Contacts of the helix formed by residues 375 - 384 (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 SER 375 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D ASP* 5.5 0.5 + - - -
361D GLY* 2.9 18.8 + - - -
363D SER 3.1 28.1 + - - -
364D ASP* 4.4 1.6 - - - -
365D PRO* 3.7 20.1 - - - +
373D VAL* 4.4 3.4 - - - -
374D ARG* 1.3 74.8 - - - +
376D LEU* 1.3 95.6 + - - +
378D ASN 3.0 6.9 + - - -
379D LEU* 2.9 17.5 + - - -
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Residues in contact with LEU 376 (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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251D PHE* 3.9 12.6 - - + -
328D PRO* 3.6 22.3 - - + +
332D ASP* 4.0 31.6 + - + +
333D VAL* 4.0 20.9 - - + -
336D CYS* 3.9 21.3 - - + -
358D THR* 3.2 26.7 - - + +
359D VAL* 3.6 21.5 - - + +
365D PRO* 4.7 2.7 - - + -
375D SER* 1.3 81.2 + - - +
377D HIS* 1.3 61.2 + - - +
379D LEU* 3.0 8.5 + - - +
380D ALA* 2.8 29.1 + - - +
406D PHE* 6.2 0.2 - - + -
410D VAL* 6.4 1.8 - - + -
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Residues in contact with HIS 377 (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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215D HIS* 4.9 5.6 - + - -
220D PHE* 3.6 24.3 - + - -
251D PHE* 4.1 12.4 - - + -
359D VAL* 3.1 18.1 + - + +
360D GLU* 3.1 15.1 + - + +
375D SER 3.2 0.6 + - - -
376D LEU* 1.3 78.9 - - - +
378D ASN* 1.3 73.5 + - - +
380D ALA* 3.3 3.7 + - - +
381D HIS* 2.9 33.2 + + - -
403D LEU* 3.5 17.5 - - + -
404D HIS* 2.9 17.2 + + - -
407D THR* 3.9 16.4 - - + +
519D ZN 1.9 38.2 - - - -
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Residues in contact with ASN 378 (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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360D GLU* 2.8 32.2 + - - +
361D GLY 3.2 22.9 + - - +
362D TYR* 3.2 36.9 + - - -
374D ARG* 4.3 12.7 - - - +
375D SER 3.0 7.6 + - - +
377D HIS* 1.3 90.9 + - - +
379D LEU* 1.3 63.6 + - - +
381D HIS* 3.3 6.6 + - - +
382D LEU* 3.1 29.8 + - + +
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Residues in contact with LEU 379 (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 MET* 3.5 24.0 - - + +
324D VAL* 3.7 21.3 - - + -
326D ARG 3.5 23.6 - - - +
327D LEU* 4.1 2.0 - - - +
328D PRO* 3.9 25.1 - - + -
332D ASP* 5.8 0.7 - - - +
374D ARG 3.7 21.3 - - - +
375D SER* 2.9 18.2 + - - +
376D LEU 3.4 7.9 - - - +
378D ASN* 1.3 74.0 - - - +
380D ALA* 1.3 59.9 + - - +
382D LEU* 3.1 4.9 + - - +
383D PHE* 2.8 32.7 + - + +
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Residues in contact with ALA 380 (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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249D TRP* 4.6 2.5 - - + -
251D PHE* 3.7 41.1 - - + -
327D LEU* 4.1 12.9 - - + +
328D PRO* 4.7 0.8 - - - +
376D LEU 2.8 10.4 + - - +
377D HIS 3.7 3.8 - - - +
378D ASN 3.3 0.2 - - - -
379D LEU* 1.3 77.4 - - - +
381D HIS* 1.3 63.2 + - - +
383D PHE* 3.6 7.1 + - - +
384D LEU* 3.5 18.4 - - - +
403D LEU* 3.7 21.3 - - + +
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Residues in contact with HIS 381 (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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377D HIS* 2.9 36.2 + + - -
378D ASN* 3.4 10.1 - - - +
379D LEU 3.2 0.2 - - - -
380D ALA* 1.3 80.3 - - - +
382D LEU* 1.3 63.9 + - + +
384D LEU* 3.3 20.0 + - - +
385D ASN 4.2 0.7 + - - -
388D GLY 2.6 24.9 + - - +
389D GLY* 3.5 18.8 - - - -
394D SER* 3.6 19.8 - - - -
400D PHE* 3.7 14.6 - + + -
403D LEU* 3.7 18.6 - - + +
404D HIS* 3.4 1.6 + - - -
519D ZN 2.1 36.0 - - - -
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Residues in contact with LEU 382 (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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318D ASN* 4.9 4.1 + - - +
321D ARG* 4.1 17.9 - - - +
324D VAL* 3.8 38.0 - - + +
374D ARG* 3.8 36.3 - - + +
378D ASN* 3.1 19.0 + - + +
379D LEU* 3.1 2.2 + - - +
381D HIS* 1.3 73.0 - - + +
383D PHE* 1.3 65.4 + - - +
384D LEU 3.1 2.5 - - - -
385D ASN* 3.0 17.4 + - - +
389D GLY* 4.2 21.5 - - - +
1W NAG 5.5 2.2 - - - +
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Residues in contact with PHE 383 (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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249D TRP* 4.9 1.6 - + - -
256D ASN 3.5 21.5 - - - -
257D VAL* 3.7 22.7 - - - -
258D CYS* 4.0 6.5 - - + -
314D ASN 3.9 0.5 - - - +
315D PRO* 3.4 19.4 - - + +
316D ALA* 2.9 46.4 + - + -
324D VAL* 3.4 11.2 + - - +
325D GLN 3.5 34.5 - - - -
326D ARG* 3.8 9.6 - - - +
327D LEU* 3.5 38.6 - - + -
379D LEU* 2.8 17.4 + - + +
380D ALA 3.6 3.6 - - - +
382D LEU* 1.3 78.4 - - - +
384D LEU* 1.3 68.6 + - + +
385D ASN* 3.3 2.3 + - - +
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D TRP* 4.6 7.4 - - + -
258D CYS* 5.0 2.5 - - - -
313D ARG* 3.8 15.8 - - + -
314D ASN 2.9 25.3 + - - -
315D PRO* 4.2 9.2 - - + -
380D ALA 3.5 15.7 - - - +
381D HIS* 3.5 15.9 - - - +
382D LEU 3.1 1.0 - - - -
383D PHE* 1.3 88.8 - - + +
385D ASN* 1.3 66.4 + - - +
386D GLY 3.3 3.4 + - - +
388D GLY* 4.1 24.2 - - - +
397D ASP* 4.6 5.8 - - + +
399D ILE* 4.1 43.7 - - + -
400D PHE 5.7 1.6 - - - +
403D LEU* 4.6 5.4 - - + -
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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