Contacts of the helix formed by residues 557 - 570 (chain A) in PDB entry 6PUO
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 GLN 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A LEU* 4.6 13.2 - - - +
555A ARG* 4.3 13.8 + - + +
556A LEU* 1.3 87.6 - - - +
558A MET* 1.3 67.9 + - - +
559A HIS* 3.3 31.6 + - + +
560A HIS* 3.2 31.9 + - + +
561A VAL* 3.8 2.6 + - - +
580A PRO* 4.9 11.5 - - - +
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Residues in contact with MET 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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516A TRP* 3.9 31.4 - - + +
519A LEU* 3.8 26.0 - - + -
520A LEU* 3.7 46.0 - - + +
523A TYR* 4.4 8.7 - - + -
557A GLN* 1.3 78.4 + - - +
559A HIS* 1.3 59.0 + - + +
561A VAL* 3.0 36.0 + - - +
562A ALA* 3.0 11.1 + - - +
577A TYR* 3.6 36.2 - - + -
578A PRO 6.2 0.2 - - - +
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Residues in contact with HIS 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ASP* 5.7 0.4 - - - -
557A GLN* 3.5 23.3 + - + +
558A MET* 1.3 76.2 - - - +
560A HIS* 1.3 93.5 + + - +
562A ALA* 3.3 10.2 + - + +
563A GLN* 2.9 29.5 + - - +
577A TYR* 4.3 12.5 - - - +
578A PRO 4.5 2.6 + - - +
579A ARG* 3.1 56.3 + - + +
580A PRO* 3.6 22.1 - - + +
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Residues in contact with HIS 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 4.3 10.2 - - + +
539A VAL* 4.4 13.5 + - + +
540A LEU* 3.6 24.8 - - + +
543A ASP* 4.0 34.0 + - + +
555A ARG 3.7 9.3 + - - -
556A LEU* 4.2 8.5 - - + -
557A GLN* 3.2 37.5 - - + +
558A MET 3.1 0.4 - - - -
559A HIS* 1.3 103.0 + + - +
561A VAL* 1.3 57.6 + - - +
563A GLN* 3.2 14.6 + - - +
564A VAL* 3.0 28.8 + - - +
579A ARG* 5.3 0.7 - - - -
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A TYR* 4.0 43.5 - - + +
532A PHE* 4.3 14.1 - - + -
536A LEU* 4.5 9.0 - - + -
556A LEU* 4.4 14.4 - - + -
557A GLN 3.9 11.4 - - - +
558A MET* 3.0 24.8 + - - +
560A HIS* 1.3 72.3 - - - +
562A ALA* 1.3 61.2 + - - +
564A VAL* 3.3 7.8 - - - +
565A LEU* 2.9 37.7 + - + +
577A TYR* 4.9 4.3 - - + -
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Residues in contact with ALA 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A MET 3.0 8.8 + - - +
559A HIS* 3.6 7.0 - - - +
560A HIS 3.3 0.2 - - - -
561A VAL* 1.3 77.9 - - - +
563A GLN* 1.3 56.1 + - - +
565A LEU* 3.3 7.0 + - - +
566A ARG* 3.0 29.6 + - - +
575A PRO* 4.6 9.6 - - + +
576A LEU* 4.2 9.2 + - - +
577A TYR* 3.5 50.6 - - + +
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Residues in contact with GLN 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 3.5 27.5 - - + +
559A HIS 2.9 18.3 + - - +
560A HIS* 3.2 15.6 + - - +
562A ALA* 1.3 77.4 - - - +
564A VAL* 1.3 60.5 + - - +
566A ARG* 3.5 15.3 + - - +
567A GLU* 3.6 10.9 + - - +
579A ARG* 4.7 10.2 + - - -
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Residues in contact with VAL 564 (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 PHE* 3.6 32.1 - - + -
535A LYS* 4.2 38.8 - - + +
536A LEU* 4.3 8.5 - - + -
539A VAL* 4.3 13.2 - - + -
560A HIS 3.0 15.3 + - - +
561A VAL* 3.3 14.8 - - - +
563A GLN* 1.3 77.3 - - - +
565A LEU* 1.3 65.1 + - - +
567A GLU* 3.5 23.8 + - - +
568A LEU* 3.6 15.5 + - + +
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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
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523A TYR* 5.3 0.2 - - - +
532A PHE* 4.7 15.9 - - + -
561A VAL* 2.9 36.3 + - + +
562A ALA* 3.3 6.2 + - - +
564A VAL* 1.3 76.4 - - - +
566A ARG* 1.3 59.4 + - - +
568A LEU* 3.2 10.8 + - + +
569A LEU* 2.9 37.4 + - + +
576A LEU* 5.0 16.6 - - + -
577A TYR* 4.6 14.1 - - + -
627A ILE* 3.8 38.8 - - + -
631A VAL* 5.1 3.6 - - + -
658A ILE* 4.4 18.4 - - + -
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Residues in contact with ARG 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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562A ALA 3.0 16.3 + - - +
563A GLN* 3.8 8.7 - - - +
564A VAL 3.3 0.4 - - - -
565A LEU* 1.3 77.1 - - - +
567A GLU* 1.3 60.9 + - - +
569A LEU* 4.7 3.1 - - - +
570A GLY 3.0 35.6 + - - +
571A ASP* 2.6 33.1 + - - +
573A THR* 2.4 34.7 + - - +
574A GLN* 3.7 5.9 + - - +
575A PRO* 3.4 36.1 - - + +
576A LEU* 6.2 1.8 - - - +
853A GLU 5.5 4.2 + - - -
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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
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535A LYS* 4.2 22.1 + - - -
563A GLN 3.6 7.9 + - - +
564A VAL* 3.5 23.3 + - - +
565A LEU 3.2 0.4 - - - -
566A ARG* 1.3 80.4 - - - +
568A LEU* 1.3 65.9 + - + +
570A GLY* 3.9 5.5 + - - -
661A GLU* 5.2 1.7 - - - +
665A GLU* 5.4 1.0 - - - +
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Residues in contact with LEU 568 (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 PHE* 4.4 21.5 - - + -
535A LYS* 4.6 12.3 - - - -
564A VAL* 3.6 12.7 + - + +
565A LEU* 3.2 13.3 + - + +
567A GLU* 1.3 83.6 - - + +
569A LEU* 1.3 64.6 + - - +
570A GLY* 3.3 1.0 + - - -
631A VAL* 5.5 0.9 - - + -
657A LYS* 3.6 11.4 + - - +
658A ILE* 4.7 23.6 - - + -
661A GLU* 3.6 40.3 - - + +
662A LEU* 3.7 35.2 - - + +
665A GLU* 4.4 12.1 - - - +
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Residues in contact with LEU 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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565A LEU* 2.9 20.8 + - + +
566A ARG* 4.9 2.0 - - - -
568A LEU* 1.3 77.3 - - - +
570A GLY* 1.3 60.6 + - - +
572A PHE* 4.0 13.5 - - - -
573A THR* 4.3 20.1 - - + +
576A LEU* 4.3 24.5 - - + -
654A ALA* 4.2 21.3 - - + +
657A LYS* 3.6 26.6 - - + +
658A ILE* 3.8 29.8 - - + -
712A TRP* 4.9 18.6 - - + +
720A LEU* 4.8 8.6 - - + +
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Residues in contact with GLY 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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566A ARG* 3.0 17.4 + - - +
567A GLU 3.9 4.6 + - - -
568A LEU 3.2 4.4 - - - -
569A LEU* 1.3 81.7 - - - +
571A ASP* 1.3 64.5 + - - -
572A PHE* 3.2 16.2 + - - -
573A THR* 3.7 15.4 + - - +
657A LYS* 5.0 4.0 - - - -
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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