Contacts of the helix formed by residues 549 - 563 (chain A) in PDB entry 5N6R
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 LYS 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A ILE 4.9 0.6 + - - -
547A PHE 3.8 0.2 - - - -
548A PHE* 1.3 117.5 + - + +
550A VAL* 1.3 66.5 + - - +
551A PRO* 3.4 4.7 - - - -
552A GLU* 3.0 31.8 + - + +
553A LEU* 2.8 48.0 + - + +
556A ILE* 6.0 0.7 - - + -
590A VAL* 3.3 43.1 - - + +
594A PHE* 5.6 6.0 - - + +
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Residues in contact with VAL 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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517A LEU* 4.1 18.4 - - + +
520A LEU* 3.9 29.6 - - + -
521A LEU* 4.3 7.2 - - + +
546A ILE* 3.9 9.9 - - + +
547A PHE* 3.4 43.2 + - + -
549A LYS* 1.3 76.2 - - - +
551A PRO* 1.3 70.5 - - + +
553A LEU* 3.5 10.7 + - + +
554A TYR* 3.3 16.6 + - - +
643A LEU* 5.1 12.3 - - + -
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Residues in contact with PRO 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 3.8 31.6 - - + +
524A MET* 3.7 33.2 - - + -
547A PHE 3.9 4.7 - - - +
549A LYS* 3.7 1.3 - - - -
550A VAL* 1.3 94.8 - - + +
552A GLU* 1.3 70.5 + - + +
554A TYR* 3.3 4.9 + - - +
555A GLU* 3.2 31.1 + - - +
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Residues in contact with GLU 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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548A PHE 5.3 0.4 - - - +
549A LYS* 3.0 40.4 + - + +
551A PRO* 1.3 81.2 - - + +
553A LEU* 1.3 54.2 + - - +
555A GLU* 3.2 17.2 + - - +
556A ILE* 2.8 52.2 + - + +
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Residues in contact with LEU 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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513A TYR* 5.3 5.5 - - - +
517A LEU* 4.2 10.0 - - + +
549A LYS* 2.8 41.0 + - + +
550A VAL* 3.7 8.7 - - + +
552A GLU* 1.3 71.2 - - - +
554A TYR* 1.3 60.2 + - - +
556A ILE* 4.0 10.5 - - + -
557A HIS* 3.1 34.3 + - + +
590A VAL* 4.8 3.6 - - + -
591A TYR* 3.4 47.8 - - + +
594A PHE* 5.5 15.9 - - + -
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Residues in contact with TYR 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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514A LEU* 3.3 47.5 - - + +
515A SER* 5.9 0.2 - - - -
517A LEU* 3.5 22.2 - - + +
518A GLU* 3.7 25.2 + - + +
521A LEU* 3.4 30.3 - - + -
550A VAL 3.3 7.4 + - - +
551A PRO 3.3 8.0 + - - +
552A GLU 3.1 0.2 - - - -
553A LEU* 1.3 74.9 - - - +
555A GLU* 1.3 74.4 + - + +
557A HIS 3.4 1.6 + - - -
558A LYS* 2.9 69.2 + - + +
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Residues in contact with GLU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 6.1 0.6 - - + +
551A PRO* 3.2 16.2 + - - +
552A GLU* 3.2 19.5 + - - +
554A TYR* 1.3 90.5 - - + +
556A ILE* 1.3 57.8 + - + +
558A LYS* 3.9 4.4 - - + +
559A GLU* 2.8 45.3 + - + +
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Residues in contact with ILE 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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549A LYS* 6.0 0.2 - - + -
552A GLU* 2.8 43.8 + - + +
553A LEU* 4.2 14.4 - - + +
555A GLU* 1.3 73.5 - - + +
557A HIS* 1.3 62.0 + - + +
559A GLU* 4.3 5.4 - - - +
560A PHE* 3.7 17.2 + - - +
584A LEU* 4.0 12.1 - - + +
587A GLN* 3.5 46.3 + - + +
590A VAL* 5.0 10.3 - - + -
591A TYR* 3.8 19.3 - - - +
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Residues in contact with HIS 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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510A GLU* 2.7 32.8 + - - +
513A TYR* 4.5 12.7 + + - -
514A LEU* 3.8 17.7 - - + -
553A LEU* 3.1 30.7 + - + +
555A GLU 3.2 0.6 - - - -
556A ILE* 1.3 80.0 - - + +
558A LYS* 1.3 60.0 + - - +
560A PHE* 3.2 14.8 + + + -
561A TYR* 2.9 27.7 + - - +
584A LEU* 4.7 11.4 - - + +
591A TYR* 3.3 30.0 + - - -
650A VAL* 4.5 20.7 - - + +
653A SER* 5.9 2.0 - - - -
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Residues in contact with LYS 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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514A LEU* 3.6 35.2 - - + +
554A TYR* 2.9 63.1 + - + +
555A GLU* 3.9 5.4 - - + +
557A HIS* 1.3 71.0 - - - +
559A GLU* 1.3 56.2 + - + +
561A TYR* 4.0 11.2 - - + -
562A ASP* 2.7 63.4 + - - +
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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
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555A GLU* 2.8 30.7 + - + +
556A ILE* 4.3 6.2 - - - +
558A LYS* 1.3 71.9 - - - +
560A PHE* 1.3 62.4 + - - +
562A ASP* 5.1 1.3 - - - -
563A GLY* 3.2 19.4 + - - -
580A LEU* 4.9 2.6 - - - +
583A LYS* 4.9 11.2 + - - -
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Residues in contact with PHE 560 (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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506A ILE* 3.5 33.7 - - + -
510A GLU* 4.4 11.2 - - + -
556A ILE 3.7 11.3 + - - +
557A HIS* 3.2 17.7 + + - +
559A GLU* 1.3 80.3 - - - +
561A TYR* 1.3 78.3 + - + +
563A GLY* 3.5 1.2 + - - -
564A LEU* 3.2 61.3 + - + +
580A LEU* 4.0 34.1 - - + +
581A PHE* 4.9 14.1 - + - -
584A LEU* 4.2 33.9 - - + -
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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
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507A LEU* 3.2 54.1 - - + +
510A GLU* 4.3 6.5 - - + -
511A GLU* 3.1 39.8 - - + +
514A LEU* 3.4 25.8 - - + -
557A HIS 2.9 16.1 + - - +
558A LYS* 4.0 12.8 - - + -
560A PHE* 1.3 85.5 - - + +
562A ASP* 1.3 81.7 + - - +
563A GLY 3.1 1.6 - - - -
564A LEU* 2.9 28.7 + - - +
565A PHE* 3.3 7.6 + - + -
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Residues in contact with ASP 562 (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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558A LYS* 2.7 54.4 + - - +
559A GLU* 4.7 1.8 - - - +
561A TYR* 1.3 89.4 + - - +
563A GLY* 1.3 54.7 + - - +
565A PHE* 3.8 15.1 - - - +
566A PRO* 3.2 20.6 - - - +
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Residues in contact with GLY 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 3.2 18.4 + - - -
560A PHE 3.8 2.0 - - - -
561A TYR 3.1 0.8 - - - -
562A ASP* 1.3 75.4 - - - +
564A LEU* 1.3 62.3 + - - +
566A PRO* 3.7 13.3 - - - +
567A ARG* 3.6 18.2 - - - +
580A LEU* 5.2 7.5 - - - +
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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