Contacts of the helix formed by residues 377 - 389 (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 SER 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373D GLN 3.2 13.8 + - - -
374D TRP* 2.6 38.9 + - - -
376D ASN* 1.3 77.1 - - - +
378D GLU* 1.3 59.7 + - - +
379D ALA* 3.8 4.7 + - - -
380D MET* 3.1 27.9 + - - +
381D GLN* 3.1 15.0 + - - +
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Residues in contact with GLU 378 (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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376D ASN 3.8 1.2 + - - +
377D SER* 1.3 71.0 - - - +
379D ALA* 1.3 60.3 + - - +
381D GLN* 4.1 13.2 - - - +
382D LYS* 2.9 31.7 + - - +
385D ARG* 3.1 29.9 + - - -
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Residues in contact with ALA 379 (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* 4.6 8.8 - - + +
374D TRP* 4.2 17.5 - - + -
377D SER* 3.2 10.0 - - - +
378D GLU* 1.3 76.8 - - - +
380D MET* 1.3 58.2 + - - +
382D LYS* 4.1 6.5 - - - +
383D HIS* 3.2 25.6 + - - +
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Residues in contact with MET 380 (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* 5.4 1.1 - - - -
341D VAL* 3.7 14.6 - - + -
374D TRP* 3.4 58.1 - - + +
375D LEU* 3.5 31.2 - - + +
377D SER* 3.1 12.0 + - - +
379D ALA* 1.3 79.5 - - - +
381D GLN* 1.3 64.5 + - - +
383D HIS* 3.3 13.9 + - - +
384D VAL* 3.2 23.7 + - - +
403D LEU* 3.8 27.8 - - + -
404D PRO* 4.0 15.0 - - + +
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Residues in contact with GLN 381 (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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339D THR 4.7 0.3 - - - +
340D ARG* 3.5 19.4 + - + +
341D VAL* 2.8 48.8 + - - +
342D VAL* 5.1 0.8 - - - +
375D LEU 3.0 16.6 + - - -
376D ASN 3.8 9.2 - - - +
377D SER 3.1 21.1 + - - +
378D GLU* 3.3 18.1 + - - +
380D MET* 1.3 75.0 - - - +
382D LYS* 1.3 58.6 + - - +
384D VAL* 3.3 8.3 - - - +
385D ARG* 3.1 50.7 + - - +
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Residues in contact with LYS 382 (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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249D GLU* 2.8 37.2 + - - +
378D GLU* 2.9 17.7 + - - +
379D ALA* 4.1 6.5 - - - +
381D GLN* 1.3 73.8 - - - +
383D HIS* 1.3 58.3 + - - +
385D ARG* 3.6 19.3 - - + +
386D THR* 2.7 45.3 + - - +
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Residues in contact with HIS 383 (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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250D THR* 3.7 37.1 - - - +
253D LEU* 3.5 25.1 - - + +
254D GLU* 3.9 17.2 + - + +
379D ALA 3.2 20.9 + - - +
380D MET* 3.4 9.9 - - - +
381D GLN 3.3 0.4 - - - -
382D LYS* 1.3 77.9 - - - +
384D VAL* 1.3 62.2 + - + +
386D THR* 4.0 4.8 - - - -
387D LEU* 3.5 50.2 + - + +
402D ARG 5.3 1.2 + - - -
403D LEU* 4.3 22.1 - - + +
404D PRO* 4.1 13.4 - - + +
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Residues in contact with VAL 384 (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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339D THR* 3.4 40.5 - - + +
340D ARG* 4.1 2.0 - - - -
341D VAL* 3.8 19.3 - - + -
380D MET 3.4 9.6 - - - +
381D GLN* 3.3 19.1 - - - +
383D HIS* 1.3 78.5 - - + +
385D ARG* 1.3 64.9 + - - +
386D THR 3.2 0.7 - - - -
388D TYR* 3.1 36.7 + - + -
395D LEU* 4.1 11.0 - - + -
403D LEU* 3.8 28.3 - - + -
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Residues in contact with ARG 385 (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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339D THR 4.2 13.2 - - - +
340D ARG* 5.5 7.5 - - + +
378D GLU* 3.1 28.3 + - - -
381D GLN* 3.1 31.0 + - - +
382D LYS* 3.4 30.7 + - + +
384D VAL* 1.3 76.2 - - - +
386D THR* 1.3 58.4 - - - +
389D ARG* 3.1 37.2 + - - +
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Residues in contact with THR 386 (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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232D TRP* 5.1 5.6 - - + -
245D PHE* 3.2 33.6 - - - +
247D THR* 4.0 13.7 - - + -
249D GLU* 3.9 21.8 + - - +
250D THR* 4.0 12.1 - - + -
382D LYS* 2.7 32.2 + - - +
383D HIS* 4.0 4.8 - - - -
384D VAL 3.2 0.2 - - - -
385D ARG* 1.3 80.4 - - - +
387D LEU* 1.3 62.2 + - - +
388D TYR 3.6 0.2 + - - -
389D ARG* 4.0 7.0 + - - +
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Residues in contact with LEU 387 (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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244D ARG* 3.4 56.2 - - + +
245D PHE* 3.0 34.1 + - - +
246D GLU* 3.9 10.8 - - + -
250D THR* 4.0 16.6 - - + +
254D GLU* 4.1 1.6 - - - +
383D HIS* 3.5 47.3 + - + +
386D THR* 1.3 80.5 - - - +
388D TYR* 1.3 84.8 + - + +
389D ARG* 5.1 0.2 - - - -
391D PHE* 3.9 4.7 - - - -
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Residues in contact with TYR 388 (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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170D VAL* 3.7 23.1 - - + -
242D ILE* 4.7 4.7 - - + -
244D ARG* 3.4 45.0 + - + -
339D THR* 3.8 10.2 + - + +
383D HIS* 6.0 0.2 - + - -
384D VAL* 3.1 31.0 + - + +
387D LEU* 1.3 95.5 - - + +
389D ARG* 1.3 72.1 + - - +
390D ASP 3.0 3.8 + - - -
391D PHE* 3.1 31.0 + - + +
392D VAL 5.0 0.2 + - - -
398D ARG 4.6 2.8 + - - -
399D MET* 3.6 64.0 + - + -
402D ARG* 4.8 5.2 - - - +
403D LEU* 6.0 0.9 - - + -
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Residues in contact with ARG 389 (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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191D TYR* 3.2 32.0 - - - +
219D ASP* 2.9 43.2 + - - -
232D TRP* 3.7 23.8 - - - -
245D PHE* 3.7 37.3 - - + +
339D THR* 3.3 23.2 + - - +
384D VAL 3.8 1.4 + - - -
385D ARG* 3.1 27.9 + - - +
386D THR* 4.0 8.8 + - - +
388D TYR* 1.3 75.5 - - - +
390D ASP* 1.3 69.0 + - - +
391D PHE* 4.2 4.9 - - + -
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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