Contacts of the helix formed by residues 299 - 320 (chain A) in PDB entry 5M4G
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 THR 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLY* 5.8 4.3 - - - +
295A ASN* 6.2 1.8 - - - +
297A LYS 4.6 3.8 - - - +
298A PHE* 1.3 76.7 - - - +
300A ALA* 1.3 60.1 + - - +
301A ASP* 3.5 7.0 + - - +
302A GLN* 3.0 41.7 + - - +
303A LYS* 2.8 28.3 + - - +
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Residues in contact with ALA 300 (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 THR* 1.3 74.6 - - - +
301A ASP* 1.3 62.7 + - - +
303A LYS* 3.4 7.6 + - - +
304A ALA* 3.0 28.8 + - - +
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Residues in contact with ASP 301 (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 THR* 3.3 7.0 + - - +
300A ALA* 1.3 82.7 - - - +
302A GLN* 1.3 62.7 + - + +
304A ALA* 3.3 5.4 + - - +
305A VAL* 3.1 28.4 + - - +
442A ARG* 2.8 50.9 + - - +
443A PHE* 3.6 24.1 - - + -
446A PHE* 4.2 7.4 - - + -
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Residues in contact with GLN 302 (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 GLY* 3.0 30.7 + - - -
271A ASP 4.2 1.4 + - - -
272A MET* 3.4 37.7 - - - +
293A PRO* 3.8 6.2 - - - +
297A LYS 3.8 4.5 - - - +
298A PHE* 3.6 13.8 - - + -
299A THR* 3.0 43.3 + - - +
301A ASP* 1.3 76.7 - - + +
303A LYS* 1.3 59.1 + - - +
305A VAL* 3.4 1.2 + - - +
306A TYR* 2.8 32.7 + - - +
446A PHE* 3.8 22.5 - - + -
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Residues in contact with LYS 303 (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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298A PHE* 3.9 17.6 - - + -
299A THR 2.8 18.3 + - - +
300A ALA* 3.6 8.1 - - - +
302A GLN* 1.3 76.3 - - - +
304A ALA* 1.3 58.2 + - - +
306A TYR* 4.5 1.1 - - - -
307A GLU* 2.7 71.1 + - - +
472A VAL* 4.1 18.8 - - + -
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Residues in contact with ALA 304 (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 ALA 3.0 16.6 + - - +
301A ASP* 3.7 7.4 - - - +
302A GLN 3.3 0.4 - - - -
303A LYS* 1.3 78.0 - - - +
305A VAL* 1.3 62.7 + - - +
307A GLU* 4.1 4.4 - - - +
308A ALA* 3.2 22.9 + - - +
340A GLU* 5.2 1.9 - - - +
344A MET* 3.6 31.7 - - + +
443A PHE* 6.1 0.2 - - + -
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP 3.1 14.3 + - - +
304A ALA* 1.3 74.6 - - - +
306A TYR* 1.3 65.3 + - - +
308A ALA* 3.2 12.9 + - - +
309A VAL* 3.3 12.8 + - - +
341A LEU* 5.3 0.2 - - + -
344A MET* 4.1 17.3 - - + -
415A ILE* 4.1 29.8 - - + +
417A PHE* 4.1 11.2 - - + -
443A PHE* 3.9 22.0 - - + -
446A PHE* 3.7 32.3 - - + -
449A VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 306 (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 MET* 4.9 0.4 - - + -
291A SER* 3.3 28.1 + - - -
298A PHE* 3.6 26.7 - + + -
302A GLN 2.8 23.6 + - - +
303A LYS 3.9 2.0 - - - +
305A VAL* 1.3 74.2 - - - +
307A GLU* 1.3 61.8 + - + +
309A VAL* 3.1 5.9 + - - +
310A LEU* 2.9 31.8 + - + -
449A VAL* 3.7 25.2 - - + +
451A ILE* 3.5 32.1 - - + +
470A ARG* 2.7 40.6 + - - -
472A VAL* 4.1 14.4 - - + -
475A ILE* 3.2 17.5 - - + +
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Residues in contact with GLU 307 (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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303A LYS* 2.7 64.5 + - - +
304A ALA* 4.3 3.8 - - - +
306A TYR* 1.3 73.9 - - + +
308A ALA* 1.3 57.4 + - - +
310A LEU* 3.6 16.6 - - + +
311A ARG* 2.8 29.5 + - - +
340A GLU* 5.5 2.1 - - - +
472A VAL* 3.7 24.1 + - + +
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Residues in contact with ALA 308 (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 3.2 12.8 + - - +
305A VAL 3.3 10.8 - - - +
306A TYR 3.2 0.4 - - - -
307A GLU* 1.3 78.5 - - - +
309A VAL* 1.3 57.1 + - - +
311A ARG* 3.3 5.0 + - - +
312A SER* 3.1 25.6 + - - -
336A ILE* 4.0 5.0 - - - +
337A HIS* 4.0 4.8 - - + -
340A GLU* 3.5 39.2 + - + -
344A MET* 4.3 3.1 - - + -
415A ILE* 3.8 16.8 - - + -
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Residues in contact with VAL 309 (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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305A VAL 3.6 13.2 - - - +
306A TYR 3.1 7.5 + - - +
308A ALA* 1.3 73.0 - - - +
310A LEU* 1.3 60.9 + - - +
312A SER* 3.1 7.2 + - - -
313A SER* 2.8 29.5 + - - -
337A HIS* 4.3 1.8 - - - +
413A PRO* 3.3 33.0 - - + +
414A GLY* 4.1 2.0 - - - -
415A ILE* 3.8 38.1 - - + +
449A VAL* 3.9 16.2 - - + -
451A ILE* 3.8 24.0 - - + +
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Residues in contact with LEU 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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306A TYR* 2.9 22.3 + - + +
307A GLU* 3.6 18.2 - - + +
308A ALA 3.3 0.2 - - - -
309A VAL* 1.3 74.7 - - - +
311A ARG* 1.3 62.4 + - - +
313A SER* 3.4 2.7 + - - -
314A ARG* 3.0 63.7 + - + +
451A ILE* 3.5 19.8 - - + +
470A ARG* 3.9 30.3 - - + +
471A THR* 4.2 18.8 - - + -
472A VAL 5.1 0.7 - - - +
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Residues in contact with ARG 311 (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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307A GLU 2.8 19.0 + - - +
308A ALA* 3.5 5.6 - - - +
310A LEU* 1.3 77.4 - - - +
312A SER* 1.3 57.2 + - - +
314A ARG* 3.4 4.3 + - - +
315A ALA* 2.9 31.3 + - + +
336A ILE* 3.7 33.7 - - + +
339A GLU* 2.9 34.5 + - - +
340A GLU* 2.8 41.0 + - - +
343A HIS* 5.1 2.8 - - - -
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Residues in contact with SER 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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308A ALA 3.1 6.6 + - - -
309A VAL* 3.1 9.0 + - - -
311A ARG* 1.3 72.8 - - - +
313A SER* 1.3 63.0 + - - +
315A ALA* 3.8 0.3 - - - +
316A VAL* 2.9 35.4 + - - +
333A ALA* 4.0 18.6 - - - -
336A ILE* 3.8 18.1 - - - +
337A HIS* 2.8 38.8 + - - -
413A PRO* 3.3 9.6 - - - +
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Residues in contact with SER 313 (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 VAL 2.8 18.8 + - - -
310A LEU* 3.6 6.5 - - - -
312A SER* 1.3 78.6 + - - +
314A ARG* 1.3 61.6 + - - +
316A VAL* 3.4 1.9 + - - +
317A MET* 3.0 46.3 + - - +
411A VAL* 4.1 5.6 - - - +
413A PRO* 3.8 19.3 - - - -
451A ILE* 4.0 24.0 - - - +
453A GLU* 4.2 7.8 - - - +
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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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310A LEU* 3.0 38.6 + - + +
311A ARG* 4.0 4.3 - - - +
313A SER* 1.3 76.2 + - - +
315A ALA* 1.3 66.0 + - - +
317A MET* 3.7 22.2 - - - +
318A GLY* 3.0 21.1 + - - -
453A GLU* 3.4 24.4 + - - -
464A LEU* 5.6 3.2 - - - +
470A ARG* 3.4 29.1 - - - +
471A THR* 4.8 10.7 - - - +
474A GLU* 5.1 1.2 + - - -
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Residues in contact with ALA 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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311A ARG* 2.9 13.2 + - + +
312A SER 3.2 1.3 + - - +
314A ARG* 1.3 78.9 - - - +
316A VAL* 1.3 62.9 + - - +
318A GLY* 3.4 0.9 + - - -
319A ALA* 3.1 25.5 + - - +
332A LEU* 4.0 10.9 - - + +
336A ILE* 3.3 34.1 - - + -
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Residues in contact with VAL 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 SER 2.9 21.6 + - - +
313A SER 3.8 3.4 - - - +
315A ALA* 1.3 76.6 - - - +
317A MET* 1.3 64.4 + - - +
319A ALA* 3.1 2.3 + - - +
320A MET* 3.0 43.5 + - + +
326A TRP* 4.3 1.3 - - + -
329A MET* 3.8 29.1 - - + +
332A LEU* 4.4 13.2 - - + -
333A ALA* 4.3 11.9 - - + +
368A LEU* 3.9 23.3 - - + -
411A VAL* 3.8 20.6 - - + -
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Residues in contact with MET 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 SER* 3.0 28.3 + - - +
314A ARG* 3.7 41.5 - - - +
316A VAL* 1.3 77.3 - - - +
318A GLY* 1.3 60.9 - - - +
319A ALA 3.4 0.5 + - - -
320A MET* 3.4 15.1 + - - +
411A VAL* 4.2 14.8 - - + -
453A GLU* 4.0 14.6 - - + +
455A VAL* 4.0 12.8 - - + -
462A ILE* 3.6 38.3 - - + +
464A LEU* 4.0 31.0 - - + -
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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
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314A ARG 3.0 17.8 + - - -
315A ALA 3.9 1.3 - - - -
317A MET* 1.3 77.2 - - - +
319A ALA* 1.3 59.3 + - - +
320A MET 4.4 2.8 - - - +
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Residues in contact with ALA 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 ALA 3.1 17.4 + - - +
316A VAL 3.1 0.2 + - - -
318A GLY* 1.3 77.4 - - - +
320A MET* 1.3 66.5 + - - +
321A LYS* 3.3 10.0 + - - +
324A VAL* 3.5 13.5 - - - +
329A MET* 3.7 28.0 - - + -
332A LEU* 4.3 7.2 - - + -
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Residues in contact with MET 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 VAL* 3.0 25.1 + - + +
317A MET* 3.4 11.1 + - - +
318A GLY 4.4 2.4 - - - +
319A ALA* 1.3 77.8 - - - +
321A LYS* 1.3 61.9 + - - +
324A VAL* 4.4 3.4 - - - -
326A TRP* 3.7 30.7 - - + -
329A MET* 4.3 5.4 - - - -
403A LEU* 3.8 22.2 - - + -
409A LEU* 4.3 13.5 - - + -
411A VAL* 3.7 24.9 - - + -
455A VAL* 3.6 27.1 - - + -
457A VAL* 4.5 2.2 - - + -
461A GLY* 3.3 18.4 - - - -
462A ILE* 3.6 17.5 - - + +
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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