Contacts of the helix formed by residues 293 - 300 (chain A) in PDB entry 2A8I
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A LEU* 4.1 11.0 - - + +
255A LEU* 5.9 8.1 - - - -
292A GLY* 1.3 69.1 - - - -
294A GLY* 1.3 68.4 + - - +
295A GLU* 3.9 11.7 - - - -
296A HIS* 3.0 51.1 + - + +
297A LEU* 3.2 12.5 + - - +
340A LEU* 2.9 29.7 + - + +
160B ILE* 4.9 4.7 - - - -
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Residues in contact with GLY 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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255A LEU* 5.9 3.8 - - - +
264A GLY* 5.5 3.1 - - - -
265A GLN* 3.7 29.2 - - - -
292A GLY 3.2 7.2 + - - -
293A CYS* 1.3 70.2 - - - +
295A GLU* 1.3 64.1 + - - +
297A LEU* 3.2 4.6 + - - +
298A VAL* 3.0 29.5 + - - +
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Residues in contact with GLU 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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255A LEU* 5.6 3.1 - - + -
262A ARG* 2.9 37.8 + - - +
263A VAL 5.3 4.3 - - - +
293A CYS* 3.2 8.3 - - - -
294A GLY* 1.3 74.0 - - - +
296A HIS* 1.3 61.9 + - - +
298A VAL* 3.4 6.3 + - - +
299A ARG* 3.1 66.1 + - + +
333A LEU* 5.1 0.2 - - - -
160B ILE* 4.1 30.3 - - + -
161B PRO 4.2 5.8 - - - -
163B CYS* 3.5 22.4 + - - -
164B PHE 5.3 0.2 + - - -
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Residues in contact with HIS 296 (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 CYS* 3.0 35.1 + - + +
295A GLU* 1.3 75.8 - - - +
297A LEU* 1.3 54.3 + - - +
299A ARG 3.9 0.2 + - - -
300A THR* 2.7 37.5 + - - +
327A PHE* 3.8 9.7 - - + -
333A LEU* 3.9 29.4 - - + +
336A GLU* 3.2 25.5 + - + +
338A GLY 3.3 25.8 - - - -
339A VAL* 3.5 5.3 - - + -
340A LEU* 2.9 34.9 + - + +
160B ILE* 3.9 13.4 - - + +
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Residues in contact with LEU 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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265A GLN* 3.5 41.5 - - + +
271A CYS* 4.1 9.1 - - - +
290A THR* 3.9 14.8 - - - +
291A SER 3.4 31.4 - - - +
292A GLY 4.2 0.9 - - - +
293A CYS 3.6 15.9 - - - +
294A GLY 3.2 5.7 + - - +
296A HIS* 1.3 73.8 - - - +
298A VAL* 1.3 61.4 + - - +
300A THR* 3.4 3.5 + - - -
301A ILE* 3.0 22.7 + - - -
302A LEU* 3.2 40.5 + - + -
327A PHE* 4.3 11.0 - - + -
340A LEU 5.1 0.2 - - - +
341A GLY* 4.6 1.6 - - - -
342A GLY 4.7 1.1 - - - +
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Residues in contact with VAL 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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263A VAL 5.9 0.4 - - - +
264A GLY* 4.4 1.8 - - - -
265A GLN* 3.5 29.6 - - + +
268A LEU* 3.7 26.9 - - + -
271A CYS* 3.9 9.1 - - + -
294A GLY 3.0 18.1 + - - +
295A GLU* 3.8 9.6 - - - +
297A LEU* 1.3 73.5 - - - +
299A ARG* 1.3 76.6 + - - +
300A THR 3.0 1.8 - - - -
301A ILE* 2.9 14.2 + - - +
127B PHE* 6.1 0.4 - - + -
163B CYS* 5.2 10.1 - - - -
269B TYR* 3.1 34.0 - - + -
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Residues in contact with ARG 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 GLU* 3.1 43.3 + - + +
298A VAL* 1.3 85.1 - - - +
300A THR* 1.3 59.0 + - - +
301A ILE* 4.7 0.5 - - - +
332A PHE* 3.8 29.7 + - + +
333A LEU* 4.1 23.1 - - + -
125B LEU 4.2 6.1 + - - -
126B ASN* 3.2 37.9 - - - +
127B PHE* 4.0 10.1 - - - +
160B ILE* 4.5 14.0 - - + +
161B PRO 5.0 0.8 + - - -
163B CYS* 3.5 25.7 - - - +
269B TYR* 2.9 35.7 + - - +
274B TRP* 4.9 1.4 - - - -
304B ARG* 5.9 0.3 + - - -
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Residues in contact with THR 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 HIS 2.7 23.3 + - - +
297A LEU* 3.4 6.4 + - - -
299A ARG* 1.3 82.2 - - - +
301A ILE* 1.3 71.7 + - - +
302A LEU* 2.9 10.1 + - - +
305A GLU* 4.2 12.8 - - - +
326A LYS 3.6 25.8 - - - +
327A PHE* 3.7 14.8 - - + -
330A SER* 3.7 16.8 - - - +
332A PHE* 4.7 2.0 - - + -
333A LEU* 3.8 20.4 - - + -
304B ARG* 4.4 5.7 + - - +
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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