Contacts of the helix formed by residues 311 - 332 (chain A) in PDB entry 5DO7
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 SER 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A THR* 3.0 5.4 - - - -
310A GLN* 1.3 79.3 - - - +
312A LYS* 1.3 75.8 + - - +
313A GLU* 3.2 14.4 + - - +
314A ARG* 4.1 14.2 - - - +
315A GLU* 2.8 30.9 + - - +
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 1.3 84.5 + - - +
313A GLU* 1.3 68.6 + - + +
315A GLU* 3.3 17.6 - - - +
316A ILE* 2.8 47.9 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 4.3 8.7 - - - +
312A LYS* 1.3 92.4 - - + +
314A ARG* 1.3 69.2 + - + +
316A ILE* 4.8 1.3 - - - +
317A GLU* 3.3 25.1 + - + +
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Residues in contact with ARG 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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308A ASP 3.8 2.5 - - - -
310A GLN* 4.6 7.4 - - + -
311A SER* 3.7 20.9 + - - +
312A LYS 3.6 0.2 - - - -
313A GLU* 1.3 80.2 - - + +
315A GLU* 1.3 60.4 + - - +
317A GLU* 4.0 13.6 + - - +
318A THR* 2.9 35.0 + - - +
23B LEU* 3.6 29.3 - - - +
246B PHE* 3.8 44.0 + - + -
249B HIS* 5.6 5.9 + - - -
250B ASN* 4.9 9.2 + - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 3.3 8.1 - - + +
308A ASP 3.5 10.3 + - - -
309A THR* 4.0 26.9 - - + +
311A SER 2.8 19.3 + - - +
312A LYS* 3.3 24.2 - - - +
313A GLU 3.2 0.2 - - - -
314A ARG* 1.3 76.4 - - - +
316A ILE* 1.3 77.4 + - - +
318A THR* 2.8 19.5 + - - -
319A SER* 3.2 9.0 + - - +
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Residues in contact with ILE 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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312A LYS* 2.8 35.3 + - + +
313A GLU* 4.8 1.3 - - - +
315A GLU* 1.3 86.8 - - - +
317A GLU* 1.3 67.9 + - - +
319A SER* 2.6 26.1 + - - +
320A LYS* 3.3 8.7 + - + +
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Residues in contact with GLU 317 (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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313A GLU* 3.3 18.2 + - + +
314A ARG* 4.0 13.0 + - - +
316A ILE* 1.3 79.7 - - - +
318A THR* 1.3 73.7 + - - +
320A LYS* 3.2 15.6 + - - +
321A ARG* 3.2 27.3 + - + +
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Residues in contact with THR 318 (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 LEU 5.7 0.2 - - - +
306A SER 5.1 1.8 - - - +
307A VAL* 2.9 27.8 - - - +
308A ASP 3.7 3.3 + - - -
314A ARG* 2.9 22.3 + - - +
315A GLU 2.8 20.3 + - - -
317A GLU* 1.3 83.1 - - - +
319A SER* 1.3 65.3 + - - +
321A ARG* 2.8 51.0 + - - +
322A VAL* 2.8 14.7 + - - +
246B PHE* 4.3 19.1 - - + -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 3.6 19.5 - - - -
315A GLU* 3.2 8.4 + - - +
316A ILE* 2.6 26.7 + - - +
318A THR* 1.3 78.4 + - - +
320A LYS* 1.3 56.1 + - - +
322A VAL* 3.0 14.0 - - - +
323A GLN* 2.8 29.9 + - - +
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Residues in contact with LYS 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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316A ILE* 3.3 10.7 + - + +
317A GLU* 3.2 12.9 + - - +
318A THR 3.1 0.8 - - - -
319A SER* 1.3 74.2 - - - +
321A ARG* 1.3 59.2 - - - +
323A GLN* 3.1 11.7 + - - +
324A MET* 2.8 60.6 + - + +
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Residues in contact with ARG 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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289A TYR* 4.3 20.0 + - + +
303A ASP 4.6 4.0 + - - -
304A LEU* 3.9 57.0 + - - +
306A SER 5.6 1.4 + - - -
317A GLU* 3.2 23.2 + - + +
318A THR* 2.8 46.0 + - - +
320A LYS* 1.3 74.2 - - - +
322A VAL* 1.3 62.8 + - - +
324A MET* 2.8 8.7 + - - +
325A ILE* 2.8 36.9 + - + +
246B PHE* 6.1 1.0 - - - -
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Residues in contact with VAL 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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267A SER* 4.2 9.0 - - - +
272A ILE* 3.6 19.7 - - + -
304A LEU 4.5 4.5 - - - +
305A THR* 3.0 33.7 - - - +
307A VAL* 4.5 14.8 - - + +
318A THR 2.8 12.7 + - - +
319A SER* 3.0 35.4 - - - +
321A ARG* 1.3 74.8 - - - +
323A GLN* 1.3 56.1 + - - +
325A ILE* 3.7 7.6 - - + -
326A GLU* 2.8 28.9 + - + +
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Residues in contact with GLN 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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270A GLU* 5.3 6.1 - - - +
319A SER 2.8 18.8 + - - +
320A LYS* 3.1 12.7 + - - +
322A VAL* 1.3 72.9 - - + +
324A MET* 1.3 77.9 + - + +
326A GLU* 2.8 16.9 + - - +
327A SER* 2.8 31.9 + - - -
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Residues in contact with MET 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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320A LYS* 2.8 54.8 + - + +
321A ARG* 2.8 7.3 + - - +
323A GLN* 1.3 87.6 - - - +
325A ILE* 1.3 56.3 + - + +
327A SER* 3.1 11.2 + - - -
328A ALA* 2.8 35.6 + - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.2 9.4 - - + -
284A PHE* 4.0 21.1 - - + -
287A CYS* 4.0 23.3 - - + +
289A TYR* 3.8 30.3 - - + -
304A LEU* 5.3 4.0 - - + +
305A THR* 5.7 4.9 - - + -
321A ARG* 2.8 36.6 + - + +
322A VAL* 3.9 7.2 - - + +
324A MET* 1.3 73.8 - - + +
326A GLU* 1.3 64.0 + - - +
328A ALA* 3.4 14.0 - - + +
329A TYR* 3.7 34.4 + - + +
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Residues in contact with GLU 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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270A GLU* 3.0 31.7 - - + +
271A LEU 3.3 25.8 - - - +
272A ILE* 4.2 16.7 - - + -
322A VAL* 2.8 15.1 + - + +
323A GLN* 2.8 18.5 + - - +
325A ILE* 1.3 74.1 - - - +
327A SER* 1.3 69.8 + - - +
328A ALA 3.1 0.7 + - - -
329A TYR* 3.2 5.9 + - - -
330A LYS* 2.7 56.0 + - - +
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Residues in contact with SER 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 GLN* 2.8 17.4 + - - -
324A MET* 3.1 19.6 + - - -
326A GLU* 1.3 75.5 - - - +
328A ALA* 1.3 75.8 + - - +
330A LYS* 2.8 36.4 + - - +
331A LYS* 2.8 16.5 + - - +
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Residues in contact with ALA 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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287A CYS* 3.9 24.7 - - + -
324A MET 2.8 18.5 + - - +
325A ILE* 3.4 11.7 - - + +
327A SER* 1.3 80.7 + - - +
329A TYR* 1.3 60.3 + - - +
331A LYS* 3.7 5.3 + - - +
332A SER* 3.4 17.4 + - - -
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Residues in contact with TYR 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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272A ILE* 3.2 26.2 - - + +
273A PHE* 3.1 65.8 - + + +
283A PHE* 4.4 11.4 - + + -
284A PHE* 3.2 35.7 - + - -
287A CYS* 3.1 34.1 - - - -
305A THR* 5.4 0.5 - - - +
325A ILE* 3.9 8.5 - - + +
326A GLU 3.2 5.4 + - - -
328A ALA* 1.3 76.8 - - - +
330A LYS* 1.3 57.9 + - - +
331A LYS 3.2 0.7 - - - -
332A SER* 3.5 20.3 + - - +
334A ILE* 4.6 4.7 - - + -
335A CYS* 2.4 47.4 - - - +
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Residues in contact with LYS 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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326A GLU* 2.7 43.0 + - - +
327A SER* 2.8 27.5 + - - +
329A TYR* 1.3 71.4 - - - +
331A LYS* 1.3 64.3 + - - +
335A CYS* 4.2 10.2 - - - +
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Residues in contact with LYS 331 (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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327A SER 2.8 12.8 + - - +
328A ALA 3.9 4.7 - - - +
330A LYS* 1.3 85.1 - - - +
332A SER* 1.3 68.0 + - - +
336A HIS* 4.7 5.7 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 3.8 22.3 - - - -
286A ASP* 4.6 3.7 + - - -
328A ALA 3.4 6.6 + - - -
329A TYR* 3.5 31.5 + - - -
331A LYS* 1.3 83.1 - - - +
333A ALA* 1.3 76.7 + - - +
334A ILE* 3.2 11.2 + - - +
335A CYS* 2.8 14.4 + - - -
336A HIS* 2.9 10.3 + - - -
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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