Contacts of the helix formed by residues 367 - 376 (chain D) in PDB entry 2IBS
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 367 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366D LEU* 1.3 71.7 - - - +
368D PRO* 1.4 71.8 - - - +
369D SER* 3.6 12.6 + - - -
370D SER* 3.0 30.0 + - - +
371D LEU* 2.9 23.9 + - - +
408D GLU 4.6 6.6 - - - +
409D TYR 3.1 10.1 + - - +
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Residues in contact with PRO 368 (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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345D TRP* 3.9 38.4 - - + -
366D LEU* 3.3 29.4 - - + +
367D ASP* 1.4 89.4 - - - +
369D SER* 1.3 56.9 + - - +
371D LEU* 3.4 7.6 + - + +
372D VAL* 3.0 36.0 + - - +
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Residues in contact with SER 369 (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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367D ASP* 3.6 13.3 + - - -
368D PRO* 1.3 79.2 - - - +
370D SER* 1.3 63.8 + - - +
372D VAL* 3.6 6.7 + - - +
373D GLN* 3.3 24.0 + - - +
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Residues in contact with SER 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D ASP* 3.0 38.4 + - - +
369D SER* 1.3 79.7 + - - +
371D LEU* 1.3 63.7 + - - +
373D GLN* 3.0 30.5 - - - +
374D TRP 3.1 6.2 + - - -
408D GLU* 3.7 7.9 + - - -
409D TYR* 3.2 28.4 - - - -
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Residues in contact with LEU 371 (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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260D LEU* 4.6 3.1 - - + -
264D PHE* 3.7 33.7 - - + -
331D LEU* 4.0 14.6 - - + -
345D TRP* 6.3 2.0 - - + -
366D LEU* 4.9 11.4 - - + -
367D ASP 2.9 16.9 + - - +
368D PRO* 3.7 7.2 - - + +
370D SER* 1.3 75.1 + - - +
372D VAL* 1.3 59.5 + - - +
374D TRP* 3.3 8.0 + - + +
375D LEU* 2.9 44.4 + - + +
405D VAL* 3.8 40.2 - - + -
409D TYR* 3.8 17.3 - - + +
410D GLY* 5.7 0.9 - - - -
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Residues in contact with VAL 372 (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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301D GLY* 4.0 15.9 - - - +
331D LEU* 3.8 27.1 - - + -
343D ALA* 3.6 9.6 - - - +
344D ALA* 4.4 2.2 - - - -
345D TRP* 4.2 21.3 - - + +
368D PRO 3.0 22.8 + - - +
369D SER* 3.9 7.0 - - - +
370D SER 3.4 0.2 - - - -
371D LEU* 1.3 76.5 - - + +
373D GLN* 1.3 56.0 + - - +
375D LEU* 3.3 7.9 + - - +
376D ASN* 2.8 52.3 + - - +
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Residues in contact with GLN 373 (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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369D SER 3.3 15.1 + - - +
370D SER* 3.0 27.1 - - - +
372D VAL* 1.3 77.9 - - + +
374D TRP* 1.3 68.1 + - - +
376D ASN* 3.9 6.4 - - - +
377D SER* 3.2 25.3 + - - -
409D TYR* 3.7 16.1 + - - -
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Residues in contact with TRP 374 (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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253D LEU* 4.0 34.1 - - + -
370D SER 3.1 18.9 + - - +
371D LEU* 3.5 9.0 - - + +
372D VAL 3.2 0.2 - - - -
373D GLN* 1.3 79.0 + - - +
375D LEU* 1.3 65.6 + - + +
377D SER* 2.6 39.7 + - - -
379D ALA* 4.2 16.8 - - + -
380D MET* 3.4 29.8 - - + +
404D PRO* 2.9 26.9 + - + -
405D VAL* 4.2 14.9 - - + +
406D ARG* 5.9 3.8 - - + -
409D TYR* 3.7 47.3 - + + -
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Residues in contact with LEU 375 (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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260D LEU* 4.2 18.4 - - + -
331D LEU* 3.9 30.3 - - + -
333D VAL* 4.7 4.5 - - + -
341D VAL* 3.0 44.0 - - + +
343D ALA* 3.9 20.4 - - + -
371D LEU* 2.9 31.4 + - + +
372D VAL* 3.3 4.9 + - - +
374D TRP* 1.3 80.8 - - + +
376D ASN* 1.3 57.6 + - - +
380D MET* 3.5 17.3 - - + +
381D GLN* 3.0 9.7 + - - -
400D LEU* 5.6 0.7 - - + -
403D LEU* 4.1 16.6 - - + -
405D VAL* 5.2 1.3 - - + -
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Residues in contact with ASN 376 (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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300D PRO* 3.6 19.3 - - + +
301D GLY* 3.5 11.1 - - - +
341D VAL 3.5 0.7 - - - +
342D VAL* 3.5 9.7 - - - +
343D ALA* 2.8 45.6 + - - +
372D VAL* 2.8 34.5 + - - +
373D GLN* 3.9 6.5 - - - +
375D LEU* 1.3 73.7 - - - +
377D SER* 1.3 65.8 + - - +
378D GLU* 3.8 1.2 + - - +
381D GLN* 3.8 12.8 + - - +
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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