Contacts of the helix formed by residues 316 - 328 (chain J) in PDB entry 4E2I
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 316 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276J TYR* 3.6 32.8 - + + -
279J GLU* 3.5 49.7 + - + +
280J THR* 4.6 7.0 - - + +
295J PHE* 4.6 3.8 - - + -
311J PRO 3.3 23.1 - - - -
312J SER* 3.9 18.2 - - - +
313J HIS 3.1 3.4 + - - +
315J LYS* 1.3 103.3 + - + +
317J HIS* 1.3 64.3 + - - +
318J GLU 3.5 1.6 - - - -
319J LYS* 3.3 23.2 + - + -
320J HIS* 3.0 29.4 + - + +
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Residues in contact with HIS 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294J GLU 3.7 17.3 - - - -
295J PHE* 3.3 39.3 + + + -
298J SER 3.6 9.2 - - - -
299J PHE* 3.4 31.4 + - + +
302J CYS* 3.9 5.6 - - - -
305J CYS* 5.4 0.7 - - - -
313J HIS* 2.9 16.6 + - - +
314J TYR* 4.5 3.7 - - - -
315J LYS 3.9 0.2 - - - -
316J TYR* 1.3 76.1 - - - +
318J GLU* 1.3 56.7 + - + +
319J LYS 3.0 0.4 + - - -
320J HIS 3.1 0.7 + - - -
321J TYR* 2.6 62.0 + + + +
700J ZN 2.8 28.1 - - - -
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Residues in contact with GLU 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J PHE* 3.6 51.2 - - + -
305J CYS* 5.1 6.4 - - - -
314J TYR 4.8 10.5 + - - +
315J LYS 5.6 0.2 - - - -
316J TYR* 3.5 0.4 - - - +
317J HIS* 1.3 75.6 - - + +
319J LYS* 1.3 61.0 + - - +
321J TYR* 4.1 6.4 + - - +
322J ALA 5.3 0.5 + - - -
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Residues in contact with LYS 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LEU* 4.9 8.8 - - + +
275J GLU* 3.2 37.4 + - - -
279J GLU* 5.5 6.7 - - - -
315J LYS 4.8 4.0 + - - +
316J TYR* 3.3 30.7 + - + +
317J HIS 3.0 0.8 - - - -
318J GLU* 1.3 81.1 - - - +
320J HIS* 1.3 79.1 + - + +
321J TYR 3.6 0.4 - - - -
322J ALA* 5.3 2.5 + - - +
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Residues in contact with HIS 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J LEU* 3.2 35.4 + - + +
275J GLU* 3.9 17.0 - - - -
276J TYR* 3.2 40.5 - + + +
279J GLU* 5.6 0.2 - - - +
292J TYR* 3.4 27.0 + + + +
295J PHE* 4.6 6.5 - + + -
316J TYR* 3.0 27.4 + - + +
317J HIS 3.4 1.3 - - - -
319J LYS* 1.3 102.1 + - + +
321J TYR* 1.3 60.1 + - - +
322J ALA 3.3 3.1 - - - +
323J ASN* 3.6 4.6 + - - +
324J ALA* 3.0 30.8 + - - +
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Residues in contact with TYR 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295J PHE 3.2 21.9 - - - +
296J GLN* 4.6 2.0 - - - -
297J TYR 2.9 36.2 + - - -
298J SER* 3.8 11.6 - - - -
299J PHE* 3.5 27.8 - + + -
300J GLU* 4.3 8.6 + - - -
317J HIS* 2.6 34.5 + - + +
318J GLU* 4.1 5.6 - - - +
319J LYS 3.6 1.4 - - - -
320J HIS* 1.3 73.9 - - - +
322J ALA* 1.3 65.2 + - - +
325J ALA* 3.2 27.9 + - + +
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Residues in contact with ALA 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J LEU* 5.8 3.4 - - + -
318J GLU 5.3 0.8 + - - -
319J LYS 5.8 1.8 - - - +
320J HIS* 3.3 1.3 - - - -
321J TYR* 1.3 85.4 - - - +
323J ASN* 1.3 60.6 + - - +
325J ALA* 3.5 14.4 - - - +
326J ILE* 3.9 13.7 - - - +
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Residues in contact with ASN 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J GLN 4.8 0.3 - - - +
268J VAL* 3.5 9.3 - - - +
269J SER* 2.6 51.3 + - - -
272J LEU* 3.5 23.3 - - + +
273J VAL* 3.2 12.5 - - - +
292J TYR* 2.8 29.1 + - - +
320J HIS 3.6 3.7 + - - +
322J ALA* 1.3 74.5 - - - +
324J ALA* 1.3 55.4 + - - +
325J ALA 3.0 1.8 - - - -
326J ILE* 3.0 10.6 + - - +
327J PHE* 2.7 34.1 + - - +
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Residues in contact with ALA 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J TYR* 3.9 19.6 + - + +
295J PHE* 3.1 36.1 - - + +
296J GLN* 3.2 19.5 - - + +
320J HIS 3.0 20.7 + - - +
323J ASN* 1.3 75.9 - - - +
325J ALA* 1.3 61.3 + - - +
327J PHE* 3.2 19.8 + - - +
328J ALA 3.3 5.5 + - - -
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Residues in contact with ALA 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295J PHE 4.2 0.4 + - - -
296J GLN* 4.3 12.0 - - - +
321J TYR* 3.2 29.6 + - + +
322J ALA* 3.5 10.5 - - - +
323J ASN 3.0 0.4 - - - -
324J ALA* 1.3 78.9 - - - +
326J ILE* 1.3 61.8 + - + +
328J ALA* 4.1 5.9 - - - +
329J ASP* 4.0 12.5 - - - +
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Residues in contact with ILE 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266J LYS* 4.3 35.7 - - + -
267J GLN* 3.7 24.9 - - - +
268J VAL* 3.5 24.2 - - + +
322J ALA 3.9 15.5 - - - +
323J ASN* 3.0 8.8 + - - +
325J ALA* 1.3 78.1 - - + +
327J PHE* 1.3 66.3 + - - +
328J ALA 3.1 2.7 - - - -
329J ASP* 3.0 21.6 + - + +
330J SER 3.5 4.3 + - - -
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Residues in contact with PHE 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J VAL* 4.0 8.5 - - + -
273J VAL* 4.7 1.8 - - + -
289J LEU* 3.7 9.9 - - + -
292J TYR* 3.7 31.4 - + + -
293J LEU* 3.5 33.4 - - + -
296J GLN* 5.0 0.2 - - - -
323J ASN* 2.7 16.4 + - - +
324J ALA* 3.2 16.4 + - - +
326J ILE* 1.3 78.2 - - - +
328J ALA* 1.3 60.7 + - - +
330J SER* 3.1 17.4 + - - -
333J GLN* 3.3 42.4 - - + +
336J ILE* 3.5 44.0 - - + -
337J CYS* 3.5 15.5 - - - -
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Residues in contact with ALA 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270I TRP* 5.3 1.2 - - - +
271I LYS* 4.3 26.2 + - + +
274I THR* 5.6 0.9 + - - -
339I GLN* 5.2 0.7 - - - +
296J GLN* 3.1 49.1 + - + +
324J ALA 3.3 2.4 + - - -
325J ALA 4.1 6.1 - - - +
326J ILE 3.1 0.4 - - - -
327J PHE* 1.3 80.3 - - - +
329J ASP* 1.3 66.8 + - - +
330J SER 3.1 3.5 + - - +
333J GLN* 3.0 19.3 - - - +
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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