Contacts of the helix formed by residues 643 - 661 (chain C) in PDB entry 4YFI
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 643 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C ILE* 4.1 3.4 - - - -
613C LEU* 4.5 5.8 - - + -
640C THR* 4.5 13.2 - - + -
641C ARG 3.1 14.9 + - - +
642C TYR* 1.3 94.7 - - - +
644C ILE* 1.3 69.7 + - - +
645C LYS* 3.0 24.7 + - - +
646C ALA* 3.2 11.2 + - - +
706C PRO* 4.7 8.0 - - + +
634D GLU* 4.9 3.8 + - - +
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Residues in contact with ILE 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C HIS* 3.3 59.5 - - + +
583C PRO* 5.1 1.3 - - + -
585C ILE* 4.3 11.9 - - + +
613C LEU* 4.2 24.8 - - + +
643C THR* 1.3 74.5 - - - +
645C LYS* 1.3 72.0 + - + +
647C ASP* 3.1 18.4 + - - +
648C VAL* 3.6 4.3 + - + +
711C GLU* 3.1 40.4 - - - +
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Residues in contact with LYS 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C THR* 3.0 13.1 - - - +
644C ILE* 1.3 82.9 - - + +
646C ALA* 1.3 63.4 + - - +
647C ASP 3.3 0.2 - - - -
648C VAL* 3.3 11.1 + - + +
649C PHE 3.2 14.0 + - - -
706C PRO* 3.5 35.7 + - + +
707C GLU* 4.0 11.3 + - - +
709C ARG* 2.7 51.6 + - + +
710C PRO 3.9 11.2 - - - +
711C GLU* 3.6 33.1 + - - +
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Residues in contact with ALA 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C TYR* 3.2 39.0 + - + +
643C THR* 3.2 8.8 + - - +
645C LYS* 1.3 76.4 - - - +
647C ASP* 1.3 62.6 + - - +
649C PHE* 3.4 3.6 + - - +
650C SER* 3.2 24.1 + - - -
709C ARG* 3.8 9.6 - - - +
632D ALA* 3.7 19.3 + - + +
634D GLU* 3.9 5.3 + - - +
635D VAL* 3.8 7.6 - - + -
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Residues in contact with ASP 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C MET* 3.5 17.8 - - + +
578C HIS* 3.0 27.9 + - + +
585C ILE* 3.2 10.6 - - - +
586C HIS* 3.0 22.0 + - - +
587C ARG* 3.0 15.0 + - - -
588C ASP 4.7 0.3 + - - -
589C LEU* 3.8 8.6 - - + +
642C TYR* 2.6 24.7 + - - -
644C ILE 3.1 11.1 + - - +
646C ALA* 1.3 74.4 - - - +
648C VAL* 1.3 56.4 + - - +
650C SER* 3.3 6.7 + - - -
651C TYR* 2.8 34.5 + - - +
712C PHE* 4.2 2.5 - - + -
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Residues in contact with VAL 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C HIS* 4.8 1.3 - - + -
644C ILE* 4.0 11.4 - - + +
645C LYS* 3.4 18.2 - - + +
646C ALA 3.3 0.4 - - - -
647C ASP* 1.3 74.4 - - - +
649C PHE* 1.3 65.2 + - - +
651C TYR* 3.3 4.3 + - + +
652C ALA* 3.0 22.0 + - - +
701C GLY* 4.0 12.3 - - - +
709C ARG* 3.9 16.6 - - + -
710C PRO* 3.4 33.4 - - + +
711C GLU* 5.1 0.7 - - - +
712C PHE* 3.6 34.1 - - + +
715C VAL* 4.9 7.4 - - + -
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Residues in contact with PHE 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C LYS 3.2 5.5 + - - -
646C ALA 3.6 7.9 - - - +
647C ASP 3.3 0.4 - - - -
648C VAL* 1.3 76.3 - - - +
650C SER* 1.3 66.2 + - - +
652C ALA* 2.9 19.4 + - - +
653C LEU* 3.3 25.8 + - + +
677C MET* 4.1 12.6 - - - -
683C ARG* 3.7 19.5 - - - -
701C GLY 3.3 10.2 + - - -
702C TRP* 3.4 41.9 - - + +
709C ARG* 3.6 33.4 - - - +
630D TRP 4.4 0.4 - - - -
631D MET 3.4 19.1 - - - -
632D ALA* 3.5 19.7 - - + -
633D PRO* 3.5 19.3 - - + -
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Residues in contact with SER 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C ARG 5.8 0.9 - - - -
588C ASP 5.7 0.7 + - - -
589C LEU* 3.5 29.8 + - - -
642C TYR* 4.6 5.8 + - - -
646C ALA 3.2 12.2 + - - -
647C ASP* 3.6 9.0 - - - -
649C PHE* 1.3 78.6 - - - +
651C TYR* 1.3 63.7 + - - +
653C LEU* 3.3 7.5 + - - +
654C CYS* 3.2 26.3 + - - -
630D TRP* 2.7 30.1 + - - -
631D MET* 4.4 1.2 - - - -
632D ALA 4.4 4.2 + - - -
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Residues in contact with TYR 651 (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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567C ALA* 2.5 40.7 + - + +
570C VAL* 3.3 35.2 - - + -
571C ALA* 3.9 9.9 - - + -
589C LEU* 3.8 9.6 - - + +
647C ASP 2.8 17.6 + - - +
648C VAL* 3.5 8.1 - - + +
649C PHE 3.1 0.2 - - - -
650C SER* 1.3 77.4 - - - +
652C ALA* 1.3 55.5 + - - +
654C CYS* 2.9 11.2 + - + +
655C LEU* 2.8 51.3 + - + -
658C ILE* 6.0 1.8 - - + -
697C LEU* 6.4 0.2 - - + -
712C PHE* 3.5 26.9 - + + -
715C VAL* 3.6 21.3 - - + -
719C LEU* 3.3 12.8 - - - +
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Residues in contact with ALA 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C VAL 3.0 11.9 + - - +
649C PHE 2.9 12.2 + - - +
651C TYR* 1.3 80.9 - - - +
653C LEU* 1.3 61.0 + - - +
655C LEU* 3.2 5.2 + - - +
656C TRP* 3.1 18.2 + - - +
697C LEU 5.0 0.9 - - - +
698C LEU* 3.2 19.7 - - + +
701C GLY* 3.7 26.2 - - - -
702C TRP* 3.8 17.3 - - + +
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Residues in contact with LEU 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C PHE* 3.3 30.1 + - + +
650C SER 3.8 4.9 - - - +
651C TYR 3.2 0.4 - - - -
652C ALA* 1.3 73.4 - - - +
654C CYS* 1.3 62.0 + - - +
656C TRP* 3.2 5.7 + - - +
657C GLU* 2.8 29.6 + - - +
664C PRO* 4.1 14.4 - - + +
677C MET* 4.1 13.9 - - + -
683C ARG* 5.6 0.2 - - - -
684C PRO* 4.0 21.3 - - + -
702C TRP* 3.7 25.6 - - + -
629D ARG 3.4 25.1 - - - +
630D TRP* 3.6 29.2 - - + +
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Residues in contact with CYS 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C LEU* 5.4 2.9 - - + -
589C LEU* 4.2 5.8 - - - -
590C ASN* 3.8 35.4 - - - -
591C SER 4.4 0.9 - - - +
594C ILE* 4.2 19.3 - - + -
650C SER 3.2 17.9 + - - -
651C TYR* 2.9 15.1 + - + +
653C LEU* 1.3 77.1 - - - +
655C LEU* 1.3 58.2 + - - +
657C GLU* 3.1 12.3 + - - +
658C ILE* 2.8 40.2 + - + +
630D TRP* 4.0 7.2 - - - -
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Residues in contact with LEU 655 (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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563C LYS 6.3 0.2 - - - -
564C LEU* 5.1 5.2 - - + -
567C ALA* 3.8 26.7 - - + -
651C TYR* 2.8 37.9 + - + +
652C ALA* 3.6 10.1 - - - +
653C LEU 3.2 0.4 - - - -
654C CYS* 1.3 73.2 - - - +
656C TRP* 1.3 60.8 + - - +
658C ILE* 3.3 11.7 + - + +
659C LEU* 3.1 44.9 + - + +
694C ILE* 4.3 15.7 - - + -
697C LEU* 4.3 28.5 - - + -
698C LEU* 4.2 9.0 - - + +
719C LEU* 4.7 7.6 - - + -
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Residues in contact with TRP 656 (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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688A TYR* 3.3 21.3 - + - -
652C ALA 3.1 12.0 + - - +
653C LEU* 3.4 9.0 - - - +
655C LEU* 1.3 73.1 - - - +
657C GLU* 1.3 70.7 + - - +
659C LEU* 3.2 6.0 + - - +
660C THR* 2.9 56.9 + - + +
662C GLU* 3.5 33.7 - - + -
663C ILE 4.0 0.2 - - - -
664C PRO* 3.8 21.5 - - + -
684C PRO* 3.4 25.3 - - + +
685C PRO* 2.8 37.1 + - + -
686C ILE* 5.1 0.4 - - + -
690C ILE* 4.4 6.4 - - + +
698C LEU* 3.7 22.1 - - + +
702C TRP* 4.0 21.3 - + + -
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Residues in contact with GLU 657 (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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547C LEU* 5.5 1.1 - - + -
551C LEU* 3.8 7.7 - - + +
552C HIS* 2.6 29.9 + - + +
591C SER* 2.6 34.7 + - - -
653C LEU 2.8 12.1 + - - +
654C CYS* 3.3 12.7 - - - +
656C TRP* 1.3 78.8 - - - +
658C ILE* 1.3 54.3 + - + +
661C GLY* 2.7 34.8 + - - -
662C GLU 3.3 23.6 - - - +
663C ILE* 4.6 0.2 - - - -
664C PRO* 4.1 7.8 - - + +
630D TRP* 3.0 36.8 + - - -
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Residues in contact with ILE 658 (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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547C LEU* 3.6 32.1 - - + -
551C LEU* 4.1 15.1 - - + +
558C LEU* 5.4 3.8 - - + -
563C LYS* 3.3 53.6 - - + +
566C ILE* 4.2 17.5 - - + -
567C ALA* 4.3 19.1 - - + -
570C VAL* 5.8 1.8 - - + -
594C ILE* 5.8 2.2 - - + -
651C TYR* 6.0 1.8 - - + -
654C CYS* 2.8 27.1 + - + +
655C LEU* 3.5 17.9 - - + +
656C TRP 3.2 0.2 - - - -
657C GLU* 1.3 74.1 - - - +
659C LEU* 1.3 64.0 + - + +
661C GLY* 3.8 3.3 + - - -
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Residues in contact with LEU 659 (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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560C LEU* 4.2 25.4 - - + -
563C LYS* 2.8 33.2 + - + +
564C LEU* 5.6 1.3 - - + -
655C LEU* 3.1 30.5 + - + +
656C TRP* 3.7 8.7 - - - +
658C ILE* 1.3 77.5 - - + +
660C THR* 1.3 65.4 + - + +
690C ILE* 4.4 18.6 - - + -
691C PRO* 4.6 10.3 - - + -
694C ILE* 3.2 40.8 - - + -
698C LEU* 4.6 4.7 - - + -
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Residues in contact with THR 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LYS* 5.5 0.7 - - - -
656C TRP* 2.9 55.8 + - + +
657C GLU 3.8 0.2 + - - -
659C LEU* 1.3 76.8 - - - +
661C GLY* 1.3 62.6 + - - +
662C GLU* 3.1 31.7 + - - +
685C PRO 5.2 0.9 - - - +
690C ILE* 4.5 13.7 - - + -
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Residues in contact with GLY 661 (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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551C LEU* 3.6 26.2 - - - +
552C HIS* 3.0 24.2 + - - -
563C LYS* 5.6 0.2 - - - +
657C GLU 2.7 18.6 + - - -
658C ILE 3.8 1.4 + - - -
659C LEU 3.5 1.8 - - - -
660C THR* 1.3 73.1 - - - +
662C GLU* 1.3 62.6 + - - +
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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