Contacts of the helix formed by residues 385 - 399 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B GLU* 4.6 6.3 - - - +
372B ALA* 3.4 12.0 - - - +
383B ALA 4.3 4.6 + - - +
384B MET* 1.3 76.6 - - - +
386B TYR* 1.3 62.9 + - - +
387B ASP* 3.5 16.4 + - - +
388B LYS* 2.8 51.0 + - - +
389B LEU* 3.0 19.8 + - - +
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Residues in contact with TYR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU* 3.7 22.9 - - + -
368B PRO* 3.5 23.6 - - + +
369B GLU* 3.4 35.1 + - - +
372B ALA* 3.5 5.0 - - - +
385B ASN* 1.3 73.6 - - - +
387B ASP* 1.4 56.0 + - - +
389B LEU* 3.9 18.2 - - + -
390B SER* 2.7 56.6 + - - -
393B LEU* 4.5 3.8 - - + -
404B LYS* 5.2 2.3 + - - -
409B ARG 3.6 4.2 + - - -
410B TYR* 3.3 32.3 - + - -
412B TYR* 2.7 23.9 + - - -
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Residues in contact with ASP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ASN* 3.2 19.5 + - - +
386B TYR* 1.4 79.5 - - - +
388B LYS* 1.3 66.1 + - - +
390B SER* 2.8 21.4 + - - -
391B ARG* 3.4 9.9 + - - +
394B ARG* 4.4 3.6 + - - -
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 4.3 7.0 - - - +
383B ALA* 2.8 31.7 + - - +
384B MET* 3.7 19.1 - - + -
385B ASN* 2.8 30.4 + - - +
387B ASP* 1.3 75.3 - - - +
389B LEU* 1.3 64.3 + - - +
391B ARG* 3.2 9.7 + - - +
392B SER* 3.2 24.7 + - - -
1427B EDO 3.0 40.9 + - - -
364D LYS* 4.1 10.5 - - - +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 3.7 22.4 - - + +
341B LEU* 5.8 0.7 - - + -
365B LEU* 4.4 10.1 - - + -
368B PRO 4.1 3.4 - - - +
371B VAL* 3.8 25.8 - - + -
372B ALA* 4.1 14.6 - - + +
375B TRP* 3.6 37.2 - - + -
384B MET* 4.2 4.4 - - - -
385B ASN 3.0 16.5 + - - +
386B TYR* 3.6 25.1 - - + +
388B LYS* 1.3 77.1 - - - +
390B SER* 1.3 55.5 + - - +
392B SER* 3.2 10.7 + - - -
393B LEU* 2.9 34.0 + - + +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B TYR* 2.7 45.2 + - - -
387B ASP* 2.8 25.1 + - - -
389B LEU* 1.3 69.0 - - - +
391B ARG* 1.4 59.6 + - - +
393B LEU* 3.3 13.8 + - - +
394B ARG* 2.9 47.5 + - - +
397B TYR* 5.2 0.5 + - - -
412B TYR* 5.1 0.9 - - - -
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASP 3.9 5.8 - - - +
388B LYS* 3.2 12.6 + - - +
390B SER* 1.4 78.0 + - - +
392B SER* 1.3 63.2 + - - +
394B ARG* 3.3 30.2 + - - +
395B TYR* 3.2 19.9 + - - +
359D ARG* 5.2 5.4 - - - -
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.5 22.4 - - - -
375B TRP* 5.1 5.7 + - - -
388B LYS 3.2 12.7 + - - -
389B LEU* 3.2 11.1 + - - -
391B ARG* 1.3 74.9 - - - +
393B LEU* 1.4 62.8 + - - +
395B TYR* 3.2 20.4 + - - +
396B TYR* 3.3 19.4 + - - -
357D THR 4.3 14.2 + - - -
359D ARG* 5.8 4.2 - - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 4.2 9.6 - - + -
341B LEU* 3.7 31.0 - - + -
363B PHE* 5.1 3.4 - - + -
365B LEU* 3.8 20.0 - - + -
386B TYR* 4.5 2.5 - - + -
389B LEU* 2.9 24.5 + - + +
390B SER* 3.3 13.4 + - - +
392B SER* 1.4 73.3 - - - +
394B ARG* 1.4 60.4 - - - +
396B TYR* 3.1 22.0 + - + +
397B TYR* 3.4 15.1 - - - +
402B MET* 4.0 17.7 - - + +
412B TYR* 3.5 41.7 - - + +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASP* 4.4 3.0 + - - -
390B SER* 2.9 31.7 + - - +
391B ARG* 3.4 39.0 - - - +
392B SER 3.2 0.2 - - - -
393B LEU* 1.4 72.5 - - - +
395B TYR* 1.4 63.8 + - - +
397B TYR* 3.2 47.1 + - + +
398B GLU* 3.7 5.0 + - - +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 5.6 2.2 - - - -
391B ARG 3.2 12.4 + - - +
392B SER* 3.2 11.8 + - - +
394B ARG* 1.4 74.8 - - - +
396B TYR* 1.4 80.4 + + - +
398B GLU* 3.3 14.4 + - + +
399B LYS* 3.2 56.5 + - + +
358D GLY 3.8 16.3 + - - -
359D ARG* 3.6 44.9 - - + -
360D GLY* 3.4 18.0 + - - -
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 3.8 12.8 + - - +
337B LEU* 3.2 32.2 + - + +
338B TRP* 3.0 54.2 + + + -
392B SER* 3.3 13.7 + - - -
393B LEU* 3.1 15.7 + - + +
395B TYR* 1.4 93.9 - + - +
397B TYR* 1.4 61.6 + - - +
399B LYS* 3.6 2.9 + - + -
400B GLY 3.2 2.6 + - - -
401B ILE* 3.0 47.5 + - + +
402B MET* 3.3 39.4 + - + -
358D GLY 6.0 0.7 - - - -
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER 5.2 0.2 + - - -
393B LEU* 3.4 15.4 - - - +
394B ARG* 3.2 40.5 + - + +
396B TYR* 1.4 74.7 - - - +
398B GLU* 1.4 55.3 + - - +
400B GLY* 2.8 25.1 + - - -
402B MET* 3.3 24.1 - - + +
403B GLN* 4.1 8.3 - - + -
404B LYS* 3.4 47.9 + - + +
412B TYR* 3.4 20.9 + + - -
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ARG 3.7 4.5 + - - +
395B TYR* 3.3 18.6 + - + +
397B TYR* 1.4 77.3 - - - +
399B LYS* 1.3 61.5 + - + +
400B GLY 3.4 0.5 + - - -
419B GLU* 4.3 6.2 - - - +
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B TYR* 3.2 52.8 + - + +
396B TYR* 4.0 4.7 - - - +
397B TYR 3.3 0.8 - - - -
398B GLU* 1.3 77.2 - - + +
400B GLY* 1.3 60.4 + - - +
401B ILE* 3.6 25.7 + - + -
419B GLU* 3.6 13.3 - - - +
423B SER* 2.8 34.5 + - - +
426B PHE 6.1 1.6 - - - -
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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