Contacts of the helix formed by residues 288 - 297 (chain A) in PDB entry 3V6C
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 THR 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A CYS 2.9 14.1 + - - -
285A LEU* 3.0 20.9 + - - +
287A ASN* 1.3 72.9 - - - +
289A ARG* 1.3 66.2 + - - +
290A GLU 4.7 1.1 - - - +
291A LEU* 3.0 23.2 + - + +
292A ARG* 2.9 22.4 + - - +
414A LEU* 4.6 2.5 - - + -
415A PHE* 4.5 9.1 - - + -
497A ILE* 4.0 24.2 - - + -
544A TYR* 2.6 30.7 + - - +
595A PHE* 4.7 0.5 - - - -
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Residues in contact with ARG 289 (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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287A ASN 3.3 6.4 + - - +
288A THR* 1.3 72.3 - - - +
290A GLU* 1.3 84.8 + - - +
292A ARG* 3.5 24.6 - - - +
293A ASP* 2.9 41.2 + - - +
565A PRO* 3.9 30.7 - - + -
597A GLU* 3.5 27.1 + - - +
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Residues in contact with GLU 290 (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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288A THR* 3.3 2.5 - - + +
289A ARG* 1.3 105.8 + - - +
291A LEU* 1.3 58.8 + - - +
293A ASP* 3.8 8.8 - - - +
294A TYR* 2.9 28.1 + - - +
410A ARG* 2.6 33.2 + - - +
414A LEU* 3.8 18.3 - - + +
496A LYS* 3.0 35.1 + - - +
497A ILE* 6.0 3.4 - - + +
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Residues in contact with LEU 291 (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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285A LEU* 3.8 43.3 - - + +
288A THR* 3.0 14.2 + - + +
290A GLU* 1.3 76.7 - - - +
292A ARG* 1.3 66.3 + - - +
294A TYR* 3.2 17.8 + - + +
295A CYS* 3.1 22.7 + - - -
318A PHE* 4.1 25.6 - - + -
366A LEU* 4.9 4.9 - - + -
369A LEU* 5.4 0.7 - - + -
410A ARG* 6.2 0.4 - - + -
411A ILE* 3.9 28.5 - - + -
414A LEU* 3.8 22.1 - - + +
415A PHE* 4.4 11.2 - - + -
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Residues in contact with ARG 292 (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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285A LEU 4.3 2.7 + - - -
286A SER 3.4 20.9 - - - +
288A THR 2.9 12.9 + - - +
289A ARG* 3.5 24.3 + - - +
291A LEU* 1.3 71.7 - - - +
293A ASP* 1.3 82.9 + - - +
295A CYS* 2.9 6.8 + - - +
296A LEU* 2.8 42.3 + - + +
322A ILE* 3.9 13.2 - - + -
326A TRP* 3.3 66.8 - - + +
565A PRO* 3.8 19.2 - - - +
566A GLY 5.1 2.8 - - - +
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Residues in contact with ASP 293 (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 ARG* 2.9 35.3 + - - +
290A GLU* 3.8 9.5 - - - +
291A LEU 3.3 0.2 - - - -
292A ARG* 1.3 99.9 + - - +
294A TYR* 1.3 57.0 + - - +
296A LEU* 4.3 7.9 - - - +
297A GLN* 2.9 56.9 + - - +
299A LEU* 5.5 0.4 - - - -
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Residues in contact with TYR 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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290A GLU 2.9 15.9 + - - +
291A LEU* 3.3 24.5 - - + +
293A ASP* 1.3 74.5 - - - +
295A CYS* 1.3 64.1 + - - +
298A ARG 3.4 1.0 + - - -
299A LEU* 2.9 55.5 + - + +
300A TYR* 3.4 40.9 - - + -
303A ASP* 2.8 33.9 + - - +
315A VAL* 5.6 1.8 - - + -
373A VAL* 3.5 16.0 - - + +
410A ARG* 3.5 38.3 - - + +
411A ILE* 4.2 17.3 - - + -
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Residues in contact with CYS 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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291A LEU* 3.1 18.5 + - - -
292A ARG 2.9 8.8 + - - +
294A TYR* 1.3 82.7 - - - +
296A LEU* 1.3 65.0 + - - +
297A GLN 3.3 0.2 - - - -
298A ARG 3.2 8.0 + - - -
300A TYR* 3.5 9.2 - - - -
318A PHE* 3.7 31.0 - - - -
319A ALA* 3.8 24.0 - - - +
322A ILE* 3.8 22.4 - - + -
323A GLN* 2.9 23.6 + - + -
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Residues in contact with LEU 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 ARG* 2.8 48.0 + - + +
293A ASP* 3.2 7.6 + - - +
295A CYS* 1.3 72.7 - - - +
297A GLN* 1.3 61.4 + - + +
298A ARG* 3.2 11.0 + - - +
322A ILE* 3.9 6.7 - - + +
323A GLN* 3.6 38.2 + - + +
326A TRP* 3.7 31.0 - - + -
327A THR* 5.8 2.7 - - + -
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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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293A ASP* 2.9 42.2 + - - +
296A LEU* 1.3 78.7 - - + +
298A ARG* 1.3 68.3 + - - +
299A LEU* 3.1 33.9 + - + +
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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