Contacts of the helix formed by residues 385 - 399 (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 ASN 385 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369D GLU* 5.9 1.6 - - - -
372D ALA* 3.4 11.0 - - - +
383D ALA 4.3 3.3 + - - +
384D MET* 1.3 76.8 - - - +
386D TYR* 1.4 64.1 + - - +
387D ASP* 3.5 17.0 + - - +
388D LYS* 2.8 51.4 + - - +
389D LEU* 3.1 19.2 + - - +
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Residues in contact with TYR 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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365D LEU* 3.7 22.4 - - + -
368D PRO* 3.6 20.0 - - + +
369D GLU* 3.6 29.2 - - - -
372D ALA* 3.5 9.1 - - - +
385D ASN* 1.4 73.4 - - - +
387D ASP* 1.4 55.2 + - - +
389D LEU* 4.0 17.0 - - + -
390D SER* 2.7 53.8 + - - -
393D LEU* 5.0 0.4 - - + -
404D LYS* 5.0 3.8 + - - -
409D ARG 3.5 4.3 + - - -
410D TYR* 3.3 34.8 - + - -
412D TYR* 2.6 23.6 + - - -
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Residues in contact with ASP 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D ASN* 3.2 19.1 + - - +
386D TYR* 1.4 78.0 - - - +
388D LYS* 1.4 67.5 + - - +
390D SER* 2.7 23.6 + - - -
391D ARG* 3.4 18.2 + - - +
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Residues in contact with LYS 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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381D ARG* 4.3 20.7 - - - +
383D ALA* 2.8 39.7 + - - +
384D MET* 3.7 19.1 - - + -
385D ASN* 2.8 31.1 + - - +
387D ASP* 1.4 76.3 - - - +
389D LEU* 1.3 64.9 + - - +
391D ARG* 3.3 8.2 + - - +
392D SER* 3.1 26.4 + - - -
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Residues in contact with LEU 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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337D LEU* 3.7 21.9 - - + +
341D LEU* 5.5 1.8 - - + -
365D LEU* 4.4 10.3 - - + -
368D PRO 4.3 1.6 - - - +
371D VAL* 3.8 26.5 - - + -
372D ALA* 4.0 14.4 - - + +
375D TRP* 3.7 35.0 - - + -
384D MET* 4.2 4.4 - - - -
385D ASN 3.1 13.8 + - - +
386D TYR* 3.5 26.7 - - + +
388D LYS* 1.3 77.3 - - - +
390D SER* 1.3 56.7 + - - +
392D SER* 3.3 7.4 + - - -
393D LEU* 2.9 39.0 + - + +
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Residues in contact with SER 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D TYR* 2.7 42.7 + - - -
387D ASP* 2.7 25.6 + - - -
389D LEU* 1.3 73.8 - - - +
391D ARG* 1.4 52.9 + - - +
393D LEU* 3.1 15.1 + - - +
394D ARG* 2.9 47.0 + - - +
397D TYR* 4.9 1.9 + - - -
412D TYR* 4.9 2.2 - - - -
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Residues in contact with ARG 391 (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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387D ASP* 3.4 22.0 - - - +
388D LYS* 3.3 11.4 + - - +
389D LEU 3.3 0.6 - - - -
390D SER* 1.4 73.4 + - - +
392D SER* 1.3 61.1 + - - +
394D ARG* 3.2 29.2 + - - +
395D TYR* 3.1 23.7 + - - +
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Residues in contact with SER 392 (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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337D LEU* 3.7 20.0 - - - -
375D TRP* 5.1 6.4 + - - -
384D MET* 6.0 1.9 - - - +
388D LYS* 3.1 14.5 + - - +
389D LEU* 3.6 8.7 - - - -
391D ARG* 1.3 72.6 - - - +
393D LEU* 1.4 65.9 + - - +
395D TYR* 3.2 18.6 + - - +
396D TYR* 3.3 16.2 + - - -
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Residues in contact with LEU 393 (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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337D LEU* 3.8 13.0 - - + -
341D LEU* 3.7 29.8 - - + -
363D PHE* 5.4 1.3 - - + -
365D LEU* 4.4 12.6 - - + -
386D TYR* 5.0 0.2 - - + -
389D LEU* 2.9 28.3 + - + +
390D SER* 3.3 13.9 - - - +
392D SER* 1.4 74.6 - - - +
394D ARG* 1.4 58.0 + - - +
396D TYR* 3.0 22.4 + - + +
397D TYR* 3.2 32.0 + - + +
402D MET* 4.4 17.0 - - + +
412D TYR* 3.7 37.5 - - + +
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Residues in contact with ARG 394 (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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390D SER* 2.9 26.4 + - - +
391D ARG* 3.4 32.3 - - - +
392D SER 3.2 0.4 - - - -
393D LEU* 1.4 73.2 - - - +
395D TYR* 1.4 63.2 + - - +
397D TYR* 3.1 42.3 + - + +
398D GLU* 3.4 10.2 + - - +
404D LYS* 5.3 10.1 - - - +
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Residues in contact with TYR 395 (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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336D GLN* 5.9 3.1 - - - -
391D ARG 3.1 12.2 + - - +
392D SER* 3.2 12.3 + - - +
394D ARG* 1.4 76.6 - - - +
396D TYR* 1.4 72.6 + + - +
398D GLU* 3.2 26.7 + - + +
399D LYS* 3.2 38.0 + - + +
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Residues in contact with TYR 396 (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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336D GLN* 3.4 24.3 + - - +
337D LEU* 3.0 44.2 + - + +
338D TRP* 3.2 36.5 + + + -
392D SER* 3.3 11.8 + - - -
393D LEU* 3.0 13.0 + - - +
395D TYR* 1.4 90.9 - + - +
397D TYR* 1.3 63.4 + - - +
399D LYS* 3.5 6.1 + - + +
400D GLY 3.3 2.6 + - - -
401D ILE* 3.0 47.6 + - + -
402D MET* 3.4 34.2 + - + +
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Residues in contact with TYR 397 (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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390D SER 4.9 1.3 + - - -
393D LEU* 3.2 21.1 - - + +
394D ARG* 3.1 41.6 + - + +
396D TYR* 1.3 74.6 - - - +
398D GLU* 1.3 59.2 + - - +
400D GLY* 2.9 20.3 + - - -
402D MET* 3.2 27.9 - - + +
403D GLN* 3.7 10.5 - - + -
404D LYS* 3.3 35.5 - - + +
412D TYR* 2.8 36.8 - + - -
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Residues in contact with GLU 398 (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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394D ARG 3.4 4.8 + - - +
395D TYR* 3.3 20.9 - - + +
397D TYR* 1.3 79.6 - - - +
399D LYS* 1.3 59.9 + - + +
400D GLY* 3.3 1.4 + - - -
419D GLU* 4.5 4.9 - - - +
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Residues in contact with LYS 399 (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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395D TYR* 3.2 45.2 + - + +
396D TYR* 3.8 8.1 - - + +
397D TYR 3.3 0.4 - - - -
398D GLU* 1.3 75.5 - - + +
400D GLY* 1.3 59.4 + - - +
401D ILE* 3.8 25.1 - - + -
419D GLU* 3.6 10.0 - - - +
423D SER* 2.8 31.8 + - - +
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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