Contacts of the helix formed by residues 295 - 306 (chain A) in PDB entry 3VZC
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A LEU* 4.9 1.3 - - - -
293A GLY 3.8 1.4 + - - -
294A VAL* 1.3 77.8 - - - +
296A ARG* 1.3 64.9 + - - +
297A ALA* 3.9 8.3 + - - +
298A MET* 3.1 24.7 + - - +
299A LEU* 3.1 18.2 + - - +
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Residues in contact with ARG 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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200A LEU* 2.9 31.0 + - + +
201A ALA* 2.7 30.4 + - - +
202A ALA* 4.4 2.2 - - - +
203A LEU* 4.1 32.6 + - + +
294A VAL 4.0 0.8 + - - -
295A SER* 1.3 70.0 - - - +
297A ALA* 1.3 64.6 + - - +
299A LEU* 3.1 10.8 + - - +
300A LEU* 3.0 22.2 + - - +
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Residues in contact with ALA 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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295A SER* 3.2 8.5 + - - +
296A ARG* 1.3 77.7 - - - +
298A MET* 1.3 57.8 + - - +
300A LEU* 3.2 9.8 + - - +
301A ARG* 2.8 44.3 + - + +
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Residues in contact with MET 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 VAL* 4.5 6.1 - - + -
295A SER* 3.1 25.8 + - - +
297A ALA* 1.3 74.4 - - - +
299A LEU* 1.3 55.8 + - - +
301A ARG* 3.3 20.6 + - - +
302A LEU* 2.7 53.7 + - + +
314A TYR* 3.5 45.1 - - + +
316A CYS* 4.0 26.2 - - + -
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Residues in contact with LEU 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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173A PHE* 4.3 10.8 - - + -
200A LEU* 3.6 26.0 - - + -
203A LEU* 4.2 21.3 - - + -
258A VAL* 4.1 26.0 - - + -
259A LEU* 4.8 3.6 - - + -
290A VAL* 5.0 4.5 - - + -
294A VAL* 4.3 15.5 - - + +
295A SER 3.1 10.7 + - - +
296A ARG* 3.4 9.6 - - - +
298A MET* 1.3 73.8 - - - +
300A LEU* 1.3 52.3 + - - +
302A LEU* 3.1 14.7 + - + +
303A PHE* 2.8 33.7 + - - +
1001A UUL 3.4 37.9 - - + -
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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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193A THR* 6.0 4.0 - - + +
196A THR* 4.6 3.4 - - + -
197A PHE* 4.9 22.2 - - + -
200A LEU* 3.7 29.1 - - + +
296A ARG 3.0 8.5 + - - +
297A ALA* 3.5 10.8 - - - +
299A LEU* 1.3 72.9 - - - +
301A ARG* 1.3 61.1 + - + +
303A PHE* 3.2 22.8 + - + +
304A LEU* 2.8 54.9 + - + +
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Residues in contact with ARG 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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297A ALA* 2.8 37.7 + - + +
298A MET* 3.6 25.2 - - - +
300A LEU* 1.3 77.5 - - + +
302A LEU* 1.3 54.8 + - - +
304A LEU* 4.0 7.4 - - + +
305A ALA* 3.0 31.5 + - - +
314A TYR* 3.8 33.8 + - + +
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Residues in contact with LEU 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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290A VAL* 5.1 5.4 - - + -
294A VAL* 5.0 5.4 - - + -
298A MET* 2.7 42.9 + - + +
299A LEU* 3.4 15.3 - - + +
301A ARG* 1.3 72.9 - - - +
303A PHE* 1.3 63.3 + - - +
305A ALA* 4.6 0.2 - - - -
306A MET* 3.1 20.1 + - - +
311A HIS* 3.4 41.9 - - + +
314A TYR* 3.8 13.7 - - + -
316A CYS* 4.0 28.7 - - + -
319A LEU* 4.4 20.0 - - + -
1001A UUL 4.4 16.9 - - + -
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Residues in contact with PHE 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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192A PHE* 4.2 3.1 - - + -
193A THR* 3.7 48.0 - - + -
196A THR* 3.7 17.9 - - + -
272A MET* 4.1 12.8 - - + +
299A LEU 2.8 12.8 + - - +
300A LEU* 3.2 22.2 - - + +
302A LEU* 1.3 77.1 - - - +
304A LEU* 1.3 70.2 + - + +
306A MET* 3.0 39.2 - - + +
307A GLU 4.0 1.9 + - - -
1001A UUL 3.4 55.5 - + - +
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Residues in contact with LEU 304 (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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193A THR* 5.2 8.7 - - + -
300A LEU* 2.8 47.9 + - + +
301A ARG* 4.2 6.1 - - + +
303A PHE* 1.3 85.6 - - + +
305A ALA* 1.3 65.6 + - - +
306A MET 3.1 1.8 - - - -
307A GLU* 3.3 24.9 + - - +
308A LYS* 4.5 1.0 + - - +
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Residues in contact with ALA 305 (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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301A ARG 3.0 18.4 + - - +
302A LEU 3.9 0.9 - - - +
304A LEU* 1.3 74.0 - - - +
306A MET* 1.3 64.1 + - - +
308A LYS* 3.0 15.3 + - - +
310A ARG* 3.0 27.7 + - + +
311A HIS* 3.6 17.5 - - - +
314A TYR* 3.6 24.9 - - + +
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Residues in contact with MET 306 (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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268A LEU* 4.1 4.5 - - + -
272A MET* 3.7 38.1 - - + -
273A PHE 2.9 23.1 + - - +
274A ALA* 3.8 27.8 - - - -
302A LEU 3.1 10.2 + - - +
303A PHE* 3.0 46.9 - - + +
305A ALA* 1.3 74.8 - - - +
307A GLU* 1.3 64.2 + - - +
309A GLY 3.0 7.6 + - - -
311A HIS* 3.7 14.3 + - + +
1001A UUL 3.7 44.0 - - + +
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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