Contacts of the helix formed by residues 309 - 327 (chain A) in PDB entry 5FMH
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 GLY 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A GLY 3.5 2.8 - - - -
308A GLY* 1.3 78.4 - - - +
310A PHE* 1.3 68.3 + - - -
311A LEU* 3.4 2.9 - - - -
312A GLY 3.4 4.0 + - - +
313A SER* 2.9 25.1 + - - -
340A MET* 3.9 9.6 - - - -
343A ILE* 6.4 1.6 - - - -
397A ALA 4.9 4.9 + - - -
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Residues in contact with PHE 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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309A GLY* 1.3 71.5 - - - +
311A LEU* 1.3 58.8 + - - +
313A SER* 3.5 1.6 - - - -
314A GLU* 2.8 36.5 + - - +
340A MET* 3.6 41.0 - - + +
343A ILE* 3.8 40.8 - - + -
344A LEU* 4.8 7.6 - - + -
482A PHE* 3.5 38.6 - + + -
484A SER* 3.3 30.4 + - - +
492A TYR* 4.0 22.0 - + + -
494A ALA* 5.9 4.5 - - + -
577A VAL* 6.1 1.8 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.7 18.2 - - - +
284A PHE* 3.8 22.4 - - + +
285A ARG* 5.8 2.2 - - - -
309A GLY 3.4 0.6 - - - -
310A PHE* 1.3 76.8 - - - +
312A GLY* 1.3 57.9 + - - +
314A GLU* 3.2 7.4 + - - +
315A LEU* 2.8 48.8 + - + +
397A ALA* 4.1 20.4 - - + +
1000A FAD 3.6 41.1 - - + -
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 3.7 12.2 - - - +
307A GLY 3.8 17.3 - - - -
309A GLY* 3.4 5.7 + - - +
311A LEU* 1.3 79.2 - - - +
313A SER* 1.3 56.2 - - - +
315A LEU* 3.4 2.7 + - - +
316A ALA* 2.9 27.7 + - - +
332A GLN* 3.4 8.2 + - - -
397A ALA* 3.8 19.0 + - - +
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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
----------------------------------------------------------
308A GLY 3.3 5.4 + - - -
309A GLY 2.9 18.5 + - - -
310A PHE 3.5 3.6 - - - -
312A GLY* 1.3 73.7 - - - +
314A GLU* 1.3 64.2 + - - +
316A ALA* 3.3 5.1 + - - +
317A CYS* 3.1 27.7 + - - -
332A GLN* 3.3 9.0 + - - +
339A ASN* 3.0 26.6 + - - -
340A MET* 3.4 15.6 - - - -
356A VAL* 4.7 4.8 - - - +
486A LEU* 3.9 12.6 - - - -
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 2.6 45.6 + - - +
177A LYS* 2.8 22.5 + - + -
181A PHE* 5.7 0.9 - - - -
310A PHE* 2.8 23.8 + - - +
311A LEU* 3.6 11.3 - - - +
313A SER* 1.3 72.0 - - - +
315A LEU* 1.3 61.9 + - - +
317A CYS* 3.2 5.2 + - - +
318A ALA* 3.0 22.3 + - - +
482A PHE* 5.4 0.7 - - - -
483A TRP 4.7 0.2 - - - +
484A SER* 2.5 37.9 + - - +
485A ASP 3.3 19.7 + - - +
486A LEU* 3.8 7.6 - - + +
1000A FAD 4.3 5.6 + - - +
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Residues in contact with LEU 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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176A SER* 3.9 22.7 - - - -
180A TRP* 4.2 13.5 - - + +
284A PHE* 3.8 51.4 - - + -
293A LEU* 4.9 4.0 - - + -
305A ILE* 3.7 11.7 - - + -
311A LEU* 2.8 35.0 + - + +
312A GLY* 3.8 7.4 - - - +
314A GLU* 1.3 74.8 - - - +
316A ALA* 1.3 57.5 + - - +
318A ALA* 3.5 2.9 - - + +
319A LEU* 2.8 39.8 + - + +
395A VAL* 4.2 14.6 - - + -
397A ALA* 4.9 2.9 - - + -
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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
----------------------------------------------------------
305A ILE* 3.2 18.4 - - + +
312A GLY 2.9 17.8 + - - +
313A SER 3.5 6.5 - - - +
314A GLU 3.3 0.2 - - - -
315A LEU* 1.3 75.3 - - - +
317A CYS* 1.3 57.5 + - - +
319A LEU* 4.3 0.2 - - - +
320A GLY 2.8 23.7 + - - -
330A VAL* 4.3 1.5 - - - +
332A GLN* 3.6 21.8 - - + +
356A VAL* 3.9 12.3 - - + -
361A VAL* 3.2 22.7 - - + +
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Residues in contact with CYS 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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181A PHE* 4.6 14.8 - - + -
313A SER 3.1 17.1 + - - +
314A GLU 3.8 6.1 - - - +
316A ALA* 1.3 75.3 - - - +
318A ALA* 1.3 64.6 + - - +
320A GLY* 3.4 0.5 + - - -
321A ARG* 3.0 24.9 + - - +
355A LYS* 4.3 7.0 - - - -
356A VAL* 4.0 23.6 - - - -
359A GLU* 4.1 29.9 - - + +
361A VAL* 4.9 0.2 - - - -
486A LEU* 4.1 28.9 - - - -
487A GLY 5.1 0.2 - - - +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER 4.1 7.0 - - - +
180A TRP* 3.4 47.7 - - + +
181A PHE* 4.3 12.2 - - + -
314A GLU 3.0 13.6 + - - +
315A LEU* 3.5 10.5 - - - +
317A CYS* 1.3 78.1 - - - +
319A LEU* 1.3 61.8 + - + +
321A ARG* 3.3 10.2 + - - +
322A LYS* 3.4 16.8 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TRP* 3.5 34.8 - - + -
293A LEU* 4.3 17.3 - - + -
297A SER* 4.0 19.7 + - - -
303A ILE* 3.8 34.5 - - + -
305A ILE* 4.0 16.8 - - + -
315A LEU* 2.8 24.8 + - + +
318A ALA* 1.3 73.2 - - + +
320A GLY* 1.3 56.1 + - - +
322A LYS* 3.2 5.9 + - - +
323A ALA* 2.8 36.2 + - - +
330A VAL* 3.8 18.3 - - + +
395A VAL* 4.8 0.7 - - + -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 2.8 19.5 + - - -
317A CYS 3.7 1.3 - - - -
319A LEU* 1.3 77.9 - - - +
321A ARG* 1.3 55.5 + - - +
323A ALA* 3.4 2.7 + - - +
324A ARG* 3.0 28.8 + - - +
330A VAL* 3.9 8.4 - - - +
359A GLU* 3.8 15.8 - - - +
360A GLY* 5.7 1.1 - - - -
361A VAL* 4.1 15.3 - - - -
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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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180A TRP 3.5 15.0 + - - -
181A PHE* 3.2 55.3 + - + +
182A SER 4.2 1.4 + - - -
183A ASP* 2.7 40.2 + - - -
317A CYS 3.0 13.1 + - - +
318A ALA* 3.6 9.4 - - - +
319A LEU 3.2 0.2 - - - -
320A GLY* 1.3 76.2 - - - +
322A LYS* 1.3 70.6 + - - +
323A ALA 3.4 0.3 + - - -
324A ARG* 3.4 15.0 + - - +
325A ALA* 3.4 11.8 + - - +
359A GLU* 5.1 10.0 + - - +
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Residues in contact with LYS 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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179A LEU 5.2 1.4 + - - -
180A TRP* 3.2 52.6 + - + +
182A SER 3.7 15.2 + - - -
183A ASP* 5.2 1.0 + - - +
187A VAL* 6.0 4.0 - - - +
294A GLU* 5.2 12.1 - - - -
297A SER* 3.6 20.0 - - - +
318A ALA 3.4 13.2 + - - +
319A LEU* 3.2 7.1 + - - +
321A ARG* 1.3 85.3 - - + +
323A ALA* 1.3 63.0 + - - +
325A ALA* 3.3 8.0 + - + +
326A LEU* 3.1 33.4 + - + +
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Residues in contact with ALA 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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297A SER* 5.7 1.3 - - - +
319A LEU 2.8 17.4 + - - +
320A GLY* 3.9 4.0 - - - +
321A ARG 3.2 0.2 - - - -
322A LYS* 1.3 75.4 - - - +
324A ARG* 1.3 55.9 + - - +
326A LEU* 3.1 1.0 + - - +
327A GLY* 2.7 33.3 + - - -
328A THR* 3.1 46.0 + - - +
330A VAL* 3.8 17.9 - - + +
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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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320A GLY 3.0 17.2 + - - +
321A ARG* 3.4 9.4 + - - +
323A ALA* 1.3 74.3 - - - +
325A ALA* 1.3 62.3 + - - +
327A GLY* 3.7 7.4 + - - -
358A ARG 3.2 28.1 + - - -
359A GLU* 3.2 32.9 + - - +
360A GLY* 3.4 9.5 - - - +
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Residues in contact with ALA 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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321A ARG 3.4 8.0 + - - +
322A LYS* 3.3 13.4 + - - +
323A ALA 3.2 0.8 - - - -
324A ARG* 1.3 80.5 - - - +
326A LEU* 1.3 66.0 + - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A SER 4.2 18.8 - - - +
298A ARG* 4.7 24.0 - - + +
322A LYS* 3.1 27.5 + - + +
323A ALA* 3.1 2.9 + - - -
325A ALA* 1.3 83.4 - - + +
327A GLY* 1.3 60.7 + - - +
328A THR* 3.8 26.4 - - + +
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Residues in contact with GLY 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 ALA 2.7 13.4 + - - -
324A ARG* 3.7 6.0 + - - -
325A ALA 3.4 3.8 + - - -
326A LEU* 1.3 75.2 - - - +
328A THR* 1.3 59.1 + - - +
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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
------------------------------------------------------------
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