Contacts of the helix formed by residues 316 - 328 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C TYR* 3.6 31.2 - + + -
279C GLU* 3.5 50.5 + - + +
280C THR* 4.6 6.0 - - + +
295C PHE* 4.6 3.6 - - + -
311C PRO 3.3 23.1 - - - -
312C SER* 3.9 18.2 - - - +
313C HIS 3.1 4.6 + - - +
315C LYS* 1.3 100.3 + - + +
317C HIS* 1.3 65.0 + - - +
318C GLU 3.5 2.0 - - - -
319C LYS* 3.3 25.5 + - + -
320C HIS* 3.0 28.6 + - + +
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Residues in contact with HIS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C GLU 3.7 17.0 - - - -
295C PHE* 3.2 40.5 - + + -
298C SER 3.6 9.1 - - - -
299C PHE* 3.4 28.3 + + + +
302C CYS* 3.9 3.4 - - - -
305C CYS* 5.4 0.9 - - - -
313C HIS* 2.9 16.6 + - - +
314C TYR* 4.5 3.9 - - - -
315C LYS 4.5 0.2 - - - +
316C TYR* 1.3 76.3 - - - +
318C GLU* 1.3 57.4 + - + +
319C LYS 3.1 0.3 + - - -
320C HIS 3.1 0.3 + - - -
321C TYR* 2.6 63.2 + + + +
700C ZN 2.4 35.7 - - - -
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 3.6 51.5 - - + -
305C CYS* 5.1 6.6 - - - -
314C TYR 4.8 10.1 + - - +
315C LYS 5.6 0.6 - - - -
316C TYR 3.5 0.2 - - - -
317C HIS* 1.3 76.5 - - + +
319C LYS* 1.3 59.6 + - - +
321C TYR* 4.1 6.2 + - - +
322C ALA 5.3 0.5 + - - -
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 4.9 8.6 - - + +
275C GLU* 3.2 37.3 + - - +
279C GLU* 5.5 5.8 - - - -
315C LYS 4.8 3.6 - - - +
316C TYR* 3.3 32.8 + - + +
317C HIS 3.0 0.6 - - - -
318C GLU* 1.3 81.8 - - - +
320C HIS* 1.3 76.5 + - + +
321C TYR 3.6 0.4 - - - -
322C ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 3.2 35.6 + - + +
275C GLU* 3.9 17.7 - - - -
276C TYR* 3.2 40.7 - + + +
279C GLU* 5.6 0.4 - - - +
292C TYR* 3.4 27.3 + + + +
295C PHE* 4.6 6.3 - + + -
316C TYR* 3.0 27.7 + - + +
317C HIS 3.4 1.8 - - - -
319C LYS* 1.3 103.1 + - + +
321C TYR* 1.3 59.9 + - - +
322C ALA 3.3 2.9 - - - -
323C ASN* 3.6 4.4 + - - +
324C ALA* 3.0 30.9 + - - +
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Residues in contact with TYR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PHE 3.2 20.2 - - - -
296C GLN* 4.6 2.0 - - - -
297C TYR 2.9 36.9 + - - -
298C SER* 3.8 11.8 - - - -
299C PHE* 3.6 27.8 - + + -
300C GLU* 4.3 8.6 + - - -
317C HIS* 2.6 34.3 + - + +
318C GLU* 4.1 5.3 - - - +
319C LYS 3.6 1.6 - - - -
320C HIS* 1.3 73.7 - - - +
322C ALA* 1.3 64.2 + - - +
325C ALA* 3.2 29.2 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 5.8 3.8 - - + -
318C GLU 5.3 0.6 + - - -
319C LYS 5.4 1.8 - - - +
320C HIS* 3.3 1.1 - - - +
321C TYR* 1.3 85.3 - - - +
323C ASN* 1.3 60.9 + - - +
325C ALA* 3.5 15.1 - - - +
326C ILE* 3.9 13.0 - - - +
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Residues in contact with ASN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C GLN 4.8 0.7 - - - +
268C VAL* 3.5 8.7 - - - +
269C SER* 2.6 50.8 + - - +
272C LEU* 3.5 24.5 - - + +
273C VAL* 3.2 13.1 - - - +
292C TYR* 2.8 27.3 + - - +
320C HIS 3.6 3.6 + - - +
321C TYR 3.4 0.2 - - - -
322C ALA* 1.3 74.2 - - - +
324C ALA* 1.3 56.8 + - - +
325C ALA 3.0 2.0 - - - -
326C ILE* 2.9 9.1 + - - +
327C PHE* 2.8 33.2 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 3.9 19.7 + - + +
295C PHE* 3.1 36.8 - - + +
296C GLN* 3.2 19.2 - - + +
320C HIS 3.0 20.5 + - - +
323C ASN* 1.3 77.2 - - - +
325C ALA* 1.3 61.6 + - - +
327C PHE* 3.2 18.7 + - + +
328C ALA 3.3 5.7 + - - -
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C PHE 4.2 0.2 + - - -
296C GLN* 4.3 12.7 - - - +
321C TYR* 3.2 30.1 + - + +
322C ALA* 3.5 10.3 - - - +
323C ASN 3.0 0.4 - - - -
324C ALA* 1.3 78.4 - - - +
326C ILE* 1.3 62.0 + - + +
328C ALA* 4.0 6.2 - - - +
329C ASP* 4.0 12.3 - - - +
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Residues in contact with ILE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LYS* 4.9 16.8 - - + -
267C GLN* 3.7 33.7 - - - +
268C VAL* 3.5 23.2 - - + +
322C ALA 3.9 14.4 - - - +
323C ASN* 2.9 9.3 + - - +
325C ALA* 1.3 77.2 - - + +
327C PHE* 1.3 66.5 + - - +
328C ALA 3.1 2.2 - - - -
329C ASP* 3.0 22.2 + - + +
330C SER 3.5 4.3 + - - -
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C VAL* 3.9 8.9 - - + +
273C VAL* 4.8 2.0 - - + -
289C LEU* 3.7 11.0 - - + -
292C TYR* 3.7 31.4 - + + -
293C LEU* 3.5 32.8 - - + -
323C ASN* 2.8 15.6 + - - +
324C ALA* 3.4 16.4 - - - +
326C ILE* 1.3 77.7 - - - +
328C ALA* 1.3 60.8 + - - +
330C SER* 3.1 17.5 + - - -
333C GLN* 3.3 41.1 - - + +
336C ILE* 3.5 42.4 - - + -
337C CYS* 3.5 15.0 - - - -
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B TRP* 5.7 2.3 - - - +
271B LYS* 4.5 25.3 + - + +
339B GLN* 5.5 0.5 - - - +
296C GLN* 3.2 47.5 + - + +
324C ALA 3.3 2.0 + - - -
325C ALA 4.0 5.8 - - - +
326C ILE 3.1 0.6 - - - -
327C PHE* 1.3 80.0 - - - +
329C ASP* 1.3 67.6 + - - +
330C SER 3.1 3.2 + - - +
333C GLN* 3.0 18.6 - - - +
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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