Contacts of the helix formed by residues 295 - 306 (chain I) in PDB entry 3A2C
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 SER 295 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160I GLU* 4.4 7.3 + - - -
293I GLU 3.8 2.9 + - - -
294I VAL* 1.3 79.3 - - - +
296I GLU* 1.3 63.7 + - - +
297I GLU* 4.0 11.8 - - - +
298I VAL* 3.2 25.8 + - - +
299I LYS* 3.1 21.8 + - - +
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Residues in contact with GLU 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294I VAL 4.0 0.2 + - - -
295I SER* 1.3 73.0 - - - +
297I GLU* 1.3 58.4 + - - +
299I LYS* 3.2 18.6 + - - +
300I MET* 2.8 33.4 + - + +
303I ARG* 2.7 36.6 + - - +
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Residues in contact with GLU 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295I SER* 3.2 12.5 - - - +
296I GLU* 1.3 78.9 - - - +
298I VAL* 1.3 66.4 + - + +
300I MET* 3.5 6.2 + - - +
301I LEU* 3.1 25.8 + - - +
322I HIS* 3.7 29.2 + - + -
323I PRO* 4.5 13.5 - - - +
324I TRP* 4.3 18.0 + - - +
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Residues in contact with VAL 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I GLU* 4.0 5.8 - - - +
253I MET* 5.2 2.9 - - - -
257I LEU* 3.5 32.5 - - + -
294I VAL* 3.5 12.1 - - + -
295I SER* 3.2 23.2 + - - +
297I GLU* 1.3 81.7 - - + +
299I LYS* 1.3 65.4 + - - +
301I LEU* 3.3 6.9 + - - +
302I ILE* 3.1 25.9 + - + +
324I TRP* 3.2 48.9 - - + +
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Residues in contact with LYS 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I PHE* 3.3 65.6 + - + +
291I TRP* 4.2 22.3 + - + +
292I SER* 6.0 0.6 - - - +
294I VAL* 4.1 14.7 + - + +
295I SER 3.1 18.3 + - - +
296I GLU* 3.5 31.4 + - - +
298I VAL* 1.3 78.8 - - - +
300I MET* 1.3 56.1 + - - +
302I ILE* 3.3 5.0 + - - +
303I ARG* 2.9 33.1 + - - +
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Residues in contact with MET 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296I GLU* 2.8 19.1 + - + +
297I GLU* 3.8 7.2 - - - +
299I LYS* 1.3 74.4 - - - +
301I LEU* 1.3 64.1 + - - +
303I ARG* 3.0 56.5 + - + +
304I ASN* 3.1 44.6 + - - +
307I LYS* 5.5 6.5 - - - +
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Residues in contact with LEU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253I MET* 3.3 31.2 - - + -
297I GLU 3.1 17.6 + - - +
298I VAL* 3.6 6.5 - - - +
299I LYS 3.2 0.2 - - - -
300I MET* 1.3 73.2 - - - +
302I ILE* 1.3 63.9 + - - +
304I ASN* 3.4 8.3 + - - +
305I LEU* 3.3 21.6 + - + +
314I MET* 3.2 35.4 - - + -
319I PHE* 4.2 12.1 - - + -
322I HIS* 3.7 39.5 - - + +
324I TRP* 4.2 15.5 - - + -
325I ILE* 4.7 3.6 - - + -
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Residues in contact with ILE 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I GLY 4.6 4.0 - - - +
253I MET* 3.8 22.4 - - + -
254I TYR* 4.1 16.4 - - + +
257I LEU* 3.9 15.5 - - + -
284I TYR* 4.5 0.7 - - + -
286I PHE* 3.9 19.5 - - + -
291I TRP* 3.4 36.1 - - + -
298I VAL 3.1 13.2 + - - +
299I LYS 3.3 7.6 + - - +
301I LEU* 1.3 75.7 - - - +
303I ARG* 1.3 56.4 + - - +
305I LEU* 3.3 7.6 + - + +
306I LEU* 3.0 51.0 + - + +
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Residues in contact with ARG 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284I TYR* 2.9 26.5 + - - +
286I PHE* 3.7 27.1 - - + -
296I GLU* 2.7 32.7 + - - +
299I LYS* 2.9 15.3 + - - +
300I MET* 3.0 57.9 + - + +
302I ILE* 1.3 74.3 - - - +
304I ASN* 1.3 67.1 + - - +
306I LEU 3.5 1.9 + - - -
307I LYS* 3.2 27.9 + - - +
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Residues in contact with ASN 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300I MET* 3.1 33.3 + - - +
301I LEU* 3.9 1.2 - - - +
302I ILE 3.4 0.2 - - - -
303I ARG* 1.3 74.2 - - - +
305I LEU* 1.3 61.0 - - - +
307I LYS* 2.8 42.1 - - + +
312I GLN 5.4 2.9 + - - +
313I ARG* 3.2 9.2 - - - +
314I MET* 3.3 41.7 - - + +
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Residues in contact with LEU 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246I MET* 3.8 41.5 - - + +
247I TRP* 3.7 11.1 - - - -
249I LEU* 4.4 3.4 - - + -
250I GLY* 3.8 24.2 - - - +
253I MET* 4.4 9.4 - - + -
301I LEU* 3.3 19.3 + - + +
302I ILE* 3.3 9.0 + - - +
304I ASN* 1.3 76.4 - - - +
306I LEU* 1.3 59.4 + - - +
307I LYS 3.1 0.2 - - - -
313I ARG* 3.1 26.9 - - - -
314I MET* 3.6 28.5 - - + +
319I PHE* 4.1 25.1 - - + -
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Residues in contact with LEU 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I TRP* 2.8 42.1 - - + +
250I GLY* 3.9 6.5 - - - +
251I VAL* 3.8 33.4 - - + +
262I PRO* 4.0 28.7 - - + -
263I PHE* 4.4 5.6 - - + -
282I GLY* 5.7 2.4 - - - -
284I TYR* 4.0 28.8 - - + +
302I ILE* 3.0 38.5 + - + +
303I ARG 3.7 3.1 - - - +
305I LEU* 1.3 75.8 - - - +
307I LYS* 1.3 65.8 + - - +
308I THR* 3.2 3.3 + - - -
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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