Contacts of the helix formed by residues 545 - 557 (chain A) in PDB entry 4ASQ
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 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A SER 3.9 0.4 + - - -
310A MET* 3.4 14.7 - - - +
525A ALA* 3.4 33.9 - - - +
542A ILE* 3.2 18.5 + - - -
543A TYR 3.2 2.5 + - - -
544A GLY* 1.3 75.1 - - - +
546A ALA* 1.3 63.1 + - - +
547A ALA* 3.6 4.0 + - - +
548A ALA* 3.1 22.7 + - - +
549A GLY 3.3 14.0 + - - -
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A SER 5.1 0.9 - - - +
310A MET 3.9 10.3 - - - +
311A ASN* 4.3 13.7 + - + +
544A GLY 3.4 6.5 + - - +
545A SER* 1.3 71.4 - - - +
547A ALA* 1.3 60.3 + - - +
549A GLY* 3.3 1.0 + - - -
550A ALA* 2.9 29.5 + - - +
1622A NAG 4.0 34.4 - - + +
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LYS* 3.4 34.2 - - + +
525A ALA* 5.1 0.2 - - - -
545A SER* 3.3 4.2 - - - +
546A ALA* 1.3 76.3 - - - +
548A ALA* 1.3 62.9 + - - +
550A ALA* 3.4 7.5 + - - +
551A ALA* 3.4 18.7 + - - +
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Residues in contact with ALA 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A MET* 3.8 17.3 - - + -
521A ALA* 3.9 33.7 - - + +
524A LYS* 4.4 5.5 - - - +
542A ILE* 4.4 5.4 - - + -
545A SER* 3.1 23.9 + - - +
547A ALA* 1.3 75.7 - - - +
549A GLY* 1.3 63.3 + - - +
551A ALA* 3.3 8.1 + - - +
552A PHE* 3.2 25.3 + - - -
571A PHE* 4.7 0.5 - - - -
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Residues in contact with GLY 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A MET* 3.2 37.1 - - - +
311A ASN* 5.7 1.3 - - - -
312A LEU* 3.4 16.8 - - - +
545A SER 3.3 7.7 + - - -
546A ALA 3.3 0.9 + - - -
547A ALA 3.3 0.4 - - - -
548A ALA* 1.3 77.3 - - - +
550A ALA* 1.3 57.4 + - - +
552A PHE* 3.3 2.2 + - - -
553A HIS* 2.8 27.0 + - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A ALA 2.9 16.7 + - - +
547A ALA* 3.6 9.6 - - - +
548A ALA 3.3 0.4 - - - -
549A GLY* 1.3 73.5 - - - +
551A ALA* 1.3 59.7 + - - +
553A HIS* 3.3 7.8 + - - +
554A ASN* 2.9 42.5 + - - +
1622A NAG 6.0 1.3 - - - +
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LYS* 3.8 24.7 - - + +
547A ALA 3.4 3.0 + - - +
548A ALA 3.3 10.4 + - - +
550A ALA* 1.3 78.5 - - - +
552A PHE* 1.3 60.5 + - - +
554A ASN* 3.4 10.9 + - - +
555A MET* 3.2 18.4 + - - +
571A PHE* 3.4 47.8 - - + +
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Residues in contact with PHE 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A MET* 3.7 24.2 - - + -
312A LEU* 4.2 17.7 - - + -
397A VAL* 4.1 33.9 - - + -
400A VAL* 3.7 37.9 - - + -
401A LEU* 4.4 9.2 - - + -
517A PHE* 5.1 2.0 - + + -
521A ALA* 4.5 3.1 - - + -
542A ILE* 4.5 3.4 - - + -
548A ALA 3.2 22.3 + - - -
549A GLY 3.3 7.6 + - - +
551A ALA* 1.3 76.4 - - - +
553A HIS* 1.3 59.7 + - - +
555A MET* 3.2 10.3 + - + -
556A LEU* 2.8 48.9 + - + +
571A PHE* 3.9 26.7 - + - -
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Residues in contact with HIS 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASN 6.0 0.7 - - - +
312A LEU* 4.1 8.2 - - + +
377A GLN* 3.0 35.2 - - - +
549A GLY 2.8 19.2 + - - +
550A ALA* 3.3 8.3 + - - +
552A PHE* 1.3 70.9 - - - +
554A ASN* 1.3 68.8 + - - +
557A SER* 2.7 50.1 + - - -
1622A NAG 4.8 19.5 + - - -
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Residues in contact with ASN 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ALA* 2.9 28.4 + - - +
551A ALA* 3.6 7.3 - - - +
553A HIS* 1.3 89.7 + - - +
555A MET* 1.3 60.0 + - - +
557A SER* 3.7 5.4 + - - -
558A MET* 3.4 23.0 - - - +
570A ALA* 3.7 25.8 + - + +
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Residues in contact with MET 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A TYR* 4.8 3.5 + - - +
393A PHE* 3.6 18.6 - - + -
397A VAL* 5.3 2.9 - - + -
517A PHE* 3.6 39.7 - - + -
551A ALA 3.2 15.3 + - - +
552A PHE* 3.9 7.6 - - + +
554A ASN* 1.3 77.2 - - - +
556A LEU* 1.3 86.2 + - + +
557A SER 3.3 0.2 - - - -
558A MET* 3.2 22.0 + - - +
559A GLY 4.1 1.7 + - - +
567A ALA* 3.2 39.3 - - + +
570A ALA* 4.3 2.9 - - - +
571A PHE* 3.7 28.9 - - + +
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU* 5.6 0.7 - - + -
373A GLN* 4.2 13.7 - - + -
374A TYR* 3.4 46.4 - - + +
377A GLN* 3.6 29.1 - - + +
378A TYR* 3.7 9.0 - - - +
397A VAL* 3.7 37.9 - - + -
552A PHE* 2.8 37.9 + - + +
555A MET* 1.3 91.4 - - + +
557A SER* 1.3 61.5 + - - +
559A GLY 3.1 11.8 + - - -
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Residues in contact with SER 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN* 3.3 28.5 - - - +
378A TYR* 4.5 0.4 - - - -
380A HIS* 3.3 18.2 + - - -
381A GLN* 2.9 21.3 - - - +
553A HIS* 2.7 37.7 + - - -
554A ASN* 3.7 8.5 + - - -
556A LEU* 1.3 76.1 - - - +
558A MET* 1.3 61.1 + - - +
559A GLY 3.3 0.6 + - - -
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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