Contacts of the helix formed by residues 539 - 553 (chain A) in PDB entry 1N35
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 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A LEU* 4.9 3.8 - - - +
535A GLN 2.7 18.7 + - - -
536A GLN* 3.1 17.6 + - - -
537A GLN 3.0 1.2 - - - -
538A VAL* 1.3 78.4 - - - +
540A ALA* 1.3 63.5 + - - +
541A PRO* 3.4 1.1 - - - -
542A HIS* 3.1 15.1 + - - +
543A THR* 3.1 14.6 + - - -
651A LEU* 3.5 25.5 - - - +
655A TYR* 4.6 1.7 + - - -
684A SER* 4.2 18.5 + - - -
685A THR* 4.5 4.7 - - - -
686A ALA* 4.9 3.6 - - - -
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Residues in contact with ALA 540 (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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451A MET* 5.6 3.6 - - + -
455A TYR* 5.9 0.7 - - + -
536A GLN 3.6 4.4 + - - +
537A GLN 3.1 17.9 + - - +
539A SER* 1.3 76.6 - - - +
541A PRO* 1.3 65.7 - - + +
543A THR* 3.0 8.9 + - - -
544A LEU* 2.8 37.3 + - + +
619A PHE* 4.4 3.1 - - + -
620A MET* 3.5 32.5 - - + -
647A MET* 3.9 1.8 - - + -
685A THR* 5.4 0.9 - - - -
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Residues in contact with PRO 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A MET* 6.0 1.6 - - - -
538A VAL 3.4 10.5 - - - +
539A SER 3.5 1.3 - - - -
540A ALA* 1.3 95.6 - - + +
542A HIS* 1.3 58.7 + - - +
544A LEU* 4.1 9.2 - - + +
545A THR* 3.0 31.5 + - - -
606A ILE* 3.9 9.1 - - + +
610A VAL* 6.0 0.2 - - + -
619A PHE* 4.9 1.8 - - + -
644A MET* 3.8 23.1 - - + +
647A MET* 3.3 35.7 - - + -
648A ILE* 3.6 22.7 - - + -
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Residues in contact with HIS 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TRP* 3.8 15.5 - + - -
539A SER 3.1 11.1 + - - +
541A PRO* 1.3 78.6 - - - +
543A THR* 1.3 62.8 + - - +
546A ALA* 3.2 19.2 + - - +
599A LEU* 4.0 7.2 - - + -
602A ILE* 4.1 12.0 - - + +
603A MET* 5.2 1.8 - - - -
606A ILE* 3.9 10.7 - - + +
648A ILE* 4.4 1.7 - - + +
651A LEU* 3.9 13.9 - - + -
655A TYR* 2.7 39.6 + + - -
680A PHE* 4.0 12.3 - + - -
686A ALA* 4.1 6.5 - - + +
690A GLU* 2.6 45.6 + - + +
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Residues in contact with THR 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A MET* 6.0 3.6 - - - -
454A GLN* 5.0 9.2 - - - +
539A SER 3.1 9.4 + - - -
540A ALA* 3.0 10.4 + - - -
542A HIS* 1.3 78.8 - - - +
544A LEU* 1.3 58.9 + - + +
546A ALA* 3.2 3.6 + - - +
547A ASP* 2.9 39.5 + - - +
685A THR* 3.0 43.5 + - - +
686A ALA* 3.3 15.7 - - - +
689A THR* 4.0 11.2 - - + -
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Residues in contact with LEU 544 (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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436A MET* 3.9 33.9 - - + +
447A PHE* 3.7 21.3 - - + -
451A MET* 3.6 30.3 - - - -
540A ALA* 2.8 28.1 + - + +
541A PRO* 4.1 5.2 - - + +
543A THR* 1.3 70.9 - - + +
545A THR* 1.3 61.3 + - - +
547A ASP* 3.2 13.3 + - + +
548A TYR* 2.9 27.7 + - - +
619A PHE* 3.8 34.1 - - + -
644A MET* 4.9 1.1 - - + -
1114A LYS* 6.4 0.2 - - - +
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Residues in contact with THR 545 (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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429A TRP* 3.4 48.7 - - + +
432A ALA* 3.8 6.5 - - + -
433A ALA* 3.7 21.7 - - - +
436A MET* 4.5 9.7 - - - +
541A PRO 3.0 17.7 + - - -
544A LEU* 1.3 78.3 - - - +
546A ALA* 1.3 62.9 + - - +
548A TYR* 3.2 7.2 + - - +
549A ILE* 3.1 22.4 + - + +
606A ILE* 3.8 15.1 - - + +
610A VAL* 5.1 0.9 - - - +
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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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429A TRP* 3.7 21.5 - - + -
542A HIS 3.2 16.4 + - - +
543A THR 3.4 5.4 - - - +
545A THR* 1.3 80.0 - - - +
547A ASP* 1.3 60.7 + - - +
549A ILE* 3.3 3.7 + - - +
550A ASN* 2.8 28.8 + - - -
689A THR* 3.4 35.4 - - + +
690A GLU* 3.7 3.1 - - + +
693A ALA* 4.2 4.4 - - + +
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Residues in contact with ASP 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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543A THR* 2.9 27.0 + - - +
544A LEU* 3.5 15.8 - - + +
546A ALA* 1.3 73.6 - - - +
548A TYR* 1.3 62.2 + - - +
550A ASN* 3.2 4.9 + - - +
551A TYR* 2.9 32.5 + - - +
689A THR* 2.7 31.9 + - - +
1114A LYS* 5.3 7.1 + - - -
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Residues in contact with TYR 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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432A ALA* 3.9 22.0 - - + +
435A ARG* 3.4 40.5 + - + +
436A MET* 3.9 24.2 - - + -
439A GLN* 3.8 23.3 - - + -
544A LEU 2.9 13.4 + - - +
545A THR 3.2 8.7 + - - +
547A ASP* 1.3 77.2 - - - +
549A ILE* 1.3 62.4 + - - +
551A TYR* 4.8 0.4 - - - -
552A HIS* 3.0 69.2 + + + +
553A MET* 3.9 17.7 - - + -
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Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR* 4.1 16.8 - - + -
429A TRP* 3.8 36.8 - - + +
432A ALA* 3.4 22.0 - - + -
545A THR 3.1 14.7 + - - +
546A ALA 3.6 5.6 - - - +
547A ASP 3.2 0.2 - - - -
548A TYR* 1.3 77.3 - - - +
550A ASN* 1.3 58.1 + - - +
553A MET* 2.7 48.5 + - + -
554A ASN* 3.3 17.8 + - - +
693A ALA* 3.9 18.8 - - + +
696A SER* 4.5 1.8 - - - +
697A THR* 4.5 8.5 - - - +
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Residues in contact with ASN 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 2.8 12.0 + - - +
547A ASP* 3.8 4.9 + - - +
549A ILE* 1.3 77.7 - - - +
551A TYR* 1.3 59.0 + - - +
554A ASN* 3.0 38.7 + - - +
556A SER* 3.4 15.5 + - - +
558A THR* 5.4 7.4 + - - +
689A THR* 2.7 45.0 + - - +
692A THR* 3.3 20.4 - - - +
693A ALA* 3.4 9.4 + - - -
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Residues in contact with TYR 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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547A ASP* 2.9 17.7 + - + +
550A ASN* 1.3 79.1 - - - +
552A HIS* 1.3 95.1 + + + +
554A ASN 5.3 2.1 - - - +
1104A LYS* 5.5 9.9 - - - -
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Residues in contact with HIS 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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435A ARG* 6.0 1.1 - - - +
439A GLN* 4.3 11.3 + - - -
548A TYR* 3.0 75.0 + + + +
551A TYR* 1.3 114.4 - + + +
553A MET* 1.3 63.1 + - + +
554A ASN 3.8 2.2 - - - -
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Residues in contact with MET 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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428A THR* 4.5 14.6 - - + +
431A LEU* 4.5 7.2 - - + -
432A ALA* 4.0 29.4 - - - +
435A ARG* 3.5 34.8 - - - +
548A TYR* 3.9 16.4 - - + +
549A ILE* 2.7 38.7 + - + +
552A HIS* 1.3 81.1 - - + +
554A ASN* 1.3 57.9 + - - +
725A ILE* 3.5 17.5 - - + +
726A GLN* 3.9 15.3 + - - +
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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