Contacts of the helix formed by residues 308 - 324 (chain A) in PDB entry 4Q44
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 ASN 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.4 6.1 - - - -
286A GLN* 2.9 20.8 + - - +
304A TRP* 2.3 41.0 + - - -
306A ARG* 3.0 9.5 - - - +
307A LEU* 1.3 76.7 - - - +
309A LYS* 1.3 65.8 + - - +
310A ALA* 4.1 3.0 - - - +
311A ASP* 3.4 29.2 + - - +
312A LEU* 3.7 3.5 + - - +
849G G 3.9 23.3 + - - +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 5.0 3.1 - - + +
264A GLU* 2.6 42.9 + - - +
267A TYR* 3.4 55.8 + - + +
268A PRO* 6.3 0.2 - - - +
308A ASN* 1.3 71.1 - - - +
310A ALA* 1.3 66.7 + - - +
312A LEU* 3.1 7.5 + - - +
313A ILE* 2.9 35.0 + - + +
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Residues in contact with ALA 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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308A ASN* 3.4 2.6 - - + +
309A LYS* 1.3 78.8 - - - +
311A ASP* 1.3 57.0 + - - +
313A ILE* 3.2 11.5 + - - +
314A ALA* 2.9 27.9 + - - +
848G A 4.2 34.5 - - - +
849G G 4.2 12.8 - - - +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 3.8 7.2 - - - +
302A HIS* 2.3 42.9 + - - -
304A TRP* 3.1 30.1 - - + -
308A ASN* 3.4 20.7 - - - +
309A LYS 3.3 0.6 - - - -
310A ALA* 1.3 75.5 - - - +
312A LEU* 1.3 60.4 + - - +
314A ALA* 3.2 7.6 + - - +
315A THR* 2.9 37.4 + - - +
849G G 4.7 9.5 - - - +
850G G 3.7 6.9 + - - -
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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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263A ILE* 5.1 5.2 - - + -
267A TYR* 4.0 19.7 - - + -
270A LEU* 3.9 21.5 - - + -
286A GLN* 3.4 41.5 - - + +
287A GLY* 3.3 34.8 - - - +
288A VAL* 3.4 5.8 - - + +
302A HIS* 5.8 1.3 - - + -
308A ASN 3.7 0.8 + - - +
309A LYS* 3.1 9.9 + - - +
311A ASP* 1.3 78.1 - - - +
313A ILE* 1.3 57.0 + - - +
315A THR* 2.7 17.7 + - - +
316A ALA* 2.9 19.6 + - - +
334A LEU* 3.8 24.7 - - + -
335A HIS 4.9 0.4 - - - +
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TRP* 3.4 21.3 - - + -
260A GLU* 4.0 20.6 - - + +
263A ILE* 3.8 22.9 - - + -
264A GLU* 3.4 28.5 - - - +
309A LYS* 2.9 32.5 + - + +
310A ALA* 3.5 10.8 - - - +
312A LEU* 1.3 76.8 - - - +
314A ALA* 1.3 56.9 + - - +
316A ALA* 3.4 4.3 + - - -
317A ARG* 2.9 36.6 + - - +
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Residues in contact with ALA 314 (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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310A ALA 2.9 13.6 + - - +
311A ASP* 3.2 14.3 + - - +
313A ILE* 1.3 76.5 - - - +
315A THR* 1.3 64.6 + - + +
317A ARG* 3.0 20.2 + - - +
318A LYS* 3.0 35.3 + - - +
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Residues in contact with THR 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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286A GLN 5.8 0.2 - - - +
287A GLY* 5.1 0.8 - - - -
288A VAL* 3.1 15.5 - - - +
300A GLN* 3.5 20.9 - - + +
301A GLU 6.5 0.2 - - - -
302A HIS* 3.4 36.3 - - + +
311A ASP* 2.9 18.9 + - - +
312A LEU* 2.7 26.4 + - + +
314A ALA* 1.3 75.9 - - + +
316A ALA* 1.3 51.8 + - - +
318A LYS* 3.1 12.3 + - + +
319A THR* 2.7 36.8 + - - -
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Residues in contact with ALA 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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256A TRP* 3.5 7.7 - - + -
259A CYS* 4.7 3.7 - - - -
263A ILE* 3.4 29.2 - - + -
288A VAL* 3.8 18.8 - - + -
290A LEU* 4.5 4.4 - - + +
312A LEU 2.9 18.8 + - - +
313A ILE 3.7 2.7 - - - +
315A THR* 1.3 73.8 + - - +
317A ARG* 1.3 60.1 + - - +
319A THR* 3.8 8.1 - - - -
320A TRP* 2.9 30.3 + - - +
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TRP* 3.3 34.5 - - + +
260A GLU* 3.6 9.7 + - - -
313A ILE* 2.9 24.2 + - - +
314A ALA* 3.0 29.7 + - - +
316A ALA* 1.3 77.6 - - - +
318A LYS* 1.3 58.7 + - + +
320A TRP* 3.5 1.0 + - - +
321A ASP* 2.9 50.2 + - - +
296F GLN* 4.8 6.1 - - - +
867H A 5.4 0.2 - - - -
868H G 3.3 46.1 + - - -
869H G 3.0 26.9 + - - -
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLN* 4.1 15.0 - - - +
314A ALA* 3.0 25.8 + - - +
315A THR* 3.1 13.8 + - + +
317A ARG* 1.3 78.4 - - + +
319A THR* 1.3 60.1 - - - +
321A ASP* 4.3 5.2 - - - +
322A GLU* 2.9 54.6 + - - +
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Residues in contact with THR 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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288A VAL* 4.9 5.5 - - + +
289A LYS 6.0 0.2 - - - -
290A LEU* 3.7 22.8 - - + +
298A THR* 3.7 26.7 - - + +
300A GLN* 2.3 40.4 + - + +
315A THR 2.7 17.8 + - - -
316A ALA* 3.8 8.3 - - - -
318A LYS* 1.3 76.4 - - - +
320A TRP* 1.3 57.2 + - - +
323A ARG* 2.9 43.1 + - - +
324A ARG 3.5 2.9 + - - -
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Residues in contact with TRP 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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253A ILE* 3.6 25.4 - - + -
254A HIS 3.4 18.2 - - - -
255A HIS 3.2 32.5 - - - -
256A TRP* 3.8 32.3 - + + +
259A CYS* 3.7 23.6 - - + -
290A LEU* 3.9 12.9 - - + +
316A ALA 2.9 19.1 + - - +
317A ARG 3.7 3.8 - - - +
319A THR* 1.3 77.6 - - - +
321A ASP* 1.3 72.1 + - - +
324A ARG* 3.1 57.7 + - - +
325A GLY 5.1 0.3 + - - -
329A VAL* 3.6 24.2 - - + -
294F ASP* 4.4 6.3 + - - -
296F GLN* 4.7 3.2 + - - -
327F ARG* 5.0 3.0 - - - +
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Residues in contact with ASP 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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317A ARG* 2.9 35.5 + - - +
318A LYS* 3.7 7.9 - - - +
319A THR 3.3 0.2 - - - -
320A TRP* 1.3 92.5 - - - +
322A GLU* 1.3 64.2 + - + +
324A ARG 5.0 0.2 - - - -
325A GLY 5.8 1.1 + - - -
296F GLN* 3.9 18.7 + - - +
323F ARG* 4.7 22.2 - - + +
324F ARG 5.8 1.0 + - - -
325F GLY* 5.5 8.0 + - - -
327F ARG* 4.7 13.7 + - - +
868H G 5.4 2.3 + - - -
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Residues in contact with GLU 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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300A GLN* 4.7 7.8 + - - -
318A LYS* 2.9 41.0 + - - +
321A ASP* 1.3 87.2 - - + +
323A ARG* 1.3 71.8 + - + +
324A ARG 3.7 0.9 - - - -
325A GLY* 5.0 2.7 + - - -
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Residues in contact with ARG 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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292A PHE* 3.6 3.4 - - + -
298A THR* 2.8 38.9 + - + -
299A THR 2.9 25.3 + - - -
300A GLN* 3.4 28.7 + - - +
319A THR* 2.9 21.2 + - - +
322A GLU* 1.3 90.0 + - + +
324A ARG* 1.3 62.4 + - - +
325A GLY* 3.3 3.4 + - - -
327A ARG* 2.8 27.4 + - - +
867C A 3.0 37.4 + - - -
868C G 5.3 1.8 - - - -
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Residues in contact with ARG 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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254A HIS* 3.8 28.4 + - - +
292A PHE* 3.5 21.3 - - + -
319A THR 3.5 3.4 + - - -
320A TRP* 3.1 73.9 + - + +
322A GLU 3.7 0.4 - - - -
323A ARG* 1.3 79.3 - - - +
325A GLY* 1.3 63.8 + - - +
326A GLY* 3.5 26.3 + - - +
327A ARG* 2.7 77.5 + - - +
329A VAL* 4.2 1.6 - - + -
294F ASP* 4.4 8.9 + - - +
327F ARG* 4.6 15.8 - - - +
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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
------------------------------------------------------------
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