Contacts of the helix formed by residues 366 - 381 (chain D) in PDB entry 4AY6
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 LYS 366 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337D VAL* 6.2 1.4 - - - +
341D ARG* 5.1 5.5 - - - +
361D LEU* 2.8 35.9 + - + +
364D GLN* 3.4 28.8 + - + +
365D GLY* 1.3 75.4 - - - +
367D LEU* 1.3 59.3 + - - +
368D GLN* 3.4 23.8 - - - +
369D GLU* 3.3 15.9 + - - +
370D ALA* 2.9 25.8 + - - +
527D VAL* 4.2 26.7 + - + +
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Residues in contact with LEU 367 (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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362D GLN* 3.8 26.0 - - + +
365D GLY* 3.1 29.2 + - - +
366D LYS* 1.3 67.4 - - - +
368D GLN* 1.3 73.4 + - - +
369D GLU 2.7 3.7 + - - -
370D ALA* 2.8 6.9 + - - -
371D LEU* 2.7 26.1 + - - +
394D THR* 4.0 13.9 - - + +
397D GLU* 3.8 45.3 - - + +
398D MET* 3.8 20.6 - - + -
524D LYS* 6.3 0.2 - - - -
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Residues in contact with GLN 368 (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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365D GLY 4.9 1.7 - - - +
366D LYS* 3.4 35.4 - - - +
367D LEU* 1.3 77.8 + - - +
369D GLU* 1.3 77.9 + - + +
371D LEU* 3.6 15.6 - - - +
372D MET* 3.6 8.8 + - - +
398D MET* 4.6 12.5 - - - +
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Residues in contact with GLU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D ARG* 3.2 33.4 + - - -
361D LEU* 4.1 13.2 - - + +
366D LYS* 3.6 26.3 - - - +
367D LEU 2.7 1.6 + - - -
368D GLN* 1.3 86.3 + - + +
370D ALA* 1.3 67.3 + - - +
371D LEU 3.0 1.3 - - - -
372D MET* 2.9 31.3 + - + +
373D HIS* 3.3 19.9 + - + +
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Residues in contact with ALA 370 (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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358D ALA* 3.2 30.2 - - + +
361D LEU* 3.5 17.5 - - + +
362D GLN* 3.5 16.6 - - + +
366D LYS 2.9 17.8 + - - +
367D LEU* 2.8 10.2 + - - +
369D GLU* 1.3 72.0 - - - +
371D LEU* 1.3 59.2 + - - +
373D HIS* 3.4 0.9 + - - -
374D TYR* 3.1 31.4 + - + -
394D THR* 4.8 2.5 - - + -
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Residues in contact with LEU 371 (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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367D LEU 2.7 19.7 + - - +
368D GLN* 3.6 7.6 - - - +
370D ALA* 1.3 70.4 - - - +
372D MET* 1.3 68.0 + - - +
374D TYR* 2.9 10.5 + - - +
375D LYS* 2.9 48.3 + - + +
391D MET* 3.8 30.3 - - + +
394D THR* 4.5 10.4 - - + +
395D LEU* 4.1 27.6 - - + -
398D MET* 4.1 17.0 - - + -
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Residues in contact with MET 372 (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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368D GLN 3.6 7.1 + - - +
369D GLU* 2.9 26.6 + - + +
371D LEU* 1.3 75.3 - - - +
373D HIS* 1.3 73.9 + - + +
375D LYS* 3.4 16.3 + - - +
376D GLU* 3.0 32.2 + - + +
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Residues in contact with HIS 373 (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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341D ARG* 4.2 10.3 + - - -
344D LEU* 4.1 6.1 - - + -
354D HIS* 3.0 52.3 + + - +
357D LEU* 3.6 31.6 - - + +
358D ALA* 3.9 9.9 - - + -
361D LEU* 3.9 11.9 - - + -
369D GLU* 3.3 22.1 + - + +
370D ALA 3.9 1.6 - - - +
371D LEU 3.1 1.0 - - - -
372D MET* 1.3 88.5 - - + +
374D TYR* 1.3 61.5 + - - +
376D GLU* 3.1 5.7 + - + +
377D ALA* 2.9 28.4 + - - +
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Residues in contact with TYR 374 (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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355D SER* 3.9 20.2 - - - -
358D ALA* 3.6 26.2 - - + -
359D SER* 3.2 25.7 - - - -
362D GLN* 3.4 10.8 + - - -
370D ALA* 3.1 23.5 + - + -
371D LEU* 2.9 9.0 + - - +
373D HIS* 1.3 77.4 - - - +
375D LYS* 1.3 60.9 + - - +
377D ALA* 3.2 5.7 + - - +
378D ILE* 3.2 29.0 + - - +
387D ALA* 4.1 19.5 - - + +
390D ASN* 3.3 31.8 - - + +
391D MET* 4.0 25.1 - - + -
394D THR* 3.4 25.6 - - - -
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Residues in contact with LYS 375 (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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371D LEU* 2.9 47.4 + - + +
372D MET* 3.5 15.8 - - - +
374D TYR* 1.3 75.7 - - - +
376D GLU* 1.3 63.2 + - - +
378D ILE* 3.6 6.4 + - - +
379D ARG* 3.3 21.1 + - - +
391D MET* 4.2 13.7 - - + -
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Residues in contact with GLU 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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348D PRO 5.1 0.9 - - - +
349D GLU* 4.8 1.7 - - - +
354D HIS* 3.5 31.8 + - + +
372D MET* 3.0 21.9 + - + +
373D HIS* 3.1 9.2 + - + +
375D LYS* 1.3 75.7 - - + +
377D ALA* 1.3 68.2 + - - +
379D ARG* 2.8 58.8 + - - +
380D ILE* 3.2 20.1 + - - +
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Residues in contact with ALA 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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351D ALA* 4.1 19.6 - - - +
354D HIS* 4.1 10.7 - - + +
355D SER* 4.1 15.9 - - - +
373D HIS 2.9 16.0 + - - +
374D TYR* 3.2 12.3 + - - +
376D GLU* 1.3 73.6 - - - +
378D ILE* 1.3 63.8 + - - +
380D ILE* 3.3 8.1 + - - +
381D SER* 3.0 21.9 + - - -
384D PHE* 4.5 6.3 - - + -
387D ALA* 4.4 10.3 - - + -
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Residues in contact with ILE 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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374D TYR 3.2 15.4 + - - +
375D LYS* 3.8 7.6 - - - +
377D ALA* 1.3 76.5 - - - +
379D ARG* 1.3 65.9 + - - +
381D SER 2.9 26.7 + - - -
382D PRO* 3.2 12.5 - - + +
384D PHE* 4.0 4.3 - - + +
387D ALA* 3.3 35.2 - - + +
388D TYR* 3.3 58.1 - - + +
391D MET* 4.7 13.0 - - + -
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Residues in contact with ARG 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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349D GLU* 3.4 28.5 + - - -
375D LYS 3.3 10.3 + - - +
376D GLU* 2.8 45.9 + - - +
378D ILE* 1.3 79.0 - - - +
380D ILE* 1.3 88.6 + - - +
382D PRO* 4.4 8.1 - - - +
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Residues in contact with ILE 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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348D PRO 4.4 0.4 - - - +
349D GLU* 3.8 40.2 - - + +
351D ALA* 3.9 18.2 - - + +
354D HIS* 4.2 18.4 - - + -
376D GLU* 3.2 26.4 + - - +
377D ALA* 3.6 7.0 - - - +
378D ILE 3.0 0.6 - - - -
379D ARG* 1.3 110.6 - - - +
381D SER* 1.3 59.1 + - - +
382D PRO* 3.3 9.6 - - - +
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Residues in contact with SER 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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351D ALA* 3.9 18.8 - - - +
377D ALA 3.0 9.3 + - - -
378D ILE* 2.9 13.9 + - - +
380D ILE* 1.3 72.2 + - - +
382D PRO* 1.3 67.7 - - - +
383D THR* 3.1 4.7 - - - -
384D PHE* 2.9 35.0 + - - +
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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