Contacts of the helix formed by residues 316 - 330 (chain A) in PDB entry 5L26
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A VAL* 3.3 14.3 - - + +
313A PRO* 2.8 17.0 + - + +
315A SER* 1.3 89.1 + - - +
317A ALA* 1.3 62.5 + - - +
318A GLY 3.4 2.5 - - - -
319A ILE* 3.7 12.4 + - + +
320A ALA* 3.4 16.1 + - - +
350A GLN 3.7 6.9 - - - +
351A LEU* 3.4 31.4 - - + +
352A SER* 3.1 26.7 + - - -
355A THR* 2.6 33.2 + - + +
359A ILE* 5.5 0.2 - - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 3.7 24.7 - - - +
307A ALA* 3.4 13.8 - - + +
308A TRP 4.4 5.2 - - - +
312A VAL* 3.9 8.5 - - - +
313A PRO 2.9 11.3 + - - +
314A TRP* 3.3 30.1 + - + +
316A GLU* 1.3 77.5 - - - +
318A GLY* 1.3 62.0 + - - +
321A GLY* 3.0 23.9 + - - -
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Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLY* 3.4 7.9 - - - -
301A TRP* 6.2 2.5 - - - -
304A SER* 3.7 15.9 - - - -
314A TRP 4.3 3.8 + - - -
315A SER 4.9 1.8 + - - -
316A GLU* 3.4 0.6 - - - +
317A ALA* 1.3 76.7 - - - +
319A ILE* 1.3 64.9 + - - +
321A GLY 3.3 0.9 + - - -
322A SER* 3.1 24.7 + - - -
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Residues in contact with ILE 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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315A SER 5.1 4.3 - - - +
316A GLU* 3.7 15.7 + - + +
317A ALA 3.3 0.4 - - - -
318A GLY* 1.3 73.2 - - - +
320A ALA* 1.3 65.0 + - - +
322A SER* 3.0 18.2 + - - -
323A LEU* 3.1 23.4 + - + +
342A TYR* 3.5 44.0 - - + +
349A VAL* 3.6 32.3 - - + -
351A LEU* 3.7 23.3 - - + -
359A ILE* 5.0 1.1 - - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 3.9 18.4 - - + -
310A ILE* 6.1 0.2 - - + -
312A VAL* 4.4 12.1 - - + -
316A GLU 3.4 14.7 + - - +
319A ILE* 1.3 78.7 - - - +
321A GLY* 1.3 57.6 + - - +
323A LEU* 3.9 3.3 - - - +
324A ILE* 3.1 41.5 + - + +
358A ILE* 6.1 0.4 - - + -
359A ILE* 4.0 31.8 - - + +
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.4 10.3 - - - +
300A GLY* 3.5 12.1 - - - -
303A PHE* 3.5 24.4 - - - +
307A ALA* 4.1 2.0 - - - +
317A ALA 3.0 16.0 + - - -
318A GLY 3.3 4.9 + - - -
319A ILE 3.0 0.2 - - - -
320A ALA* 1.3 75.5 - - - +
322A SER* 1.3 58.8 + - - +
324A ILE* 4.8 0.7 - - - -
325A GLY* 2.9 24.1 + - - -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 2.6 30.8 + - - +
297A ALA* 4.5 1.9 - - - -
299A LEU* 4.2 2.1 - - - +
300A GLY* 3.2 16.2 - - - +
318A GLY 3.1 8.1 + - - -
319A ILE* 3.0 12.6 + - - -
321A GLY* 1.3 74.9 - - - +
323A LEU* 1.3 63.3 + - - +
325A GLY* 3.4 0.5 + - - -
326A GLN* 2.8 45.6 + - - +
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Residues in contact with LEU 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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319A ILE* 3.1 28.6 + - + +
320A ALA 4.1 3.4 - - - +
321A GLY 3.3 0.2 - - - -
322A SER* 1.3 82.0 - - - +
324A ILE* 1.3 64.0 + - - +
326A GLN* 3.5 15.4 + - - +
327A LYS* 3.1 19.2 + - - +
335A ALA* 3.3 27.6 - - - +
338A GLU* 4.4 14.4 - - + -
339A PHE* 3.5 38.6 - - + -
342A TYR* 4.6 7.6 - - + +
359A ILE* 3.6 20.6 - - + -
363A LEU* 4.0 15.3 - - + -
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Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 4.3 19.3 - - + +
306A LEU* 4.9 7.4 - - + -
307A ALA* 4.9 8.5 - - + +
310A ILE* 4.2 13.5 - - + -
320A ALA* 3.1 27.5 + - + +
321A GLY* 4.2 3.6 - - - +
323A LEU* 1.3 75.7 - - + +
325A GLY* 1.3 62.5 + - - +
327A LYS* 3.3 9.0 + - + +
328A VAL* 3.2 30.8 + - + +
358A ILE* 6.2 0.4 - - + -
359A ILE* 5.8 2.0 - - + -
362A ALA* 4.2 14.1 - - + +
363A LEU* 4.1 18.6 - - + -
406A LEU* 4.0 30.3 - - + -
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Residues in contact with GLY 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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299A LEU* 4.0 12.1 - - - -
303A PHE* 3.8 26.2 - - - -
321A GLY 2.9 18.8 + - - -
322A SER 3.7 0.9 - - - -
324A ILE* 1.3 78.4 - - - +
326A GLN* 1.3 61.0 + - - +
328A VAL* 3.2 4.0 + - - +
329A VAL* 3.2 27.2 + - - +
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Residues in contact with GLN 326 (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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274A ILE* 5.2 4.5 - - + +
296A GLN* 3.3 37.5 - - + +
299A LEU* 3.9 18.4 - - + +
322A SER* 2.8 34.7 + - - +
323A LEU* 3.8 18.3 - - - +
325A GLY* 1.3 72.9 - - - +
327A LYS* 1.3 57.1 + - - +
329A VAL* 5.1 0.2 - - - -
330A ILE* 2.9 40.1 + - + +
331A ASN 3.4 3.3 + - - +
334A VAL* 4.2 24.8 - - + +
335A ALA* 4.5 9.0 - - - -
338A GLU* 4.4 14.7 - - - +
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Residues in contact with LYS 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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323A LEU 3.1 15.3 + - - +
324A ILE* 3.4 13.5 - - + +
325A GLY 3.1 0.2 - - - -
326A GLN* 1.3 79.6 - - - +
328A VAL* 1.3 65.3 + - + +
331A ASN* 3.5 17.2 + - - -
332A GLU* 4.5 8.3 - - - +
335A ALA* 3.9 9.6 - - + +
362A ALA 3.3 26.9 + - - +
363A LEU* 3.6 28.5 - - + +
365A GLY 3.7 11.2 - - - +
367A ALA* 3.3 26.3 + - - +
368A ASN* 3.3 19.2 + - - +
402A SER* 4.4 9.5 + - - +
405A ASN* 3.4 24.3 - - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 4.9 15.9 - - + -
324A ILE* 3.2 24.1 + - + +
325A GLY* 3.2 6.9 + - - +
327A LYS* 1.3 82.2 - - - +
329A VAL* 1.3 65.1 + - + +
367A ALA 3.7 9.0 - - - +
368A ASN* 3.3 1.0 - - - -
369A LEU* 3.1 35.1 + - + +
398A VAL* 4.7 15.5 - - + -
402A SER* 4.1 19.7 - - - +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 5.9 4.7 - - + -
299A LEU* 4.4 23.1 - - + -
303A PHE* 5.7 4.7 - - + -
325A GLY 3.2 15.8 + - - +
328A VAL* 1.3 84.7 - - + +
330A ILE* 1.3 77.3 + - + +
369A LEU* 4.2 19.9 - - + +
246B ILE* 3.5 25.9 - - + +
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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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270A PHE* 3.7 34.9 - - + -
274A ILE* 4.0 26.9 - - + -
295A LEU* 5.7 6.3 - - + -
299A LEU* 6.0 1.3 - - + -
326A GLN* 2.9 20.4 + - + +
327A LYS 3.8 2.2 - - - -
329A VAL* 1.3 99.5 - - + +
331A ASN* 1.3 68.7 + - - +
334A VAL* 3.7 26.5 - - + -
368A ASN* 3.3 17.5 - - - +
370A GLY* 4.7 3.5 + - - -
246B ILE* 4.6 18.2 - - + +
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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