Contacts of the helix formed by residues 357 - 367 (chain D) in PDB entry 3ITX
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 ASP 357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ARG 5.7 1.0 - - - +
355D LEU 3.3 4.3 + - - +
356D VAL* 1.3 70.7 - - - +
358D ARG* 1.3 56.9 + - - +
359D ALA* 3.3 10.6 + - - +
360D ALA* 2.9 34.3 + - + +
361D LEU* 2.9 28.1 + - - +
376D THR* 3.8 10.6 + - + +
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Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ASN* 2.8 41.6 + - - +
310D VAL* 3.5 29.2 - - + +
311D ASP* 3.8 24.4 + - - +
314D ALA* 4.7 17.7 - - + -
353D ALA 3.1 25.1 + - - -
356D VAL* 3.0 26.0 + - - +
357D ASP* 1.3 69.3 + - - +
359D ALA* 1.3 62.1 + - - +
361D LEU* 3.7 15.3 - - - +
362D SER* 2.9 30.7 + - - -
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Residues in contact with ALA 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ASP* 3.3 7.9 + - - +
358D ARG* 1.3 78.5 - - - +
360D ALA* 1.3 64.3 + - - +
362D SER* 3.3 6.9 + - - -
363D GLY* 3.0 19.1 + - - -
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Residues in contact with ALA 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ASP* 2.9 35.0 + - + +
359D ALA* 1.3 76.7 - - - +
361D LEU* 1.3 63.5 + - - +
363D GLY* 3.2 3.0 + - - -
364D TYR* 3.0 43.4 + - + -
376D THR* 4.4 4.9 - - + -
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Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B GLY* 3.6 22.4 - - - +
307D ASN* 4.9 3.1 - - - +
356D VAL* 4.1 9.6 - - + -
357D ASP 2.9 17.4 + - - +
358D ARG* 3.7 19.3 - - - +
360D ALA* 1.3 77.3 - - - +
362D SER* 1.3 63.5 + - - +
364D TYR* 3.1 5.2 + - - -
365D GLN* 2.9 44.8 + - - +
373D ALA* 3.5 30.5 - - - +
376D THR* 3.9 12.3 - - + +
377D LEU* 3.9 23.1 - - + -
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Residues in contact with SER 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ARG* 4.4 16.3 + - - -
358D ARG 2.9 19.0 + - - -
359D ALA* 3.5 7.2 - - - -
360D ALA 3.3 0.2 - - - -
361D LEU* 1.3 76.8 - - - +
363D GLY* 1.3 62.2 + - - +
365D GLN* 3.3 13.7 + - - +
366D GLU* 3.0 33.8 + - - +
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Residues in contact with GLY 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D ALA 3.0 13.6 + - - -
360D ALA* 3.2 4.2 + - - -
361D LEU 3.2 0.4 - - - -
362D SER* 1.3 78.2 - - - +
364D TYR* 1.3 62.7 + - - +
366D GLU* 3.9 4.2 - - - +
367D ASP* 2.9 35.4 + - - +
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Residues in contact with TYR 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ARG* 5.0 2.0 - - - -
189B GLN 5.0 0.2 - - - +
360D ALA* 3.0 31.7 + - + +
361D LEU 3.1 5.4 + - - +
363D GLY* 1.3 75.1 - - - +
365D GLN* 1.3 65.2 + - - +
367D ASP* 4.9 1.3 - - + -
368D ASN* 3.2 2.1 + - - -
369D ASP* 2.8 50.6 + - + +
372D MET* 3.5 45.9 - - + +
373D ALA* 3.8 20.7 - - - +
376D THR* 3.3 26.5 - - - -
379D ARG* 5.4 1.9 + - - -
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 3.6 16.2 - - + +
188B GLY* 2.9 30.6 + - - +
189B GLN 3.7 15.7 - - - +
190B SER* 3.5 17.7 + - - -
191B ASN* 3.6 30.0 + - + +
194B ARG* 4.6 5.0 + - - -
361D LEU* 2.9 40.1 + - + +
362D SER* 3.7 15.2 - - - +
364D TYR* 1.3 76.3 - - - +
366D GLU* 1.3 70.1 + - - +
368D ASN* 3.1 15.0 + - - +
373D ALA* 4.7 0.4 - - + -
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Residues in contact with GLU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 2.9 44.7 + - - +
194B ARG* 5.3 6.9 + - - -
198B ARG* 4.1 18.1 + - - -
362D SER* 3.0 27.7 + - - +
363D GLY* 3.9 5.8 - - - +
365D GLN* 1.3 79.8 - - - +
367D ASP* 1.3 63.9 + - - +
368D ASN* 3.2 1.4 - - - +
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Residues in contact with ASP 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TYR* 5.5 0.3 - - - -
363D GLY* 2.9 23.5 + - - +
364D TYR* 4.5 4.1 - - + +
365D GLN 3.3 0.2 - - - -
366D GLU* 1.3 81.6 - - - +
368D ASN* 1.3 72.3 + - - +
369D ASP* 3.2 6.9 + - + +
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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