Contacts of the helix formed by residues 293 - 303 (chain A) in PDB entry 1XV9
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 PRO 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A GLU 4.5 1.1 - - - +
292A LEU* 1.4 91.9 - - + +
294A LEU* 1.3 66.8 + - - +
295A ASP* 4.4 2.9 - - + +
296A ASP* 3.1 40.5 + - + +
297A GLN* 3.1 10.2 + - - +
384A SER* 4.4 6.7 - - - +
388A GLU* 4.1 20.0 - - - +
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Residues in contact with LEU 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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292A LEU 3.6 1.6 + - - -
293A PRO* 1.3 72.1 - - - +
295A ASP* 1.3 66.9 + - - +
297A GLN* 3.6 13.9 - - - +
298A VAL* 3.4 23.4 + - + +
634E HIS* 5.1 7.2 - - + +
637E LEU* 3.7 39.9 - - + +
638E GLN* 3.9 30.1 - - + +
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Residues in contact with ASP 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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293A PRO* 3.1 3.2 - - + +
294A LEU* 1.3 82.3 - - - +
296A ASP* 1.3 65.3 + - - +
297A GLN 3.1 2.0 - - - -
298A VAL* 3.5 9.1 + - - +
299A ILE* 2.8 39.9 + - + +
634E HIS* 5.9 1.0 + - - -
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Residues in contact with ASP 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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292A LEU* 4.8 5.8 - - + -
293A PRO* 3.1 29.5 + - + +
295A ASP* 1.3 79.7 - - - +
297A GLN* 1.3 61.6 + - - +
299A ILE* 3.8 12.6 - - - +
300A LEU* 3.0 38.7 + - + +
383A LEU* 3.8 12.3 - - + +
384A SER* 2.6 49.2 + - - -
385A ASN* 3.5 11.8 + - - +
388A GLU* 5.5 0.7 - - - +
389A VAL* 4.6 5.0 - - + +
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Residues in contact with GLN 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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284A LYS* 5.8 0.9 - - - +
289A PHE* 3.4 46.4 - - + +
290A SER* 3.7 13.8 + - - +
292A LEU* 2.8 27.9 + - + +
293A PRO 3.1 11.1 + - - +
294A LEU* 3.6 20.3 - - - +
295A ASP 3.1 0.2 - - - -
296A ASP* 1.3 76.2 - - - +
298A VAL* 1.3 58.4 + - - +
300A LEU* 3.1 6.3 + - - +
301A LEU* 2.9 30.2 + - - +
637E LEU* 3.2 37.7 + - + +
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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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294A LEU* 3.4 15.6 + - + +
295A ASP* 3.8 11.7 - - - +
297A GLN* 1.3 78.9 - - - +
299A ILE* 1.3 55.3 + - + +
301A LEU* 4.4 2.0 - - - -
302A ARG* 2.6 48.1 + - + +
630E HIS* 4.6 10.8 - - + -
633E LEU* 3.3 26.9 - - + -
634E HIS* 4.1 25.4 - - + +
637E LEU* 3.3 24.2 - - + -
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Residues in contact with ILE 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 ASP* 2.8 29.5 + - + +
296A ASP* 3.8 21.8 - - - +
297A GLN 3.2 0.2 - - - -
298A VAL* 1.3 77.7 - - + +
300A LEU* 1.3 64.1 + - - +
301A LEU 3.1 0.2 + - - -
302A ARG* 3.6 6.3 - - - +
303A ALA* 3.0 28.0 + - + +
380A SER* 3.6 28.0 - - - -
381A LYS 4.5 11.7 - - - +
382A GLY* 3.6 26.9 - - - +
383A LEU* 3.7 11.0 - - + +
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Residues in contact with LEU 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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289A PHE* 4.4 9.6 - - + -
292A LEU* 3.9 25.6 - - + -
296A ASP 3.0 19.9 + - - +
297A GLN 3.1 4.8 + - - +
299A ILE* 1.3 79.7 - - - +
301A LEU* 1.3 62.2 + - - +
303A ALA 3.5 14.1 - - - +
304A GLY* 3.8 5.5 - - - -
374A VAL 5.0 1.2 - - - +
375A LEU* 3.1 37.9 - - + +
376A PHE* 4.6 3.1 - - + -
377A ASN* 3.5 29.8 - - + +
380A SER* 4.0 9.4 - - - +
383A LEU* 4.4 8.7 - - + -
389A VAL* 4.0 24.5 - - + -
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Residues in contact with LEU 301 (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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279A LEU* 4.9 7.9 - - + -
280A VAL* 4.5 19.5 - - + +
283A ALA* 4.0 12.6 - - + -
289A PHE* 4.0 6.5 - - + -
297A GLN 2.9 18.1 + - - +
298A VAL* 3.8 4.7 - - - +
300A LEU* 1.3 74.8 - - - +
302A ARG* 1.3 68.6 + - - +
303A ALA 3.0 0.9 - - - -
304A GLY 2.9 14.4 + - - -
305A TRP* 2.9 15.8 + - + +
308A LEU* 4.2 13.5 - - + -
375A LEU* 3.4 28.3 - - + -
454A MET* 4.0 5.6 - - + -
633E LEU* 4.1 26.0 - - + -
637E LEU* 4.3 21.5 - - + -
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Residues in contact with ARG 302 (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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298A VAL* 2.6 37.2 + - + +
299A ILE* 3.6 7.1 - - - +
301A LEU* 1.3 70.7 - - - +
303A ALA* 1.3 61.2 + - - +
305A TRP* 2.9 25.1 + - - -
381A LYS 5.6 3.2 + - - -
453A GLU 5.4 1.1 - - - -
454A MET* 3.5 26.6 + - + +
456A GLU* 4.9 14.6 + - - +
630E HIS* 3.1 38.6 + - + +
633E LEU* 3.9 8.7 - - + +
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Residues in contact with ALA 303 (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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299A ILE* 3.0 14.3 + - + +
300A LEU* 3.5 9.2 - - - +
301A LEU 3.5 1.1 - - - -
302A ARG* 1.3 80.0 - - + +
304A GLY* 1.3 56.7 + - - +
307A GLU* 6.1 0.4 - - - -
374A VAL 5.3 2.8 - - - +
377A ASN* 5.2 7.9 + - - +
380A SER* 4.7 15.4 + - - +
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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