Contacts of the helix formed by residues 367 - 379 (chain D) in PDB entry 4AVP
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 GLU 367 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352D HIS* 3.4 35.9 - - - +
353D PHE* 3.1 25.1 + - + +
365D LEU 4.4 0.2 - - - -
366D ILE* 1.3 83.3 - - + +
368D PRO* 1.4 66.4 - - - +
369D GLU 3.3 3.1 - - - -
370D GLU* 3.0 26.9 + - + +
371D VAL* 3.1 14.6 + - - +
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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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365D LEU* 3.4 27.6 - - + +
366D ILE 3.5 4.9 - - - +
367D GLU* 1.4 81.4 - - - +
369D GLU* 1.3 69.1 + - + +
371D VAL* 3.4 5.6 + - + +
372D ALA* 3.1 21.7 + - - +
386D TYR* 3.6 31.9 - - + -
389D LEU* 4.3 0.5 - - - +
410D TYR* 3.7 39.0 - - + +
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Residues in contact with GLU 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 GLU 3.3 0.8 - - - -
368D PRO* 1.3 81.9 - - + +
370D GLU* 1.4 56.1 + - - +
372D ALA* 3.5 6.7 + - - +
373D ARG* 2.9 28.8 + - - +
385D ASN* 6.0 0.9 - - - -
386D TYR* 3.6 29.2 - - - -
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Residues in contact with GLU 370 (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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352D HIS* 5.7 0.4 - - - +
353D PHE* 3.8 24.2 - - + -
367D GLU* 3.0 31.7 + - + +
369D GLU* 1.4 76.0 - - - +
371D VAL* 1.3 64.5 + - - +
373D ARG* 2.7 48.3 + - - +
374D ARG* 2.8 49.2 + - - +
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Residues in contact with VAL 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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340D PHE* 4.3 2.7 - - + -
341D LEU* 3.8 26.7 - - + -
344D LEU* 4.6 6.1 - - + -
353D PHE* 3.6 40.8 - - + +
354D ILE* 3.9 13.9 - - + -
365D LEU* 4.3 13.2 - - + -
367D GLU 3.1 8.8 + - - +
368D PRO* 3.4 8.0 + - + +
370D GLU* 1.3 75.7 - - - +
372D ALA* 1.3 56.8 + - - +
374D ARG* 3.3 5.9 + - - +
375D TRP* 2.9 27.0 + - - +
389D LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 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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368D PRO 3.1 12.9 + - - +
369D GLU* 3.5 9.9 - - - +
371D VAL* 1.3 75.2 - - - +
373D ARG* 1.3 56.2 + - - +
375D TRP* 3.1 3.8 + - - +
376D GLY 2.9 24.6 + - - -
384D MET* 3.2 15.9 - - + +
385D ASN* 3.4 38.8 - - - +
386D TYR* 3.5 7.4 - - - +
389D LEU* 4.0 11.1 - - + +
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Residues in contact with ARG 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 GLU 2.9 18.2 + - - +
370D GLU* 2.7 45.4 + - - +
372D ALA* 1.3 73.4 - - - +
374D ARG* 1.3 74.3 + - - +
376D GLY* 3.3 4.0 + - - -
377D ILE* 3.0 54.6 + - + +
384D MET* 5.0 6.0 + - - -
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Residues in contact with ARG 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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340D PHE* 3.5 20.3 - - + -
344D LEU* 5.0 5.3 - - + +
350D ASN* 3.8 9.5 + - - -
352D HIS* 4.5 9.5 + - - -
353D PHE* 3.4 45.7 - - + -
370D GLU* 2.8 41.5 + - - +
371D VAL* 3.8 5.4 - - - +
373D ARG* 1.3 87.8 - - - +
375D TRP* 1.4 64.0 + - - +
377D ILE* 3.3 12.2 + - + +
378D GLN* 3.0 18.7 + - - +
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Residues in contact with TRP 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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335D LEU 3.7 10.3 - - - -
336D GLN* 4.2 1.1 - - - -
337D LEU* 3.5 46.1 - - + +
340D PHE* 3.5 49.5 - + + -
371D VAL 2.9 14.4 + - - +
372D ALA 3.1 6.9 + - - +
374D ARG* 1.4 74.6 - - - +
376D GLY* 1.3 57.1 + - - +
378D GLN* 3.2 10.1 + - + +
379D LYS* 3.0 60.0 + - + +
381D ARG* 5.5 1.6 - - - +
384D MET* 3.6 39.6 - - + +
389D LEU* 3.7 19.9 - - + +
392D SER* 5.1 6.8 + - - -
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Residues in contact with GLY 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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372D ALA 2.9 10.3 + - - -
373D ARG 3.6 4.5 - - - -
375D TRP* 1.3 74.0 - - - +
377D ILE* 1.4 57.1 + - - +
380D ASN* 2.9 10.2 + - - -
381D ARG* 2.8 52.7 + - - -
382D PRO* 5.1 1.7 - - - +
384D MET* 3.6 12.2 - - - +
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Residues in contact with ILE 377 (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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373D ARG* 3.0 54.5 + - + +
374D ARG* 3.3 15.2 + - + +
376D GLY* 1.4 74.4 - - - +
378D GLN* 1.3 63.3 + - - +
380D ASN* 3.4 12.5 + - - +
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Residues in contact with GLN 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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335D LEU* 3.9 27.1 - - + +
340D PHE* 3.6 34.4 - - + -
374D ARG 3.0 13.4 + - - +
375D TRP* 3.3 22.2 - - + +
377D ILE* 1.3 80.0 - - - +
379D LYS* 1.4 64.0 - - + +
380D ASN* 3.5 0.7 + - - +
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Residues in contact with LYS 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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334D SER* 5.1 2.0 - - - +
335D LEU 4.1 12.6 - - - +
375D TRP* 3.0 61.0 + - + +
376D GLY 4.5 0.7 - - - +
378D GLN* 1.4 82.7 - - + +
380D ASN* 1.4 70.3 + - - +
381D ARG* 3.2 21.5 + - + +
384D MET* 5.9 0.2 - - + -
1427D EDO 2.7 48.3 + - - +
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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