - - + +
308A TYR* 3.4 48.2 - - + -
318A ILE 4.0 0.8 + - - -
319A GLY* 1.3 69.6 - - - -
321A ALA* 1.3 63.5 + - - +
323A VAL* 3.1 16.0 + - + +
324A TYR* 3.3 29.0 + - + -
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Residues in contact with ALA 321 (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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319A GLY 3.5 0.4 - - - -
320A LEU* 1.3 77.1 - - - +
322A THR* 1.3 55.8 + - - +
324A TYR* 3.4 13.7 + - - +
325A ARG* 3.1 32.8 + - - +
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Residues in contact with THR 322 (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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286A PRO* 4.1 14.8 - - + -
290A ILE* 4.8 0.4 - - + -
318A ILE* 3.9 19.3 - - + -
319A GLY* 3.1 18.6 + - - -
321A ALA* 1.3 73.8 - - - +
323A VAL* 1.3 65.8 + - - +
325A ARG* 3.2 35.2 + - - +
326A VAL* 3.0 40.1 + - + +
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Residues in contact with VAL 323 (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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290A ILE* 3.9 13.4 - - + +
304A ALA* 3.3 29.4 - - + +
307A LEU* 4.0 11.4 - - + -
308A TYR* 4.2 16.8 - - + +
311A LEU* 4.0 24.9 - - + -
318A ILE* 4.1 7.4 - - + -
319A GLY 3.5 12.8 - - - +
320A LEU* 3.1 8.9 + - + +
322A THR* 1.3 75.3 - - - +
324A TYR* 1.3 60.9 + - - +
326A VAL* 3.6 0.9 + - - +
327A LEU* 3.2 45.7 + - + +
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Residues in contact with TYR 324 (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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304A ALA* 3.5 27.8 - - + -
305A GLU* 3.3 15.0 + - + +
320A LEU* 3.3 45.2 + - + +
321A ALA* 3.5 12.1 - - - +
322A THR 3.3 0.2 - - - -
323A VAL* 1.3 78.5 - - - +
325A ARG* 1.3 61.2 + - - +
327A LEU* 3.6 2.5 + - - +
328A ASN* 2.7 39.3 + - - +
344A GLY* 2.5 45.4 + - - -
346A SER* 6.0 1.1 - - - -
348A PHE* 5.3 7.9 - + - -
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Residues in contact with ARG 325 (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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321A ALA* 3.1 14.4 + - - +
322A THR* 3.2 47.8 + - - +
324A TYR* 1.3 73.2 - - - +
326A VAL* 1.3 60.0 + - - +
328A ASN* 3.1 5.7 + - - +
329A GLN* 2.7 65.6 + - + +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 4.7 6.1 - - + -
287A ARG* 3.9 19.1 - - + +
290A ILE* 3.7 30.5 - - + -
322A THR* 3.0 29.8 + - + +
323A VAL 3.9 0.2 - - - +
325A ARG* 1.3 80.8 - - - +
327A LEU* 1.3 51.9 + - - +
329A GLN* 3.2 14.2 + - - +
330A PHE* 2.7 71.6 + - + -
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Residues in contact with LEU 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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290A ILE* 3.9 12.3 - - + -
294A LEU* 4.0 16.2 - - + -
303A SER 4.7 0.7 - - - -
304A ALA* 3.8 24.7 - - + +
307A LEU* 3.7 26.7 - - + -
323A VAL* 3.2 27.4 + - + +
324A TYR* 4.1 1.6 - - - +
326A VAL* 1.3 79.2 - - - +
328A ASN* 1.3 58.1 + - - +
330A PHE* 4.0 4.9 - - + -
331A ASP* 3.0 24.3 + - - +
336A VAL* 3.5 11.1 - - + +
348A PHE* 3.7 53.3 - - + -
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Residues in contact with ASN 328 (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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324A TYR* 2.7 36.0 + - - +
325A ARG* 3.1 5.4 + - - +
327A LEU* 1.3 76.6 - - - +
329A GLN* 1.3 64.4 + - + +
331A ASP* 3.1 10.7 + - - +
332A ASP* 3.1 22.2 + - - +
338A ARG* 2.9 43.8 + - - +
348A PHE* 4.1 12.0 - - - -
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Residues in contact with GLN 329 (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* 4.4 15.7 - - + +
287A ARG* 3.4 31.1 + - - +
325A ARG* 2.7 50.5 + - + +
326A VAL* 3.6 14.2 + - - +
328A ASN* 1.3 71.6 - - + +
330A PHE* 1.3 64.0 + - + +
332A ASP* 3.1 8.9 + - - +
333A ALA* 3.0 25.8 + - - +
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Residues in contact with PHE 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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276A LEU* 4.0 20.0 - - + -
281A LEU* 3.9 16.6 - - + -
287A ARG* 3.5 36.3 - - + -
290A ILE* 4.2 5.8 - - + -
291A LEU* 3.9 27.8 - - + -
294A LEU* 4.2 6.3 - - + -
326A VAL* 2.7 49.7 + - + +
327A LEU* 3.6 8.7 - - - +
329A GLN* 1.3 73.4 - - + +
331A ASP* 1.3 60.1 + - - +
333A ALA 3.4 1.3 + - - +
334A GLY 3.2 3.6 + - - -
335A ILE* 2.9 52.8 + - + -
336A VAL* 3.4 20.5 + - + -
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Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU 3.0 15.8 + - - +
328A ASN* 3.1 17.2 + - - +
330A PHE* 1.3 75.6 - - - +
332A ASP* 1.3 64.1 + - - +
334A GLY* 3.2 12.1 + - - -
336A VAL* 3.4 21.1 - - + +
337A THR* 3.8 2.4 - - - +
338A ARG* 3.4 40.7 + - + +
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Residues in contact with ASP 332 (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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328A ASN 3.1 11.8 + - - +
329A GLN* 3.5 11.0 - - - +
331A ASP* 1.3 79.3 - - - +
333A ALA* 1.3 58.8 + - + +
334A GLY 3.4 1.1 + - - -
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Residues in contact with ALA 333 (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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279A ALA* 3.5 38.8 - - + +
281A LEU* 3.9 23.1 - - + -
329A GLN 3.0 15.5 + - - +
330A PHE* 3.4 2.7 + - - +
331A ASP 3.2 0.2 - - - -
332A ASP* 1.3 77.3 - - - +
334A GLY* 1.3 59.4 + - - -
335A ILE* 3.3 4.4 + - + +
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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