Contacts of the helix formed by residues 388 - 403 (chain Y) in PDB entry 5A31
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 ARG 388 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383Y LEU* 3.0 23.6 + - + +
386Y MET* 3.7 35.3 - - + +
387Y GLY* 1.3 75.6 - - - +
389Y VAL* 1.3 57.9 + - - +
390Y GLN 3.5 2.0 - - - -
391Y GLU* 3.0 46.9 + - + +
392Y ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 389 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384Y ARG* 5.5 6.5 - - + +
387Y GLY 3.0 14.7 + - - +
388Y ARG* 1.3 69.0 - - - +
390Y GLN* 1.3 66.1 + - + +
392Y ALA* 3.2 6.0 + - + +
393Y ILE* 2.8 47.6 + - + +
416Y CYS* 3.6 32.8 - - + +
419Y ALA* 5.0 5.2 - - + -
420Y SER* 4.3 22.2 - - - +
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Residues in contact with GLN 390 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388Y ARG 3.5 0.2 - - - -
389Y VAL* 1.3 85.7 - - + +
391Y GLU* 1.3 60.9 + - - +
393Y ILE* 3.4 20.4 + - + +
394Y ILE* 3.4 19.2 + - + +
397Y ARG* 5.3 1.7 + - - +
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Residues in contact with GLU 391 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383Y LEU* 3.9 19.9 - - + +
388Y ARG* 3.0 55.1 + - + +
389Y VAL 3.3 0.4 - - - -
390Y GLN* 1.3 79.7 - - - +
392Y ALA* 1.3 59.2 + - - +
394Y ILE* 2.9 34.8 - - + +
395Y HIS* 3.1 13.0 + - - +
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Residues in contact with ALA 392 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380Y GLY 3.5 21.8 - - - +
383Y LEU* 3.5 16.7 - - + +
384Y ARG* 3.9 10.1 - - + +
388Y ARG 2.9 19.5 + - - +
389Y VAL* 3.5 7.9 - - - +
391Y GLU* 1.3 73.2 - - - +
393Y ILE* 1.3 66.5 - - - +
395Y HIS* 3.1 14.9 + - - +
396Y PHE* 3.1 26.0 + - + -
416Y CYS* 4.7 3.8 - - - -
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Residues in contact with ILE 393 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389Y VAL* 2.8 46.7 + - + +
390Y GLN* 3.6 11.7 - - + +
391Y GLU 3.3 0.2 - - - -
392Y ALA* 1.3 75.9 - - - +
394Y ILE* 1.3 63.6 + - - +
396Y PHE* 3.3 18.5 + - - +
397Y ARG* 3.3 27.8 + - + +
413Y LEU* 4.4 1.9 - - + +
416Y CYS* 4.2 15.0 - - + +
417Y TYR* 3.0 56.1 - - + +
420Y SER* 4.7 9.0 - - - +
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Residues in contact with ILE 394 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390Y GLN* 3.4 13.9 + - + +
391Y GLU* 2.9 31.6 + - + +
393Y ILE* 1.3 77.2 - - - +
395Y HIS* 1.3 76.2 + - + +
397Y ARG* 3.3 34.4 + - - +
398Y GLU* 3.1 29.2 + - - +
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Residues in contact with HIS 395 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Y ILE* 5.1 2.0 - - + -
376Y LEU* 3.3 39.5 - - + +
379Y LYS* 3.6 29.6 - - + +
380Y GLY* 4.2 8.7 - - - -
383Y LEU* 3.3 28.6 - - + +
391Y GLU* 3.1 29.4 + - - +
392Y ALA 3.1 7.9 + - - +
394Y ILE* 1.3 88.3 - - + +
396Y PHE* 1.3 58.0 + - - +
398Y GLU* 3.2 17.9 + - - +
399Y ALA* 2.8 29.7 + - - +
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Residues in contact with PHE 396 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377Y LEU* 3.7 36.1 - - + -
380Y GLY* 3.6 11.7 - - - -
381Y ALA* 3.4 29.8 - - + -
384Y ARG* 5.5 0.4 - - - -
392Y ALA 3.1 28.9 + - - -
393Y ILE* 3.3 8.5 + - - +
395Y HIS* 1.3 77.2 - - - +
397Y ARG* 1.3 56.4 + - - +
399Y ALA* 3.2 5.7 + - + +
400Y ILE* 2.8 36.0 + - - +
409Y CYS* 4.5 7.8 - - - +
412Y GLY* 4.1 15.5 - - - -
413Y LEU* 3.9 30.1 - - + +
416Y CYS* 3.3 32.8 - - - -
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Residues in contact with ARG 397 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390Y GLN* 5.3 1.8 + - - +
393Y ILE* 3.3 30.6 + - - +
394Y ILE* 3.3 30.4 + - - +
396Y PHE* 1.3 77.1 - - - +
398Y GLU* 1.3 58.8 + - - +
400Y ILE* 2.8 33.2 - - + +
401Y ARG* 3.6 6.9 + - - +
413Y LEU* 3.8 16.2 - - + -
417Y TYR* 3.5 17.5 + - - +
429Y MET* 6.0 1.1 - - - -
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Residues in contact with GLU 398 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376Y LEU* 3.0 32.6 - - + +
394Y ILE* 3.1 18.7 + - - +
395Y HIS* 3.2 29.2 + - - +
397Y ARG* 1.3 73.8 - - - +
399Y ALA* 1.3 61.5 + - - +
401Y ARG* 2.9 33.5 - - - +
402Y LEU* 3.3 13.9 + - + +
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Residues in contact with ALA 399 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373Y VAL* 4.0 11.2 - - + +
376Y LEU* 3.6 21.4 - - + +
377Y LEU* 4.5 16.8 - - + -
395Y HIS 2.8 21.2 + - - +
396Y PHE* 3.4 10.5 - - + +
398Y GLU* 1.3 71.6 - - - +
400Y ILE* 1.3 65.6 + - - +
402Y LEU* 3.2 6.4 + - - +
403Y ALA* 3.1 21.7 + - - +
409Y CYS* 4.7 11.6 - - + +
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Residues in contact with ILE 400 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396Y PHE 2.8 22.8 + - - +
397Y ARG* 2.8 31.6 - - + +
399Y ALA* 1.3 70.1 - - - +
401Y ARG* 1.3 65.9 + - + +
403Y ALA 3.2 3.4 - - - -
404Y PRO* 3.1 27.4 - - - +
409Y CYS* 4.0 27.8 - - + +
410Y TYR* 4.0 35.1 + - + +
413Y LEU* 4.2 17.7 - - + -
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Residues in contact with ARG 401 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397Y ARG 3.8 3.8 - - - +
398Y GLU* 2.9 39.0 - - - +
400Y ILE* 1.3 84.8 - - + +
402Y LEU* 1.3 70.1 + - + +
403Y ALA 3.5 0.3 + - - -
404Y PRO* 3.6 15.1 - - - +
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Residues in contact with LEU 402 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370Y SER 3.7 24.2 - - - +
371Y ASN* 4.3 16.7 - - + +
372Y SER 5.2 0.2 - - - -
373Y VAL* 3.4 22.8 - - + +
376Y LEU* 3.8 28.9 - - + -
398Y GLU* 3.4 8.7 - - + +
399Y ALA* 3.2 4.6 + - - +
401Y ARG* 1.3 87.0 - - + +
403Y ALA* 1.3 57.6 + - - +
404Y PRO* 3.5 6.5 - - - +
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Residues in contact with ALA 403 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373Y VAL* 3.2 35.7 - - + -
399Y ALA 3.1 7.0 + - - +
400Y ILE 3.2 4.2 - - - +
402Y LEU* 1.3 74.9 - - - +
404Y PRO* 1.3 70.1 - - - +
405Y CYS 3.5 0.2 + - - -
406Y ARG* 3.4 22.7 + - + +
409Y CYS* 3.3 25.0 - - - -
410Y TYR* 4.9 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