Contacts of the helix formed by residues 298 - 315 (chain A) in PDB entry 5FN2
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 ALA 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ARG* 3.6 5.4 - - - +
282A LEU 4.2 2.7 - - - +
283A ASP* 3.1 43.5 - - - +
284A SER* 4.0 7.4 - - - +
294A GLY 2.8 15.2 + - - +
296A GLU 3.3 0.6 - - - -
297A SER* 1.3 75.0 - - - +
299A VAL* 1.3 63.9 - - - +
300A ALA 3.3 2.2 - - - -
301A SER* 2.8 22.7 + - - -
302A PHE* 3.3 11.7 - - - -
553A HIS* 4.8 5.4 - - + -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO 3.3 26.5 - - - +
294A GLY 2.7 11.3 + - - +
295A ALA* 2.9 12.1 + - - +
298A ALA* 1.3 72.3 - - - +
300A ALA* 1.3 60.5 + - - +
302A PHE* 3.2 15.0 + - - -
303A VAL* 2.9 42.6 + - + +
522A LEU* 4.2 2.7 - - + -
525A PHE* 3.8 22.4 - - + -
526A LEU* 3.5 24.7 - - + -
553A HIS* 3.5 26.2 - - + +
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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
----------------------------------------------------------
295A ALA 2.9 16.2 + - - +
296A GLU* 4.5 8.5 - - - +
299A VAL* 1.3 82.6 - - - +
301A SER* 1.3 58.1 + - - +
303A VAL* 3.2 7.6 + - - +
304A THR* 2.9 33.3 + - - +
368A VAL 4.2 18.6 - - - +
369A ALA* 4.8 1.6 - - + -
463A ILE* 3.8 24.2 - - + -
487A LEU* 3.8 7.9 - - + +
522A LEU* 4.9 0.2 - - - -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.6 6.6 - - - +
281A ARG* 3.4 13.3 + - - +
296A GLU 5.0 0.8 + - - -
297A SER 4.5 2.6 + - - -
298A ALA* 2.8 26.1 + - - -
300A ALA* 1.3 78.3 - - - +
302A PHE* 1.3 60.4 + - - +
304A THR* 2.4 25.8 + - - -
305A GLN* 2.9 13.7 + - - +
365A LEU* 3.1 37.7 + - - +
367A GLN* 4.2 12.3 - - - -
368A VAL* 4.6 7.0 - - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.4 19.3 - - + -
281A ARG 4.0 1.1 - - - +
282A LEU* 3.3 48.0 - - + -
298A ALA 3.3 17.5 - - - -
299A VAL* 3.2 23.2 + - - -
301A SER* 1.3 81.8 + - - +
303A VAL* 1.3 56.9 + - - +
305A GLN* 3.2 4.9 + - - +
306A LEU* 2.9 38.0 + - + +
329A PHE* 3.6 6.1 - + + -
525A PHE* 3.4 30.5 - + - -
553A HIS* 3.7 28.3 - + - -
563A THR* 4.7 0.4 - - + -
567A VAL* 3.2 28.3 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 2.9 30.1 + - + +
300A ALA 3.2 7.4 + - - +
302A PHE* 1.3 77.4 - - + +
304A THR* 1.3 55.7 + - - +
306A LEU* 3.2 10.9 + - - +
307A ALA* 2.9 27.9 + - - +
487A LEU* 4.6 1.8 - - + -
518A VAL* 3.8 29.6 - - + +
521A LEU* 3.8 20.4 - - + +
522A LEU* 3.8 16.2 - - + -
525A PHE* 3.7 32.5 - - + -
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Residues in contact with THR 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 2.9 10.7 + - - +
301A SER* 2.4 33.3 + - - -
303A VAL* 1.3 75.7 - - - +
305A GLN* 1.3 55.7 + - - +
307A ALA* 3.2 6.7 + - - -
308A ALA* 2.9 26.6 + - - +
365A LEU* 3.0 18.4 - - - +
368A VAL* 4.3 10.0 - - + +
487A LEU* 3.4 49.1 - - + +
490A VAL* 4.6 13.9 - - + -
491A ALA* 3.3 13.0 - - - +
518A VAL* 5.7 0.2 - - - -
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Residues in contact with GLN 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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278A ALA* 2.7 48.8 + - - +
279A ALA 3.5 7.4 - - - +
280A THR* 3.1 20.8 + - - +
301A SER 2.9 10.5 + - - +
302A PHE 3.2 8.3 + - - +
304A THR* 1.3 78.1 + - - +
306A LEU* 1.3 55.6 - - - +
308A ALA* 3.2 7.9 + - - +
309A ALA* 2.9 27.5 + - - +
327A PHE* 3.7 12.4 - - + +
328A VAL 2.8 26.1 + - - +
329A PHE* 3.5 17.7 - - + -
365A LEU* 3.6 17.2 - - + +
494A LEU* 4.3 3.8 - - - +
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Residues in contact with LEU 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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302A PHE* 2.9 35.8 + - + +
303A VAL* 3.3 8.3 - - - +
305A GLN* 1.3 76.4 - - - +
307A ALA* 1.3 57.3 + - - +
309A ALA* 3.2 8.3 + - - +
310A GLU* 2.9 29.1 + - - +
329A PHE* 3.3 26.7 - - + -
521A LEU* 3.6 31.2 - - + -
525A PHE* 4.2 9.9 - - + -
567A VAL* 4.4 6.1 - - + +
570A ALA* 4.9 3.4 - - + -
571A LEU* 3.9 28.9 - - + +
574A LEU* 3.7 20.8 - - + +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL 2.9 12.1 + - - +
304A THR* 3.2 5.6 + - - +
306A LEU* 1.3 75.5 - - - +
308A ALA* 1.3 58.6 + - - +
310A GLU* 3.2 9.7 + - - +
311A ALA* 2.9 28.8 + - - +
491A ALA* 3.2 23.8 - - + -
513A ALA* 3.8 7.7 - - + +
517A THR* 5.4 2.2 - - - -
518A VAL* 3.2 31.4 - - + -
521A LEU* 4.5 4.0 - - - +
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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
----------------------------------------------------------
304A THR 2.9 11.7 + - - +
305A GLN* 3.2 10.5 + - - +
307A ALA* 1.3 77.1 - - - +
309A ALA* 1.3 57.0 + - - +
311A ALA* 3.2 5.8 + - - +
312A LEU* 2.9 31.0 + - - +
327A PHE* 4.1 4.7 - - + -
491A ALA* 3.1 28.2 - - - +
494A LEU* 3.9 28.3 - - + -
495A GLY* 3.9 6.4 - - - +
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Residues in contact with ALA 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 GLN* 2.9 8.7 + - + +
306A LEU* 3.2 13.0 + - - +
308A ALA* 1.3 75.8 - - - +
310A GLU* 1.3 59.0 + - - +
312A LEU* 3.3 3.5 + - - +
313A GLN* 2.9 34.1 + - - +
327A PHE* 3.2 42.3 - - + -
571A LEU* 4.4 15.9 - - + -
574A LEU* 5.6 0.7 - - + -
575A THR* 4.5 8.5 - - + -
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Residues in contact with GLU 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 LEU 2.9 12.7 + - - +
307A ALA* 3.2 12.1 + - - +
309A ALA* 1.3 76.8 - - - +
311A ALA* 1.3 62.8 + - - +
313A GLN* 3.4 1.6 + - - +
314A LYS* 3.0 35.2 + - + +
514A ASP* 3.7 23.4 - - - +
517A THR* 4.2 16.9 + - + -
573A ASN* 5.0 1.0 + - - +
574A LEU* 2.9 58.1 - - + +
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Residues in contact with ALA 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 ALA 2.9 11.0 + - - +
308A ALA* 3.3 11.0 - - - +
310A GLU* 1.3 79.8 - - - +
312A LEU* 1.3 63.3 + - - +
314A LYS* 3.2 16.4 + - - +
315A ALA 3.3 8.5 + - - -
491A ALA 5.2 0.2 - - - +
492A THR* 5.0 3.1 - - - -
511A VAL* 3.7 22.6 - - + +
512A GLN 3.2 37.9 + - - +
513A ALA* 3.5 5.4 - - + +
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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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260A LEU* 3.2 40.2 - - + -
308A ALA 2.9 14.5 + - - +
309A ALA 4.0 1.1 - - - +
311A ALA* 1.3 77.0 - - - +
313A GLN* 1.3 66.8 + - - +
315A ALA* 3.0 21.1 + - - +
318A VAL* 3.7 6.8 - - + +
321A LEU* 5.8 0.9 - - + -
325A VAL* 4.2 13.5 - - + -
327A PHE* 3.5 34.5 - - + -
495A GLY* 4.6 6.5 - - - +
498A LEU* 3.9 22.9 - - + -
499A TYR* 4.9 8.1 - - + +
511A VAL* 3.7 15.2 - - + +
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Residues in contact with GLN 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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259A MET 4.2 1.0 + - - -
260A LEU* 3.2 47.4 + - - +
309A ALA 2.9 16.9 + - - +
310A GLU* 3.8 3.6 - - - +
312A LEU* 1.3 82.2 - - - +
314A LYS* 1.3 61.9 + - - +
315A ALA 3.0 12.1 - - - +
318A VAL* 4.2 8.8 - - - +
327A PHE* 5.3 2.8 - - - -
574A LEU 4.4 3.8 - - - +
575A THR* 3.1 56.5 - - - +
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Residues in contact with LYS 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 GLU* 3.0 29.3 + - - +
311A ALA 3.2 10.0 + - - +
313A GLN* 1.3 76.9 - - - +
315A ALA* 1.3 59.6 + - - +
316A PRO* 3.6 5.2 - - - +
512A GLN* 4.3 17.5 + - - +
514A ASP* 3.9 35.2 + - - +
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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
----------------------------------------------------------
311A ALA 3.3 6.4 + - - +
312A LEU* 3.0 16.9 + - - +
313A GLN 3.0 13.5 - - - +
314A LYS* 1.3 75.0 - - - +
316A PRO* 1.4 68.1 - - + +
317A ASP 4.5 7.4 - - - +
318A VAL* 3.1 20.2 - - + +
499A TYR* 5.5 7.4 - - + -
507A PHE* 5.3 5.2 - - + +
510A THR* 4.2 15.5 - - - +
511A VAL* 4.6 11.4 - - + +
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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