Contacts of the helix formed by residues 558 - 575 (chain A) in PDB entry 3HN3
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 THR 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A THR* 3.8 7.2 + - - +
549A PHE 3.3 12.3 - - - +
550A HIS 3.9 2.9 - - - -
551A GLN* 3.8 23.8 - - + +
554A PRO* 4.3 0.5 - - - +
555A LEU 2.7 26.7 + - - +
557A PHE* 1.3 81.4 + - - +
559A GLU* 1.3 64.8 + - - +
560A GLU* 3.6 12.3 + - - +
561A TYR* 3.1 16.5 + - - +
562A GLN 3.2 16.5 + - - -
602E LEU* 3.8 30.5 - - + -
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Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A THR* 3.7 20.2 - - + -
546A ILE 4.3 1.8 - - - +
547A ALA* 3.4 4.8 - - - -
548A GLY* 2.8 26.4 + - - +
549A PHE 3.0 14.5 + - - +
550A HIS* 4.3 11.5 + - + -
558A THR* 1.3 72.3 - - - +
560A GLU* 1.3 64.1 + - - +
562A GLN* 3.3 5.2 + - - +
563A LYS* 3.0 33.8 + - + +
616A LYS* 4.5 4.3 - - + -
617A SER* 3.0 43.7 + - - +
618A ALA* 5.0 1.2 - - - +
550B HIS* 2.8 25.5 + - - -
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A PHE 3.8 0.3 - - - +
550A HIS* 2.7 39.2 + - - -
551A GLN 3.1 42.1 + - - +
552A ASP* 6.1 0.2 - - - +
554A PRO* 3.8 11.2 - - + +
558A THR* 3.2 3.2 - - - +
559A GLU* 1.3 77.7 - - - +
561A TYR* 1.3 60.2 + - - +
563A LYS* 3.3 14.5 + - + +
564A SER* 2.9 29.1 + - - -
615B PRO* 3.7 1.5 - - - +
617B SER* 4.7 3.6 + - - -
620B PHE* 3.5 39.6 - - + -
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Residues in contact with TYR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A SER* 2.8 40.3 + - - -
507A TRP* 3.9 15.3 - + - -
512A GLY* 3.1 26.4 - - - -
514A LEU* 3.6 31.1 - - + +
543A ALA* 4.2 12.1 - - + -
554A PRO* 3.6 11.1 - - + +
555A LEU* 3.2 27.1 - - - +
556A MET* 3.5 23.6 - - + -
557A PHE 4.5 0.4 - - - +
558A THR* 3.1 11.5 + - - +
560A GLU* 1.3 74.9 - - - +
562A GLN* 1.3 61.0 + - - +
564A SER* 3.2 1.9 + - - -
565A LEU* 2.8 40.6 + - + +
596E GLN* 4.0 5.4 - - - -
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Residues in contact with GLN 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLY* 6.1 0.2 - - - -
543A ALA* 4.0 20.6 + - + +
545A THR* 3.2 38.8 + - + +
558A THR 3.2 6.2 + - - +
559A GLU* 3.5 8.6 - - - +
561A TYR* 1.3 77.5 - - - +
563A LYS* 1.3 63.2 - - - +
565A LEU* 3.5 0.3 + - - +
566A LEU* 3.0 41.8 + - + +
586A ILE* 5.4 0.8 - - - +
606A LYS 3.6 12.9 + - - -
607A GLY 3.1 24.7 + - - -
608A ILE* 3.9 10.1 - - - +
616A LYS* 3.9 11.1 - - - +
618A ALA* 3.4 24.9 - - + +
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Residues in contact with LYS 563 (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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559A GLU* 3.0 21.7 + - + +
560A GLU* 3.6 16.4 - - + +
562A GLN* 1.3 75.7 - - - +
564A SER* 1.3 56.1 + - - +
566A LEU* 3.3 6.1 + - - +
567A GLU* 2.9 49.6 + - - +
617A SER* 3.9 29.4 - - - -
618A ALA* 3.8 23.6 - - - +
621A LEU* 4.7 16.4 - - + +
617B SER* 5.4 2.7 - - - +
620B PHE* 5.7 14.1 - - + +
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Residues in contact with SER 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.6 28.8 - - - +
554A PRO* 4.5 7.0 - - - -
560A GLU 2.9 17.4 + - - -
561A TYR 3.2 3.6 + - - -
563A LYS* 1.3 72.7 - - - +
565A LEU* 1.3 65.7 + - - +
567A GLU* 3.2 16.2 + - - +
568A GLN* 3.0 31.0 + - - +
90E TRP* 3.8 14.9 - - - -
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TYR 5.4 0.7 - - - -
505A TYR 3.6 9.4 - - - +
506A SER* 3.3 24.0 - - - +
507A TRP* 4.3 6.3 - - + -
514A LEU* 3.6 12.9 - - + +
517A ILE* 3.9 10.5 - - + -
541A TYR* 4.2 4.3 - - + -
542A GLY* 3.7 41.3 - - - +
543A ALA* 4.2 5.2 - - + -
561A TYR* 2.8 34.6 + - + +
562A GLN 3.9 2.9 - - - +
564A SER* 1.3 72.8 - - - +
566A LEU* 1.3 60.3 + - + +
568A GLN* 3.3 1.7 + - - +
569A TYR* 3.0 46.8 + - + -
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Residues in contact with LEU 566 (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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541A TYR* 3.8 28.7 - - + -
542A GLY* 4.6 7.2 - - - -
562A GLN* 3.0 34.4 + - + +
563A LYS 3.5 3.6 - - - +
565A LEU* 1.3 85.7 - - + +
567A GLU* 1.3 53.4 + - - +
569A TYR* 3.2 1.7 + - - +
570A HIS* 2.8 56.6 + - + +
586A ILE* 3.5 26.5 - - + -
608A ILE* 4.5 0.7 - - + -
618A ALA* 3.9 35.0 - - + +
621A LEU* 4.1 10.8 - - + -
622A LEU* 4.5 3.4 - - + -
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Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LYS* 2.9 35.2 + - - +
564A SER* 3.2 18.1 + - - +
566A LEU* 1.3 76.1 - - - +
568A GLN* 1.3 64.6 + - - +
570A HIS* 3.3 10.3 + - - +
571A LEU* 3.0 37.5 + - + +
621A LEU* 4.5 22.8 - - + +
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Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.9 24.6 - - + +
515A GLU* 5.5 2.9 - - - +
517A ILE* 3.7 26.0 - - + +
518A GLN* 2.8 37.3 + - - +
564A SER* 3.0 24.8 + - - +
565A LEU 3.7 2.9 - - - +
567A GLU* 1.3 79.0 + - - +
569A TYR* 1.3 66.5 + - - +
571A LEU* 3.3 20.7 + - - +
572A GLY* 3.1 18.4 + - - -
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Residues in contact with TYR 569 (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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503A SER* 2.9 29.3 + - - -
504A TYR* 4.8 1.1 - - - -
505A TYR* 2.8 47.6 + + + -
517A ILE* 3.6 18.2 - - + -
521A LEU* 3.6 26.3 - - + +
538A GLN* 3.8 10.3 - - + -
541A TYR* 3.5 41.7 - + + -
565A LEU* 3.0 41.9 + - + +
566A LEU 3.6 6.5 - - - +
568A GLN* 1.3 75.4 - - - +
570A HIS* 1.3 53.0 + - + +
572A GLY* 3.1 2.8 + - - -
573A LEU* 2.8 42.7 + - + +
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Residues in contact with HIS 570 (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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541A TYR* 2.9 31.1 + + - -
566A LEU* 2.8 35.0 + - + +
567A GLU* 3.5 8.9 + - - +
568A GLN 3.2 0.2 - - - -
569A TYR* 1.3 72.9 - - - +
571A LEU* 1.3 58.6 + - + +
573A LEU* 3.2 4.2 + - + +
574A ASP* 2.8 38.2 + - - +
584A GLU* 4.1 3.6 - - - -
621A LEU* 3.4 33.0 - - + +
622A LEU* 3.4 15.5 - - + +
625A ARG* 3.3 46.7 - - - +
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Residues in contact with LEU 571 (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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518A GLN* 3.6 32.8 - - - +
567A GLU* 3.0 25.2 + - + +
568A GLN* 3.6 20.0 - - - +
569A TYR 3.3 0.2 - - - -
570A HIS* 1.3 73.5 - - + +
572A GLY* 1.3 63.7 + - - +
574A ASP* 3.5 22.5 + - + +
575A GLN* 3.5 18.0 + - - +
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Residues in contact with GLY 572 (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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518A GLN* 4.3 12.4 - - - +
521A LEU* 3.8 21.8 - - - -
522A ALA* 5.9 0.9 - - - -
525A PHE* 4.3 4.8 - - - -
568A GLN 3.1 12.0 + - - -
569A TYR 3.1 3.1 + - - -
571A LEU* 1.3 73.4 - - - +
573A LEU* 1.3 64.0 + - - +
575A GLN* 3.2 20.6 + - - +
576A LYS* 3.9 10.2 + - - +
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Residues in contact with LEU 573 (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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344A TYR* 4.4 5.8 - - - +
521A LEU* 4.6 4.0 - - + -
525A PHE* 3.7 28.5 - - + -
538A GLN* 3.9 19.7 - - + -
541A TYR* 4.8 7.0 - - + -
569A TYR* 2.8 34.7 + - + +
570A HIS* 3.5 12.8 - - + +
572A GLY* 1.3 72.9 - - - +
574A ASP* 1.3 63.8 + - - +
576A LYS* 3.1 4.5 + - - +
577A ARG* 3.0 27.3 + - - +
581A VAL* 4.1 15.3 - - + +
584A GLU* 3.6 34.8 - - + +
625A ARG* 3.6 9.4 - - - +
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Residues in contact with ASP 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A HIS* 2.8 20.7 + - - +
571A LEU* 3.6 19.6 - - + +
572A GLY 3.3 0.4 - - - -
573A LEU* 1.3 77.0 - - - +
575A GLN* 1.3 65.3 + - - +
576A LYS 3.4 1.0 + - - -
577A ARG* 2.9 31.7 + - - +
578A ARG* 4.8 7.1 + - - +
625A ARG* 2.9 35.1 + - - -
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Residues in contact with GLN 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A GLN* 5.6 3.4 - - - +
571A LEU 3.6 14.0 - - - +
572A GLY* 3.2 11.4 + - - +
573A LEU 3.1 1.2 - - - -
574A ASP* 1.3 81.1 - - - +
576A LYS* 1.3 81.2 + - - +
578A ARG 5.5 0.4 - - - -
579A LYS* 3.9 14.4 - - - +
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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
------------------------------------------------------------
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