Contacts of the helix formed by residues 547 - 559 (chain A) in PDB entry 1R4L
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 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A VAL* 3.4 10.9 - - - +
533A ALA* 3.3 27.2 - - - +
544A ILE 3.8 11.9 - - - -
545A SER 3.1 6.1 + - - -
546A ASN* 1.3 75.1 - - - +
548A THR* 1.3 58.8 + - - +
549A GLU* 3.4 11.3 + - - +
550A ALA* 2.8 24.3 + - - +
551A GLY 2.8 21.0 + - - -
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Residues in contact with THR 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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317A SER 4.6 2.7 - - - +
318A VAL 4.4 1.3 - - - -
319A GLY* 3.9 22.9 - - - +
546A ASN 3.4 9.6 + - - +
547A SER* 1.3 68.2 - - - +
549A GLU* 1.3 73.0 + - - +
550A ALA 2.9 2.0 - - - -
551A GLY* 3.9 4.7 - - - +
552A GLN* 2.5 49.1 + - - +
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Residues in contact with GLU 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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532A ALA* 3.0 26.0 - - - +
533A ALA* 5.1 3.6 - - - -
547A SER* 3.4 9.6 - - - +
548A THR* 1.3 101.2 + - - +
550A ALA* 1.3 56.2 + - - +
552A GLN* 4.1 2.8 - - - +
553A LYS* 3.4 19.1 + - - +
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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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529A LEU* 3.9 21.6 - - + +
532A ALA* 3.5 8.2 + - - +
544A ILE* 3.5 33.0 - - + -
547A SER* 2.8 22.2 + - - +
548A THR 2.9 0.4 - - - -
549A GLU* 1.3 74.7 - - - +
551A GLY* 1.3 69.5 + - - +
552A GLN 3.1 1.5 + - - -
553A LYS* 3.1 11.8 + - - +
554A LEU* 3.2 13.6 + - - +
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Residues in contact with GLY 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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318A VAL* 2.7 38.7 - - - +
319A GLY* 5.2 0.7 - - - -
320A LEU* 4.0 7.4 - - - +
544A ILE* 5.7 0.4 - - - -
547A SER 2.8 14.5 + - - -
550A ALA* 1.3 73.1 - - - +
552A GLN* 1.3 63.7 + - - +
554A LEU* 3.3 7.4 + - - +
555A PHE* 2.8 23.3 + - - +
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Residues in contact with GLN 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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318A VAL 4.2 0.4 + - - -
319A GLY* 5.2 2.3 - - - -
548A THR* 2.5 30.3 + - - +
549A GLU* 4.1 3.6 - - - +
551A GLY* 1.3 65.8 - - - +
553A LYS* 1.3 71.5 + - - +
555A PHE* 2.8 28.4 + - - +
556A ASN* 2.6 48.7 + - - +
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Residues in contact with LYS 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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528A ALA* 3.9 22.1 + - - +
529A LEU* 4.3 11.4 - - + -
532A ALA* 4.2 18.6 - - + +
549A GLU 3.4 12.7 + - - +
550A ALA 3.1 8.1 + - - +
552A GLN* 1.3 84.1 - - - +
554A LEU* 1.3 65.9 + - - +
555A PHE 2.7 0.3 + - - -
556A ASN* 2.8 23.9 + - - +
557A MET* 3.4 3.7 + - - +
572A ASN 5.0 2.7 - - - -
573A VAL* 2.9 44.9 + - + +
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Residues in contact with LEU 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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315A PHE* 6.3 2.9 - - + -
318A VAL* 6.5 1.6 - - + -
320A LEU* 5.4 7.6 - - + -
404A VAL* 4.7 13.9 - - + +
407A ILE* 4.6 21.3 - - + -
408A MET* 5.3 14.6 - - + -
525A PHE* 4.7 11.4 - - + -
529A LEU* 4.3 19.2 - - + +
550A ALA 3.2 8.4 + - - +
551A GLY* 3.6 9.9 - - - +
553A LYS* 1.3 80.7 - - - +
555A PHE* 1.3 61.4 + - - +
557A MET* 2.9 21.2 + - + +
558A LEU* 2.8 54.1 - - + +
573A VAL* 5.6 3.1 - - + -
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Residues in contact with PHE 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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319A GLY* 5.9 0.9 - - - -
320A LEU* 3.8 38.8 - - + -
321A PRO* 4.6 10.8 - - + -
384A ALA* 4.8 15.3 - - + -
551A GLY 2.8 13.1 + - - +
552A GLN* 2.8 26.5 + - - +
553A LYS 2.7 4.2 + - - -
554A LEU* 1.3 67.1 - - - +
556A ASN* 1.3 59.9 + - - +
557A MET 2.7 15.5 + - - -
558A LEU* 3.0 16.9 + - - +
559A ARG* 3.1 29.0 + - + +
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Residues in contact with ASN 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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552A GLN* 2.6 49.3 + - - +
553A LYS* 2.8 14.9 + - - +
555A PHE* 1.3 74.9 - - - +
557A MET* 1.3 50.6 + - - +
559A ARG* 3.2 20.0 + - - +
560A LEU* 2.7 26.5 - - - +
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Residues in contact with MET 557 (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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381A TYR* 3.7 15.3 - - + +
396A ALA* 4.8 3.6 - - + -
400A PHE* 3.4 40.8 - - + -
525A PHE* 4.8 4.9 - - + -
553A LYS 3.4 2.2 + - - +
554A LEU* 2.9 26.4 + - + +
555A PHE 2.7 1.8 + - - -
556A ASN* 1.3 78.6 - - - +
558A LEU* 1.3 71.7 + - + +
559A ARG 3.3 1.3 - - - -
560A LEU* 3.0 20.8 + - + +
561A GLY 4.9 5.6 - - - +
569A ALA* 4.3 14.8 - - + -
573A VAL* 3.9 33.2 - - + -
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Residues in contact with LEU 558 (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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320A LEU* 4.5 13.9 - - + -
380A GLN* 4.0 13.7 - - + +
381A TYR* 3.3 43.6 + - + -
384A ALA* 3.4 26.0 - - + -
385A TYR* 3.6 5.4 - - - +
404A VAL* 4.8 11.9 - - + -
554A LEU* 2.8 65.9 + - + +
555A PHE* 3.0 6.3 + - - +
557A MET* 1.3 81.3 - - + +
559A ARG* 1.3 64.1 + - - +
560A LEU 3.1 1.4 + - - -
561A GLY 3.2 10.4 + - - -
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Residues in contact with ARG 559 (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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384A ALA* 2.8 24.5 + - - +
385A TYR* 3.8 4.2 - - - +
387A ALA 5.0 0.7 - - - +
388A GLN* 3.0 21.2 + - - +
555A PHE* 3.1 32.4 + - + +
556A ASN* 3.2 20.2 + - - +
558A LEU* 1.3 76.2 - - - +
560A LEU* 1.3 101.1 + - - +
561A GLY 2.9 7.4 + - - -
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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