Contacts of the helix formed by residues 305 - 315 (chain C) in PDB entry 2A19
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 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C VAL* 4.6 9.4 - - + +
299C LYS 3.6 23.8 - - - +
300C TYR* 4.1 14.8 - - + -
302C ASN* 3.4 13.8 + - - +
303C GLU 2.9 0.8 + - - -
304C LYS* 1.3 77.5 - - - +
306C GLU* 1.3 57.2 + - - +
307C ARG 3.1 4.0 + - - -
308C GLU* 3.8 10.4 + - - +
309C VAL* 4.1 2.4 + - - +
362C LEU* 3.3 26.8 - - + +
364C ILE* 5.2 0.7 - - - +
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Residues in contact with GLU 306 (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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288B ILE* 4.0 8.9 - - + +
300C TYR* 3.2 39.5 + - + +
303C GLU* 2.7 40.2 + - + +
305C ALA* 1.3 70.2 - - - +
307C ARG* 1.3 62.4 + - - +
308C GLU 3.6 0.2 - - - -
309C VAL* 3.8 13.2 - - + -
310C LYS* 3.3 57.4 + - + +
362C LEU* 4.9 0.2 - - - -
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Residues in contact with ARG 307 (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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303C GLU 4.0 0.6 + - - -
304C LYS* 2.7 41.2 + - - +
306C GLU* 1.3 77.0 - - - +
308C GLU* 1.3 59.9 + - - +
310C LYS* 4.3 1.1 - - - +
311C ALA* 3.0 33.6 + - + +
413C ARG* 3.3 20.6 - - - +
434C GLY 5.5 1.4 + - - -
435C LEU* 4.1 8.5 + - - +
436C VAL* 3.0 28.8 + - + +
901C PO4 2.7 45.4 + - - -
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Residues in contact with GLU 308 (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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296C LYS* 3.4 27.6 + - - +
298C VAL* 5.5 0.9 - - - +
304C LYS 4.4 0.2 + - - -
305C ALA 3.8 5.1 + - - +
306C GLU 3.6 0.2 - - - -
307C ARG* 1.3 79.5 - - - +
309C VAL* 1.3 58.2 + - - +
311C ALA* 3.8 0.2 - - - +
312C LEU* 2.8 47.3 + - + +
364C ILE* 3.8 24.2 - - + +
366C MET* 3.6 23.9 - - - +
432C ASP* 5.3 0.3 - - - +
433C PHE* 3.3 35.3 + - + +
434C GLY* 3.7 9.4 + - - +
436C VAL* 4.0 9.1 - - + +
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.5 10.5 - - + +
289B ASP* 4.3 4.0 - - + -
305C ALA 4.1 2.4 + - - +
306C GLU* 3.7 24.9 - - + +
308C GLU* 1.3 75.6 - - - +
310C LYS* 1.3 67.1 + - + +
312C LEU* 3.8 1.2 - - - +
313C ALA* 2.8 32.2 + - - +
323C TYR* 4.1 15.4 - - + +
326C CYS* 3.7 34.1 - - + -
362C LEU* 3.9 10.5 - - + -
364C ILE* 3.5 34.5 - - + -
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Residues in contact with LYS 310 (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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288B ILE 3.8 14.8 - - - +
289B ASP* 4.0 16.8 - - - +
290B GLY* 5.5 1.9 - - - +
306C GLU* 3.3 47.0 + - + +
307C ARG* 4.3 1.1 - - - +
309C VAL* 1.3 77.3 - - + +
311C ALA* 1.3 61.7 + - - +
313C ALA* 3.4 6.8 + - - +
314C LYS* 3.3 38.7 + - - +
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Residues in contact with ALA 311 (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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307C ARG* 3.0 21.8 + - + +
308C GLU 3.8 2.7 - - - +
310C LYS* 1.3 73.6 - - - +
312C LEU* 1.3 65.1 + - - +
314C LYS* 3.2 14.6 + - - +
315C LEU* 3.3 21.0 + - + +
410C LEU* 4.0 29.2 - - + +
436C VAL* 3.8 24.5 - - + -
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Residues in contact with LEU 312 (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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308C GLU* 2.8 47.9 + - + +
311C ALA* 1.3 72.9 - - + +
313C ALA* 1.3 62.2 + - - +
315C LEU* 3.1 32.1 + - + +
320C ILE* 4.6 8.1 - - + -
321C VAL* 4.8 3.8 - - + +
323C TYR* 3.8 33.0 - - + +
364C ILE* 4.5 3.1 - - + -
366C MET* 3.4 34.5 - - + -
433C PHE* 3.7 36.1 - - + -
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Residues in contact with ALA 313 (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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289B ASP* 4.0 24.2 - - + +
291B LYS* 3.7 32.5 + - + +
293B TYR* 4.9 0.6 + - - -
309C VAL 2.8 20.4 + - - +
310C LYS* 3.6 8.1 - - - +
311C ALA 3.1 0.4 - - - -
312C LEU* 1.3 76.4 - - - +
314C LYS* 1.3 62.2 + - + +
315C LEU 3.7 1.9 + - - +
323C TYR* 3.9 22.1 - - + -
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Residues in contact with LYS 314 (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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291B LYS* 4.8 11.6 + - + +
310C LYS* 3.3 21.5 + - - +
311C ALA* 3.2 9.7 + - - +
312C LEU 3.2 0.6 - - - -
313C ALA* 1.3 78.6 - - + +
315C LEU* 1.3 62.7 + - + +
316C ASP* 3.6 3.2 + - - +
404C TYR* 4.1 7.4 + - - -
408C LYS* 4.2 22.8 - - + +
410C LEU* 5.4 9.4 - - + -
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Residues in contact with LEU 315 (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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311C ALA* 3.3 22.4 - - + +
312C LEU* 3.1 25.5 + - + +
313C ALA 4.8 1.8 - - - +
314C LYS* 1.3 75.6 - - - +
316C ASP* 1.3 61.0 + - - +
317C HIS 4.0 0.7 - - - -
320C ILE* 3.9 21.1 - - + +
321C VAL 5.6 1.4 - - - +
323C TYR* 5.5 3.5 + - - +
404C TYR* 3.7 26.0 - - + -
405C ILE* 4.4 15.5 - - + -
408C LYS* 4.4 12.8 - - + -
410C LEU* 4.4 12.3 - - + -
433C PHE* 3.7 35.2 - - + -
436C VAL* 5.5 0.2 - - + -
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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