Contacts of the helix formed by residues 337 - 345 (chain D) in PDB entry 4J1R
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 HIS 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D GLU* 3.3 27.4 - - - -
315D ALA* 4.1 10.6 + - + +
316D LEU* 3.6 36.5 + - + +
319D ARG* 5.1 5.1 - - + +
329D LEU* 4.5 10.1 - - + -
333D GLU 3.3 4.4 + - - +
334D ALA 3.1 20.4 + - - +
335D CYS 3.1 1.2 - - - -
336D ALA* 1.3 79.5 - - - +
338D SER* 1.3 70.8 + - - +
339D PHE* 2.9 30.9 + - - +
340D PHE* 3.0 10.9 + - + +
341D ASP* 4.2 0.2 - - - -
344D ARG* 2.7 27.5 + - - -
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LYS* 5.7 0.3 + - - -
312D GLU* 4.5 14.2 - - - +
336D ALA 3.9 0.6 + - - -
337D HIS* 1.3 84.6 + - - +
339D PHE* 1.3 64.0 + - - +
340D PHE 3.1 0.4 - - - -
341D ASP* 3.1 36.7 + - - +
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Residues in contact with PHE 339 (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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155D VAL* 4.1 10.1 - - + -
158D VAL* 4.0 19.7 - - + -
159D LYS* 3.3 61.9 + - + +
162D MET* 4.9 0.7 - - + -
247D LEU* 4.3 14.8 - - + -
251D LEU* 5.4 0.7 - - + -
310D PRO* 5.0 0.2 - - + -
312D GLU* 3.9 18.2 - - + +
313D ALA* 3.6 38.6 - - + -
316D LEU* 3.5 15.3 - - + -
337D HIS* 2.9 20.0 + - + +
338D SER* 1.3 79.7 - - - +
340D PHE* 1.3 94.7 + + + +
341D ASP 3.3 0.4 + - - -
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Residues in contact with PHE 340 (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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159D LYS* 3.1 31.6 - - - -
162D MET* 3.8 16.6 - - + -
163D TYR* 3.6 24.5 - + + -
166D PHE* 3.9 14.4 - + - -
316D LEU* 3.8 15.3 - - + -
334D ALA 3.0 32.5 - - - -
335D CYS* 3.6 18.4 - - - +
337D HIS* 3.0 11.3 + - + +
339D PHE* 1.3 102.9 - + - +
341D ASP* 1.3 62.1 + - - +
342D GLU 3.1 3.1 - - - -
343D LEU* 3.0 29.3 + - + +
344D ARG* 3.4 13.5 + - - +
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Residues in contact with ASP 341 (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 ALA 5.3 0.2 - - - +
337D HIS 3.5 1.9 - - - +
338D SER* 3.1 36.2 + - - +
339D PHE 3.3 0.6 - - - -
340D PHE* 1.3 77.4 - - - +
342D GLU* 1.3 62.7 + - - +
344D ARG* 2.7 51.6 + - - +
345D ASP* 3.4 9.2 + - - +
376D ILE* 6.0 0.3 - - - +
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Residues in contact with GLU 342 (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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155D VAL* 5.7 0.5 - - - +
156D ILE* 3.6 33.5 + - + +
159D LYS* 2.5 48.7 + - + +
340D PHE 3.1 0.4 - - - -
341D ASP* 1.3 77.8 - - - +
343D LEU* 1.3 61.9 + - - +
344D ARG 3.5 0.3 + - - -
345D ASP* 3.5 13.3 - - + +
348D VAL* 3.5 23.5 - - + +
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Residues in contact with LEU 343 (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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156D ILE* 4.2 22.9 - - + -
159D LYS* 3.5 37.2 - - + +
160D LEU* 4.0 26.2 - - + +
163D TYR* 3.9 20.9 - - + -
340D PHE* 3.0 28.8 + - + +
342D GLU* 1.3 77.8 - - - +
344D ARG* 1.3 59.2 + - + +
345D ASP 3.3 2.3 + - - +
348D VAL* 3.7 21.4 - - + +
356D THR* 5.4 2.5 + - + -
359D LEU* 4.4 17.0 - - + +
360D PHE* 3.3 18.7 - - + -
381D HIS* 5.7 0.5 - - - -
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Residues in contact with ARG 344 (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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163D TYR* 4.2 10.5 - - + -
335D CYS 2.9 23.8 + - - -
336D ALA* 4.1 9.3 + - - +
337D HIS 2.7 23.6 + - - -
340D PHE* 3.4 17.9 - - - +
341D ASP* 2.7 38.7 + - - +
343D LEU* 1.3 77.7 - - + +
345D ASP* 1.3 60.2 + - - +
346D PRO* 3.7 1.4 - - - +
360D PHE* 3.5 26.2 - - + -
376D ILE* 3.2 29.8 + - - +
377D LEU* 4.1 11.8 + - - +
379D PRO* 3.7 12.4 - - + +
381D HIS* 2.9 25.9 + - - -
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D ASP 3.4 6.5 + - - +
342D GLU* 3.5 18.4 - - + +
343D LEU 3.3 1.1 - - - +
344D ARG* 1.3 77.9 - - - +
346D PRO* 1.3 79.4 - - - +
347D ASN* 3.0 32.9 + - - +
348D VAL* 3.1 28.4 + - + +
381D HIS* 4.0 1.4 + - - -
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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