Contacts of the helix formed by residues 286 - 300 (chain A) in PDB entry 5I94
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 CYS 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 5.9 0.7 - - - -
283A LEU* 3.0 36.1 + - + +
284A GLN 2.7 1.2 + - - -
285A SER* 1.3 78.8 - - - +
287A VAL* 1.3 56.4 + - - +
288A LYS 3.2 0.2 - - - -
289A PRO* 3.2 20.2 - - - +
290A LEU* 4.0 8.0 - - - +
480A LYS* 3.5 29.8 - - - -
481A SER 3.7 0.4 + - - -
482A GLY* 3.6 18.8 - - - -
486A GLY* 3.7 17.9 - - - -
488A LEU* 4.3 10.1 - - + +
498A MET* 4.4 11.7 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.9 23.8 - - + +
284A GLN 2.8 18.6 + - - +
286A CYS* 1.3 77.9 - - - +
288A LYS* 1.3 70.2 + - + +
289A PRO 3.3 0.4 - - - -
290A LEU* 2.9 23.0 + - + +
291A LYS* 3.1 42.4 + - + +
357A VAL* 5.7 2.2 - - + -
361A LEU* 5.1 3.8 - - + -
416A LEU* 3.8 32.8 - - + +
417A CYS* 4.5 4.3 - - - -
419A ILE* 4.5 10.5 - - + -
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER* 3.3 43.6 + - - +
287A VAL* 1.3 79.0 - - + +
289A PRO* 1.3 67.3 - - + +
291A LYS* 3.5 16.1 + - - +
292A TYR* 3.1 22.5 + - - +
331A PRO 3.9 12.9 - - - +
332A MET* 3.7 30.5 - - - +
333A VAL 4.4 0.2 - - - -
334A ASN* 3.7 20.1 + - - +
337A ALA* 3.6 30.5 - - + +
340A VAL* 5.4 0.5 - - - +
413A TYR* 3.0 24.9 + - - -
417A CYS* 4.7 4.6 - - - -
465A TYR* 6.3 0.7 - - - -
480A LYS* 4.5 1.6 - - - -
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Residues in contact with PRO 289 (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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286A CYS 3.2 18.2 - - - +
288A LYS* 1.3 95.2 - - + +
290A LEU* 1.3 58.0 + - + +
292A TYR* 3.4 1.5 + - + +
293A ALA* 3.0 24.8 + - - +
332A MET* 3.8 13.5 - - + -
433A LEU* 5.5 0.4 - - + -
455A THR* 3.3 29.7 - - + +
459A MET* 3.7 20.0 - - + -
480A LYS* 3.5 33.2 - - + -
488A LEU* 4.7 7.6 - - + -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.2 20.0 - - + -
286A CYS 4.0 11.2 - - - +
287A VAL* 2.9 12.7 + - + +
289A PRO* 1.3 81.0 - - + +
291A LYS* 1.3 58.1 + - - +
293A ALA* 3.4 5.5 - - + +
294A ILE* 3.1 31.8 + - - +
361A LEU* 3.9 22.4 - - + -
364A MET* 4.2 19.4 - - + +
429A MET* 3.7 34.5 - - + +
433A LEU* 4.4 21.1 - - + -
488A LEU* 4.5 16.2 - - + -
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Residues in contact with LYS 291 (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 VAL* 3.1 36.1 + - + +
288A LYS* 3.5 24.9 - - - +
290A LEU* 1.3 74.4 - - - +
292A TYR* 1.3 64.5 + - - +
294A ILE* 3.8 10.3 - - + -
295A ALA* 3.1 24.3 + - - +
337A ALA* 4.4 8.5 - - - +
340A VAL* 3.7 11.6 - - + +
341A THR* 3.2 23.2 + - - +
344A ILE* 3.5 19.7 - - + +
357A VAL* 5.5 3.6 - - + -
413A TYR* 3.4 24.9 + - - -
416A LEU* 3.7 30.7 - - + +
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Residues in contact with TYR 292 (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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288A LYS 3.1 18.3 + - - +
289A PRO* 3.6 6.1 - - + +
291A LYS* 1.3 75.8 - - - +
293A ALA* 1.3 65.4 + - - +
295A ALA* 3.3 2.1 + - - +
296A VAL* 2.9 46.1 + - + +
304A VAL* 3.8 14.1 - - + -
305A HIS* 2.3 36.2 + - - -
331A PRO* 3.4 38.6 - - + -
332A MET* 4.7 2.5 - - + -
340A VAL* 4.2 10.9 - - + +
451A ALA 4.7 0.2 - - - -
454A ASN* 3.5 38.5 + - + +
455A THR* 3.4 20.4 - - + -
458A LEU* 3.5 15.9 - - + -
473B PHE* 3.6 3.3 - - - -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PRO 3.0 13.5 + - - +
290A LEU* 3.4 13.9 - - + +
292A TYR* 1.3 78.2 - - - +
294A ILE* 1.3 52.5 + - - +
297A ASN* 2.8 35.3 + - - +
364A MET* 5.4 0.2 - - + -
433A LEU* 5.1 2.9 - - + -
447A LEU* 3.7 30.7 - - + -
451A ALA* 3.5 11.0 - - + +
455A THR* 3.6 19.5 - - + +
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Residues in contact with ILE 294 (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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290A LEU 3.1 18.4 + - - +
291A LYS* 3.9 9.9 - - - +
292A TYR 3.3 0.2 - - - -
293A ALA* 1.3 76.5 - - - +
295A ALA* 1.3 59.4 + - - +
297A ASN* 3.1 5.6 + - - +
298A ASP* 2.9 31.4 + - - +
344A ILE* 4.1 15.0 - - + -
356A TYR* 3.9 16.8 - - + -
357A VAL* 4.1 26.5 - - + +
360A PHE* 3.6 56.1 - - + -
361A LEU* 4.8 2.9 - - + -
364A MET* 4.1 8.1 - - + -
447A LEU* 4.1 6.5 - - - +
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Residues in contact with ALA 295 (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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291A LYS 3.1 16.7 + - - +
292A TYR* 3.6 6.1 - - - +
293A ALA 3.3 0.2 - - - -
294A ILE* 1.3 79.7 - - - +
296A VAL* 1.3 54.2 + - - +
298A ASP* 2.9 4.5 + - - +
299A LEU* 2.7 48.6 + - + +
304A VAL* 3.9 16.8 - - + -
340A VAL* 4.5 10.1 - - + +
343A LEU* 5.0 3.6 - - + -
344A ILE* 4.1 16.4 - - + -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 2.9 54.0 + - + +
293A ALA 3.7 2.9 - - - +
295A ALA* 1.3 74.0 - - - +
297A ASN* 1.3 58.6 + - - +
300A GLY* 2.7 26.5 + - - +
301A THR* 4.1 8.7 - - - +
304A VAL* 3.7 18.8 - - + +
450A GLU* 4.1 15.4 - - - +
451A ALA* 3.6 26.0 - - + +
454A ASN* 3.8 15.7 - - - +
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Residues in contact with ASN 297 (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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293A ALA 2.8 18.0 + - - +
294A ILE* 3.3 8.5 - - - +
296A VAL* 1.3 73.9 - - - +
298A ASP* 1.3 81.8 + - - +
300A GLY 4.9 0.3 + - - -
360A PHE* 3.7 20.2 - - - -
445A ARG* 4.4 7.1 + - - -
446A VAL 4.0 2.8 + - - +
447A LEU* 3.5 16.7 - - + -
448A SER* 3.0 34.0 + - - -
451A ALA* 3.8 7.8 - - + +
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Residues in contact with ASP 298 (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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294A ILE* 2.9 20.5 + - - +
295A ALA* 2.9 4.2 + - - +
297A ASN* 1.3 95.3 + - - +
299A LEU* 1.3 78.1 + - + +
344A ILE* 5.6 1.0 - - - +
345A LYS* 5.1 7.2 + - - +
356A TYR* 2.4 39.5 + - - -
360A PHE* 4.1 0.9 - - - -
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Residues in contact with LEU 299 (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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295A ALA* 2.7 29.5 + - + +
298A ASP* 1.3 90.5 - - + +
300A GLY* 1.3 62.5 + - - +
302A GLU* 5.5 0.3 - - - +
303A TYR* 3.6 50.2 + - + +
304A VAL* 4.2 5.4 - - + -
343A LEU* 3.4 36.3 - - + +
344A ILE* 5.1 1.3 - - - -
345A LYS 5.7 1.1 - - - +
346A GLN* 5.9 1.1 - - - +
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Residues in contact with GLY 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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296A VAL* 2.7 22.8 + - - -
297A ASN 4.7 0.4 + - - -
299A LEU* 1.3 84.9 - - - +
301A THR* 1.3 68.2 + - - +
302A GLU* 3.4 5.6 + - - -
303A TYR 3.6 0.4 + - - -
304A VAL* 3.3 18.2 + - - +
450A GLU* 3.7 11.0 - - - -
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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