Contacts of the helix formed by residues 364 - 374 (chain B) in PDB entry 4HNE
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 PHE 364 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ASP* 3.5 30.5 - - + -
302B TYR* 4.2 26.2 - + - -
305B ARG* 3.5 37.9 - - - -
306B ASN* 3.3 23.6 - - + -
309B ARG* 4.2 6.3 - - + -
362B TYR 4.9 0.4 - - - -
363B PRO* 1.3 72.5 - - + +
365B TYR* 1.3 59.8 + - - +
366B TRP* 3.1 39.3 - + + +
367B ALA* 3.0 25.0 + - + +
368B TRP* 4.0 5.7 - - - -
444B VAL* 3.7 23.8 - - + -
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Residues in contact with TYR 365 (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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308B ASP* 6.3 0.4 - - - -
309B ARG 3.0 31.0 + - - +
310B GLY* 3.4 24.7 - - - -
311B ASN* 3.0 21.7 + - - +
363B PRO* 3.6 37.6 - - + +
364B PHE* 1.3 72.1 - - - +
366B TRP* 1.3 59.8 + - - +
367B ALA 3.1 1.1 + - - -
368B TRP* 3.4 28.1 + + - +
369B LEU 4.4 0.2 + - - -
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Residues in contact with TRP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.7 24.0 - + + -
297B LEU* 4.0 15.3 - - + +
298B VAL* 3.7 47.1 - - + -
301B ASP* 2.9 36.6 + - + +
302B TYR* 4.9 3.8 - + - -
309B ARG* 3.7 18.3 - - + +
311B ASN* 3.4 16.9 + - - +
314B TRP* 4.5 3.1 - - - +
364B PHE* 3.7 26.9 - + + +
365B TYR* 1.3 75.8 - - - +
367B ALA* 1.3 89.2 + - + +
368B TRP 3.2 0.4 - - - -
369B LEU* 3.2 19.7 + - + +
372B ALA* 3.3 12.5 - - - +
440B PRO* 4.1 10.1 - - + -
444B VAL* 3.6 34.1 - - + -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B PHE* 3.0 18.1 + - + +
366B TRP* 1.3 94.6 - - + +
368B TRP* 1.3 63.9 + - + +
369B LEU 3.6 1.4 + - - +
372B ALA* 3.7 15.0 - - - +
441B LEU* 4.0 21.0 - - + +
444B VAL* 3.7 30.7 - - + -
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Residues in contact with TRP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASN* 5.7 0.9 - - - +
363B PRO* 3.5 36.8 - - + -
364B PHE 4.0 12.3 - - - -
365B TYR* 3.4 22.2 + + - +
366B TRP 3.2 1.0 - - - -
367B ALA* 1.3 81.3 - - + +
369B LEU* 1.3 66.9 + - + +
370B PRO* 3.8 2.4 - - - +
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Residues in contact with LEU 369 (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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271B ASP* 6.1 0.4 - - + -
274B LEU* 3.6 37.2 - - + -
294B PHE* 4.3 6.3 - - + -
311B ASN* 3.4 37.2 - - + +
314B TRP* 3.8 12.6 - - + -
366B TRP* 3.2 18.0 + - + +
367B ALA 4.0 1.4 - - - +
368B TRP* 1.3 80.5 - - - +
370B PRO* 1.3 79.3 - - + +
371B GLN* 3.8 12.3 - - + +
372B ALA* 3.1 17.3 + - - +
373B LYS* 4.3 4.6 + - - +
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Residues in contact with PRO 370 (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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278B GLU* 3.8 23.3 - - - +
368B TRP 3.8 2.7 - - - +
369B LEU* 1.3 88.3 - - + +
371B GLN* 1.3 72.7 + - - +
373B LYS* 2.9 43.3 + - + +
374B VAL* 4.4 2.8 + - - +
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Residues in contact with GLN 371 (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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274B LEU* 3.5 30.3 - - - +
277B PHE* 5.5 6.1 - - - +
287B ASN* 5.4 6.1 - - - +
290B LEU* 4.0 17.7 - - + +
291B LEU* 3.6 28.6 - - + +
294B PHE* 3.5 27.4 - - + -
369B LEU* 3.2 8.8 - - + +
370B PRO* 1.3 95.0 - - - +
372B ALA* 1.3 59.9 + - - +
373B LYS 3.1 2.4 + - - -
374B VAL* 3.5 22.4 + - - +
440B PRO* 5.0 1.0 - - - +
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Residues in contact with ALA 372 (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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294B PHE* 3.7 12.9 - - + -
366B TRP* 3.3 26.0 - - + +
367B ALA* 3.7 16.6 - - - +
369B LEU 3.1 9.9 + - - +
370B PRO 2.9 1.6 + - - -
371B GLN* 1.3 77.0 - - - +
373B LYS* 1.3 60.1 + - - +
374B VAL 3.3 1.1 - - - -
439B SER* 3.6 0.5 - - - -
440B PRO* 3.5 19.0 - - + +
441B LEU* 2.9 34.0 + - + +
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Residues in contact with LYS 373 (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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278A GLU 5.2 4.7 - - - +
279A ALA 5.0 4.7 - - - +
281A PRO* 3.4 40.0 - - + +
369B LEU 4.9 3.1 - - - +
370B PRO* 2.9 24.5 + - + +
372B ALA* 1.3 80.0 - - - +
374B VAL* 1.3 60.7 + - - +
375B PRO* 3.5 3.3 - - - +
439B SER* 3.5 13.8 + - - -
441B LEU* 4.2 26.4 - - + +
442B HIS* 5.7 2.0 - - - -
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO* 4.4 10.5 - - + -
282A LEU 3.5 18.2 - - - +
284A GLU* 3.9 24.9 - - + +
291B LEU* 4.3 20.9 - - + -
295B GLU* 5.3 3.7 - - - +
370B PRO 4.7 2.5 - - - +
371B GLN* 3.7 21.4 - - - +
372B ALA 3.3 1.4 - - - -
373B LYS* 1.3 78.4 - - - +
375B PRO* 1.3 83.8 - - - +
376B PHE* 4.3 0.3 - - - -
439B SER* 3.6 1.3 - - - -
440B PRO* 3.3 21.3 - - - +
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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