Contacts of the helix formed by residues 558 - 570 (chain C) in PDB entry 6CIM
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 ARG 558 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C PHE* 3.9 11.3 - - - -
526C VAL* 3.8 10.9 - - - +
527C SER* 3.4 25.8 + - - -
528C SER 4.7 0.8 - - - -
529C ARG* 2.8 30.5 + - - +
532C VAL* 3.4 22.4 - - + +
533C GLY 4.3 4.4 + - - -
535C ILE* 3.9 14.9 - - + +
556C ARG* 4.1 1.8 - - - +
557C PHE* 1.3 73.3 - - - +
559C TYR* 1.3 60.7 + - - +
560C ASP* 3.1 31.6 + - - +
561C SER* 3.0 13.1 + - - -
562C ALA* 2.9 26.3 + - - +
678C GLU* 3.1 27.4 - - + +
169D THR* 4.5 0.2 - - - -
170D GLU* 2.7 47.2 + - + -
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Residues in contact with TYR 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C PHE 3.5 1.6 + - - -
558C ARG* 1.3 70.6 - - - +
560C ASP* 1.3 58.2 + - - +
562C ALA* 3.3 2.8 + - - +
563C LEU* 3.0 31.1 + - + +
595C VAL* 4.4 0.2 - - - +
597C GLU* 3.5 28.0 + - - +
622C PHE* 4.1 11.4 - + - -
624C PHE* 4.1 19.0 - + - +
655C LEU* 3.5 37.9 - - + -
675C LEU* 3.6 26.5 - - + -
678C GLU* 2.9 23.5 + - + +
679C ARG* 3.7 22.4 - - + -
682C MET* 3.6 15.0 - - + -
702C PHE* 3.8 27.9 - + - -
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Residues in contact with ASP 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C PHE* 3.6 11.1 - - - -
519C TRP* 3.7 22.3 + - + +
523C LEU* 4.0 12.9 - - + +
526C VAL* 4.1 5.9 - - - +
527C SER 4.7 0.7 - - - +
558C ARG* 3.1 47.0 + - - +
559C TYR* 1.3 73.3 + - - +
561C SER* 1.3 76.5 + - - -
563C LEU* 3.1 4.8 + - - +
564C VAL* 2.9 28.3 + - - +
678C GLU* 4.9 4.0 - - + +
682C MET* 3.6 24.0 - - - -
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Residues in contact with SER 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C PRO* 4.0 5.8 - - - +
513C GLY* 3.3 18.0 + - - -
517C PHE* 4.3 15.0 - - - -
530C THR 4.4 3.1 + - - -
532C VAL* 3.1 31.9 + - - +
533C GLY 5.9 0.2 - - - -
558C ARG* 3.0 18.8 + - - -
560C ASP* 1.3 86.3 + - - +
562C ALA* 1.3 61.7 + - - +
564C VAL* 3.3 6.4 + - - +
565C SER* 3.0 22.5 + - - -
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Residues in contact with ALA 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C PRO* 4.3 7.8 - - - +
557C PHE* 4.1 9.0 - - + -
558C ARG 2.9 12.8 + - - +
559C TYR 3.5 8.5 - - - +
560C ASP 3.2 0.2 - - - -
561C SER* 1.3 73.9 - - - +
563C LEU* 1.3 65.7 + - - +
565C SER 3.1 1.6 + - - +
566C ALA* 2.9 24.4 + - - +
624C PHE* 3.8 13.5 - - + -
655C LEU* 3.8 22.9 - - + -
992C TRP* 3.6 18.0 - - + -
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Residues in contact with LEU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C TRP* 5.5 0.4 - - + -
559C TYR* 3.0 19.4 + - + +
560C ASP* 3.1 9.6 + - - +
562C ALA* 1.3 75.2 - - - +
564C VAL* 1.3 63.9 + - + +
566C ALA* 3.2 1.4 + - - +
567C LEU* 3.0 37.1 + - + +
595C VAL* 4.1 14.1 - - + -
624C PHE* 4.0 26.9 - - + -
626C VAL* 5.0 0.7 - - + -
682C MET* 3.7 18.6 - - - -
687C LEU* 5.3 1.8 - - + -
700C PHE* 3.8 34.1 - - + -
702C PHE* 3.6 33.9 - - + -
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Residues in contact with VAL 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C HIS* 4.3 17.3 - - + +
517C PHE* 3.5 46.9 - - + -
560C ASP 2.9 19.6 + - - +
561C SER* 3.4 7.6 - - - +
563C LEU* 1.3 77.4 - - - +
565C SER* 1.3 64.0 + - - +
567C LEU* 3.3 2.0 + - - +
568C MET* 3.0 24.3 + - + +
687C LEU* 4.1 16.4 - - + +
689C LEU* 3.8 29.2 - - + -
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Residues in contact with SER 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C VAL 4.7 2.6 + - - -
510C LEU* 3.3 24.4 + - - -
511C LEU 3.6 8.5 + - - -
512C PRO* 3.8 21.5 - - - -
513C GLY 5.2 0.4 - - - -
515C HIS* 5.3 3.2 + - - -
561C SER 3.0 8.3 + - - -
562C ALA 3.1 2.4 + - - -
564C VAL* 1.3 79.2 - - - +
566C ALA* 1.3 58.2 + - - +
568C MET* 3.4 5.9 + - - +
569C ASP* 2.9 28.2 + - - +
992C TRP* 3.7 17.9 + - - -
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Residues in contact with ALA 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C ALA 2.9 16.6 + - - +
563C LEU* 3.7 3.8 - - - +
565C SER* 1.3 78.4 - - - +
567C LEU* 1.3 62.1 + - + +
569C ASP* 3.3 10.2 - - - +
570C MET* 3.0 26.5 + - + +
624C PHE* 3.9 24.5 - - + -
626C VAL* 4.5 11.2 - - + -
653C LYS* 3.9 20.2 + - + +
992C TRP* 4.1 4.2 - - - -
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Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 3.0 24.1 + - + +
564C VAL 3.9 3.1 - - - +
566C ALA* 1.3 74.8 - - - +
568C MET* 1.3 67.4 + - - +
570C MET* 3.1 10.9 + - - +
571C GLU* 3.0 20.3 + - - -
574C ILE* 4.2 5.3 - - + +
593C VAL* 4.4 12.8 - - + -
626C VAL* 4.5 13.7 - - + -
629C ILE* 4.6 14.8 - - + -
687C LEU* 4.3 5.4 - - + -
689C LEU* 4.2 9.6 - - + -
691C MET* 4.5 2.9 - - - +
698C PHE* 3.7 46.0 - - + -
700C PHE* 3.9 29.2 - - + -
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Residues in contact with MET 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C HIS* 2.9 58.1 - - + +
564C VAL 3.0 19.9 + - - +
565C SER* 3.8 3.6 - - - +
567C LEU* 1.3 75.8 - - - +
569C ASP* 1.3 63.7 + - - +
571C GLU* 3.2 40.8 + - - +
689C LEU* 3.7 24.7 - - + -
690C GLU 3.5 24.5 - - - +
691C MET* 3.9 9.4 - - - -
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Residues in contact with ASP 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C LEU* 4.5 7.9 - - + +
565C SER 2.9 14.7 + - - +
566C ALA* 3.3 14.9 - - - +
567C LEU 3.2 0.2 - - - -
568C MET* 1.3 79.6 - - - +
570C MET* 1.3 57.3 + - - +
571C GLU 3.4 1.9 + - - -
572C GLU* 4.6 5.7 + - - +
573C ASP* 4.7 1.9 - - - +
653C LYS* 3.6 10.4 + - - +
996C SER* 3.0 27.7 - - - -
997C LYS* 2.4 39.0 + - - +
998C TYR* 3.3 31.6 + - - +
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Residues in contact with MET 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C ALA 3.0 17.7 - - - +
567C LEU* 3.3 12.1 - - - +
569C ASP* 1.3 74.9 - - - +
571C GLU* 1.3 64.4 + - - +
572C GLU 3.1 3.4 - - - -
573C ASP* 2.8 29.2 + - + +
574C ILE* 3.0 17.6 + - + +
626C VAL* 4.0 22.9 - - + +
629C ILE* 3.9 20.0 - - - -
641C PHE* 3.4 37.0 - - + -
643C GLU* 5.5 0.2 - - - +
653C LYS* 5.6 5.6 - - - +
997C LYS* 3.6 27.1 - - + +
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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