Contacts of the helix formed by residues 301 - 316 (chain A) in PDB entry 5HG1
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 TYR 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE* 3.7 25.3 - - + +
285A SER* 5.1 7.0 - - - -
287A ASN* 4.1 8.8 + - - -
291A GLN* 5.5 0.3 - - - +
294A GLU* 3.9 14.0 + - + -
295A LYS* 3.0 76.0 - - + +
298A SER* 3.7 10.9 + - - +
299A GLY 3.2 0.6 - - - -
300A MET* 1.3 120.7 - - + +
302A MET* 1.3 58.2 + - - +
303A GLY 3.5 1.3 - - - -
304A GLU* 3.6 10.6 + - + +
305A LEU* 3.0 28.7 + - - +
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Residues in contact with MET 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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296A MET 5.9 0.7 - - - +
297A ILE* 4.1 16.2 - - - +
298A SER 3.2 20.2 - - - +
299A GLY 3.5 4.2 + - - +
301A TYR* 1.3 76.2 - - - +
303A GLY* 1.3 67.9 + - - +
305A LEU* 3.1 18.2 + - + +
306A VAL* 3.3 15.1 + - - +
336A THR* 3.6 11.9 - - - +
339A ILE* 3.4 22.0 - - + +
378A VAL* 3.3 22.8 - - + +
379A SER* 3.2 42.2 - - - +
382A SER* 4.3 10.5 - - - -
416A VAL* 4.6 21.8 - - - -
420A HIS* 5.4 2.2 - - + -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET 5.2 0.8 + - - -
302A MET* 1.3 77.1 - - - +
304A GLU* 1.3 57.0 + - - +
306A VAL* 2.9 23.6 - - - +
307A ARG* 3.0 11.6 + - - +
334A PHE* 3.0 24.7 - - - +
335A GLU* 3.8 2.0 - - - -
336A THR* 3.2 20.9 + - - -
339A ILE* 3.4 13.1 - - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 3.9 20.2 - - + -
300A MET 4.9 4.4 + - - +
301A TYR* 3.6 17.6 + - + +
302A MET 3.2 0.6 - - - -
303A GLY* 1.3 74.2 - - - +
305A LEU* 1.3 60.9 + - - +
307A ARG* 2.7 36.2 + - - -
308A LEU* 3.2 31.4 + - + +
331A THR* 3.1 13.5 + - - -
332A GLY* 3.0 29.8 + - - +
334A PHE 3.5 4.4 + - - -
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Residues in contact with LEU 305 (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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29A MET* 4.5 7.2 - - + -
275A THR* 5.1 0.2 - - + -
277A PHE* 3.8 19.5 - - + +
278A ASP* 3.6 17.0 - - - +
281A ILE* 3.1 31.6 - - + -
295A LYS 4.6 10.5 - - - +
296A MET* 4.7 4.3 - - - +
301A TYR 3.0 18.2 + - - +
302A MET* 3.5 10.1 - - + +
303A GLY 3.0 0.8 - - - -
304A GLU* 1.3 79.9 - - - +
306A VAL* 1.3 58.3 + - - +
308A LEU* 3.9 2.8 + - - +
309A ILE* 3.0 29.8 + - + +
378A VAL* 4.2 24.5 - - + -
381A ARG* 3.5 24.9 - - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET 3.3 13.0 + - - +
303A GLY* 2.9 20.4 - - - +
305A LEU* 1.3 74.8 - - - +
307A ARG* 1.3 65.3 + - - +
309A ILE* 2.9 11.0 + - - +
310A LEU* 2.9 25.4 + - + +
334A PHE* 3.0 37.9 - - + -
339A ILE* 4.1 7.6 - - + -
371A THR* 5.1 1.1 - - + +
374A ILE* 3.1 31.9 - - + +
375A CYS* 4.4 9.2 - - - -
378A VAL* 4.3 9.8 - - + +
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Residues in contact with ARG 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 GLY 3.0 16.2 + - - +
304A GLU* 2.7 45.8 + - - +
306A VAL* 1.3 74.8 - - - +
308A LEU* 1.3 84.4 + - - +
310A LEU* 2.8 23.2 + - - +
311A VAL* 3.0 17.8 + - + +
327A GLU 5.0 0.4 - - - -
328A LEU* 3.1 39.6 + - + +
329A LEU* 3.6 18.0 + - - +
330A ASN 3.4 21.1 + - - -
331A THR* 3.4 14.7 + - - +
332A GLY 3.8 2.7 - - - +
333A ARG* 5.2 0.7 - - - -
334A PHE* 3.7 24.8 - - + +
359A LEU* 6.0 0.4 - - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 3.8 20.2 - - + +
280A GLU* 3.9 38.8 - - + +
281A ILE* 3.6 35.9 - - + +
304A GLU* 3.2 19.5 + - - +
305A LEU 4.1 3.8 - - - +
306A VAL 3.4 0.4 - - - -
307A ARG* 1.3 110.5 - - - +
309A ILE* 1.3 57.0 + - - +
311A VAL* 3.6 10.4 + - + +
312A LYS* 3.1 25.8 + - - +
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Residues in contact with ILE 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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25A TYR* 5.1 0.2 - - + -
26A LEU* 4.0 14.8 - - + -
29A MET* 4.0 27.4 - - + -
277A PHE* 3.5 29.6 - - + -
305A LEU* 3.0 19.7 - - + +
306A VAL* 2.9 9.9 + - - +
307A ARG 2.8 0.2 + - - -
308A LEU* 1.3 74.2 - - - +
310A LEU* 1.3 66.6 + - - +
312A LYS* 3.4 2.9 + - - +
313A MET* 3.0 47.4 + - + +
374A ILE* 4.0 17.3 - - + -
378A VAL* 4.1 18.2 - - + -
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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
----------------------------------------------------------
306A VAL* 2.9 23.1 + - + +
307A ARG* 2.8 9.0 + - - +
309A ILE* 1.3 74.7 - - - +
311A VAL* 1.3 55.0 + - - +
313A MET* 2.8 7.2 + - - +
314A ALA* 2.7 36.0 + - - +
319A LEU* 4.0 12.9 - - + +
320A PHE* 4.6 7.9 - - + -
328A LEU* 4.0 27.1 - - + -
334A PHE* 4.3 28.0 - - + -
356A LEU* 4.5 9.2 - - + -
359A LEU* 5.4 0.2 - - + -
371A THR* 3.6 23.3 - - - +
374A ILE* 3.6 28.3 - - + -
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Residues in contact with VAL 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 ARG* 3.0 21.1 + - - +
308A LEU* 3.8 11.4 - - + +
310A LEU* 1.3 74.3 - - - +
312A LYS* 1.3 64.6 + - - +
314A ALA* 3.8 3.0 - - - +
315A LYS* 3.0 42.6 + - + +
324A LEU* 4.4 2.7 - - + -
328A LEU* 3.6 38.3 - - + +
329A LEU* 3.6 28.9 - - + -
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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
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25A TYR* 3.1 25.4 - - - +
276A GLU* 3.2 35.7 + - - +
277A PHE* 3.6 26.5 - - + -
308A LEU 3.1 18.0 + - - +
309A ILE 3.7 4.9 - - - +
311A VAL* 1.3 78.4 - - - +
313A MET* 1.3 62.0 + - + +
315A LYS* 3.8 11.9 + - - +
316A GLU* 3.2 39.5 + - + +
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Residues in contact with MET 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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21A LYS* 5.7 2.7 - - - -
22A VAL* 4.5 12.6 - - + -
25A TYR* 2.9 52.7 - - + -
26A LEU* 4.1 11.0 - - + -
309A ILE* 3.0 27.4 + - + +
310A LEU 2.8 13.3 + - - +
312A LYS* 1.3 70.1 - - - +
314A ALA* 1.3 65.6 + - - +
316A GLU* 3.0 14.1 + - - +
318A LEU* 3.2 31.8 + - + +
319A LEU* 3.8 34.8 - - + -
374A ILE* 3.8 18.4 - - + -
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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 LEU 2.7 19.9 + - - +
311A VAL* 3.8 3.1 - - - +
313A MET* 1.3 71.4 - - - +
315A LYS* 1.3 63.6 + - - +
317A GLU* 2.8 14.0 + - - -
319A LEU* 3.6 15.5 - - - +
320A PHE* 4.0 21.5 - - + -
322A GLY* 3.5 15.6 - - - -
324A LEU* 3.1 33.0 - - + -
328A LEU* 4.8 2.7 - - + -
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Residues in contact with LYS 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 VAL* 3.0 38.0 + - + +
312A LYS* 3.9 10.4 - - - +
314A ALA* 1.3 75.0 - - - +
316A GLU* 1.3 61.9 + - + +
317A GLU* 3.6 7.4 + - - +
322A GLY* 5.6 0.2 - - - -
324A LEU* 3.8 21.9 - - + +
329A LEU* 6.0 0.2 - - + -
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Residues in contact with GLU 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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25A TYR* 3.0 33.5 + - - -
312A LYS* 3.2 40.2 + - + +
313A MET* 3.0 7.5 + - - +
315A LYS* 1.3 79.9 - - + +
317A GLU* 1.3 67.7 + - - +
318A LEU* 3.2 27.1 - - + +
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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