Contacts of the helix formed by residues 331 - 342 (chain D) in PDB entry 4MNE
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 SER 331 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D GLU* 2.8 33.4 + - - -
330D PHE* 1.3 75.0 - - - +
332D LEU* 1.3 65.7 + - - +
333D GLU* 3.1 17.5 + - - -
334D PHE* 3.3 4.3 + - - +
335D GLN* 3.1 20.3 + - - +
363D ARG* 3.1 22.3 + - - -
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Residues in contact with LEU 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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327D SER* 5.8 3.1 - - - -
328D GLY 6.0 0.7 - - - +
330D PHE 3.5 0.6 + - - -
331D SER* 1.3 74.3 + - - +
333D GLU* 1.3 66.0 + - - +
335D GLN* 3.2 24.6 + - - +
336D ASP* 2.8 29.8 + - - +
495G LEU* 4.4 23.1 - - + -
499G LYS* 6.6 0.2 - - - -
521G THR* 5.1 15.0 - - + +
522G LYS* 5.2 6.9 + - - +
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Residues in contact with GLU 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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331D SER* 3.1 11.1 + - - +
332D LEU* 1.3 86.5 + - - +
334D PHE* 1.3 56.2 + - - +
336D ASP* 3.1 6.4 + - - -
337D PHE* 2.8 30.1 + - - +
358D HIS* 3.5 5.3 - - - -
359D ALA* 3.9 22.4 - - + -
360D PHE* 3.9 24.0 - - + +
363D ARG* 3.7 23.2 + - - +
522G LYS* 6.1 0.4 - - - +
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Residues in contact with PHE 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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163D GLU* 3.2 27.8 - - + +
166D LEU* 3.7 35.2 - - + -
253D LEU* 4.6 15.3 - - + -
257D ALA* 4.0 5.2 - - + -
325D LEU* 3.5 17.9 - - + -
330D PHE* 3.5 29.6 - + - -
331D SER* 3.3 10.1 + - - +
332D LEU 3.3 0.4 - - - -
333D GLU* 1.3 77.5 - - - +
335D GLN* 1.3 63.0 + - - +
337D PHE* 3.1 5.5 + + + +
338D VAL* 2.9 43.6 + - + +
360D PHE* 3.4 40.3 - + + -
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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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325D LEU* 3.8 27.0 - - + +
326D PRO 3.7 14.0 + - - +
327D SER* 3.5 29.5 + - - +
328D GLY 3.9 2.8 - - - +
330D PHE* 2.8 26.1 + - + +
331D SER 3.1 12.2 + - - +
332D LEU* 3.5 23.4 - - + +
334D PHE* 1.3 75.6 - - - +
336D ASP* 1.3 63.6 + - - +
338D VAL* 3.6 0.9 + - - +
339D ASN* 3.1 36.8 + - - +
451G GLU* 4.8 7.6 - - - +
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Residues in contact with ASP 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 LEU 2.8 14.4 + - - +
333D GLU* 3.6 8.7 - - - +
335D GLN* 1.3 78.7 - - - +
337D PHE* 1.3 62.7 + - - +
339D ASN* 3.3 8.1 + - - +
340D LYS* 3.0 56.3 + - - +
358D HIS* 2.9 23.9 + - + +
522G LYS* 3.8 38.9 + - + +
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Residues in contact with PHE 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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170D SER* 3.7 19.1 - - - -
174D ILE* 3.8 21.1 - - + -
249D MET* 3.8 15.0 - - + -
253D LEU* 3.8 20.2 - - + -
333D GLU 2.8 17.0 + - - +
334D PHE* 3.4 8.7 - + - +
336D ASP* 1.3 72.3 - - - +
338D VAL* 1.3 68.3 + - + +
340D LYS* 3.1 13.6 + - - +
341D CYS* 3.2 15.5 + - - -
355D LEU* 3.4 30.7 - - + +
358D HIS* 3.6 28.6 - + + -
360D PHE* 3.8 24.2 - + + -
361D ILE* 3.6 24.7 - - + -
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Residues in contact with VAL 338 (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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250D GLY* 4.2 4.3 - - - +
253D LEU* 4.4 13.7 - - + -
254D VAL* 3.5 27.6 - - + -
324D LYS* 5.0 0.9 - - - -
325D LEU* 3.8 24.5 - - + +
334D PHE* 2.9 44.9 + - + +
335D GLN 4.0 2.9 - - - +
337D PHE* 1.3 79.4 - - + +
339D ASN* 1.3 70.6 + - - +
341D CYS* 3.1 10.6 + - - +
342D LEU* 3.0 29.0 + - + +
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Residues in contact with ASN 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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323D PRO 4.2 5.5 - - - +
324D LYS* 3.6 28.4 - - - +
325D LEU 5.1 0.4 + - - -
335D GLN* 3.1 30.8 + - - +
336D ASP* 3.7 8.6 + - - +
338D VAL* 1.3 79.7 - - - +
340D LYS* 1.3 61.0 + - + +
342D LEU* 3.2 14.0 + - - +
343D ILE* 3.5 18.1 + - - +
451G GLU* 5.6 3.8 + - - -
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Residues in contact with LYS 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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336D ASP* 3.0 47.6 + - - +
337D PHE* 3.1 6.2 + - - +
339D ASN* 1.3 78.9 - - + +
341D CYS* 1.3 60.6 + - - +
343D ILE* 4.2 13.8 + - + +
349D ARG* 3.5 6.4 - - - +
350D ALA* 3.0 45.5 + - + +
355D LEU* 4.9 3.4 - - + -
358D HIS* 4.3 13.9 - - + -
454G ASP* 4.6 13.9 + - - +
522G LYS* 5.1 5.7 - - - +
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Residues in contact with CYS 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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246D ILE* 3.6 27.1 - - - +
247D TRP* 3.5 11.6 - - - -
249D MET* 3.5 31.6 - - - -
250D GLY* 3.7 13.2 - - - -
253D LEU* 5.1 0.2 - - - -
337D PHE* 3.2 25.2 + - - -
338D VAL* 3.1 8.9 + - - +
340D LYS* 1.3 78.8 - - - +
342D LEU* 1.3 58.7 + - - +
343D ILE 3.4 0.4 - - - -
349D ARG* 2.9 23.2 - - - -
355D LEU* 3.9 11.4 - - - -
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Residues in contact with LEU 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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247D TRP* 3.1 53.6 - - + +
250D GLY 3.8 9.4 - - - +
251D LEU* 3.8 14.6 - - + +
254D VAL* 3.8 27.1 - - + -
322D PRO* 3.1 31.9 - - + +
323D PRO* 3.7 32.5 - - + +
338D VAL* 3.0 18.3 + - + +
339D ASN* 3.2 9.3 + - - +
341D CYS* 1.3 78.3 - - - +
343D ILE* 1.3 61.9 + - - +
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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