Contacts of the helix formed by residues 329 - 337 (chain D) in PDB entry 5M8L
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 329 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D ALA* 3.8 4.8 - - - +
253D THR 5.0 0.2 - - - +
254D GLY* 3.9 12.4 - - - +
326D ARG* 3.9 21.7 + - - -
327D LEU 4.8 1.8 - - - +
328D PRO* 1.3 75.9 - - + +
330D PRO* 1.3 80.6 - - + +
331D GLN* 3.0 6.2 + - + +
332D ASP* 2.9 38.9 + - - +
333D VAL 3.9 1.9 + - - -
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Residues in contact with PRO 330 (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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252D ALA* 3.1 22.9 - - + +
253D THR* 3.9 18.4 - - - +
329D GLU* 1.3 96.5 - - + +
331D GLN* 1.3 68.2 + - + +
333D VAL* 3.6 12.5 + - - +
469D PRO* 3.6 23.0 - - + +
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Residues in contact with GLN 331 (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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329D GLU* 3.1 4.7 - - + +
330D PRO* 1.3 80.7 - - + +
332D ASP* 1.3 58.1 + - - +
333D VAL 3.0 1.8 - - - -
334D ALA* 2.8 14.4 + - + +
335D GLN* 2.7 48.9 + - + +
469D PRO* 3.7 21.7 - - - +
470D SER 4.1 15.9 + - - +
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Residues in contact with ASP 332 (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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328D PRO* 3.6 9.2 - - + +
329D GLU* 2.9 43.8 + - - +
331D GLN* 1.3 76.4 - - - +
333D VAL* 1.3 56.2 + - - +
335D GLN* 3.7 11.4 + - - +
336D CYS* 3.1 29.1 + - - +
365D PRO* 3.5 33.6 - - + +
375D SER* 5.5 0.5 + - - -
376D LEU* 4.0 19.0 + - + +
379D LEU* 5.8 0.7 - - - +
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Residues in contact with VAL 333 (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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252D ALA* 3.6 30.7 - - + -
330D PRO 3.6 9.1 + - - +
331D GLN 3.0 0.8 - - - -
332D ASP* 1.3 76.2 - - - +
334D ALA* 1.3 65.8 + - - +
336D CYS* 3.4 7.2 + - - -
337D LEU* 3.2 30.1 + - + +
376D LEU* 4.0 14.4 - - + -
406D PHE* 4.4 14.6 - - + -
410D VAL* 4.6 8.7 - - + -
468D TRP* 3.5 37.5 - - + -
469D PRO* 4.7 5.8 - - + -
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Residues in contact with ALA 334 (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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330D PRO 3.9 1.2 + - - -
331D GLN* 2.8 27.3 + - + +
333D VAL* 1.3 80.5 - - - +
335D GLN* 1.3 62.6 + - + +
337D LEU* 3.6 13.4 + - - +
338D GLU* 3.6 19.8 + - - +
417D ARG* 4.9 2.7 + - - +
469D PRO* 3.8 33.2 - - + +
470D SER* 5.1 2.7 - - - +
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Residues in contact with GLN 335 (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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331D GLN* 2.7 32.7 + - + +
332D ASP* 3.7 21.4 + - - +
334D ALA* 1.3 73.6 - - + +
336D CYS* 1.3 62.9 + - - +
338D GLU* 3.1 28.2 + - - +
339D VAL* 3.9 5.7 + - - +
365D PRO* 3.2 23.1 - - - +
366D THR* 3.2 31.7 + - + +
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Residues in contact with CYS 336 (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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332D ASP 3.1 17.3 + - - +
333D VAL* 3.4 13.6 + - - -
335D GLN* 1.3 76.7 - - - +
337D LEU* 1.3 60.5 + - - +
338D GLU 3.2 0.9 - - - -
339D VAL* 3.2 17.3 + - - +
355D PHE* 3.4 26.3 - - - -
358D THR* 3.5 27.8 - - + -
359D VAL* 4.4 5.4 - - - -
365D PRO 3.2 7.8 + - - +
376D LEU* 3.9 14.4 - - + -
410D VAL* 3.9 26.7 - - - -
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Residues in contact with LEU 337 (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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333D VAL* 3.2 35.6 + - + +
334D ALA* 3.9 6.1 - - - +
335D GLN 3.2 0.4 - - - -
336D CYS* 1.3 81.5 - - - +
338D GLU* 1.3 55.4 + - - +
339D VAL 3.3 0.7 - - - -
355D PHE* 4.5 3.4 - - + -
410D VAL* 3.8 29.8 - - + +
413D GLU* 3.8 28.0 - - + +
414D TRP* 3.9 18.6 - - + +
417D ARG* 3.3 31.4 - - - +
418D TYR* 2.9 23.6 + - - -
468D TRP* 4.1 15.7 - - + -
469D PRO* 6.0 0.2 - - + -
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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