Contacts of the helix formed by residues 668 - 685 (chain A) in PDB entry 2YT4
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 ASN 668 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A PHE* 5.0 2.5 - - - -
651A SER* 5.1 1.3 - - - -
666A CYS* 3.2 7.0 - - - -
667A LYS* 1.3 89.1 - - + +
669A LYS* 1.3 62.5 + - - +
670A ARG* 2.5 43.7 + - - +
671A VAL* 2.8 33.4 + - - +
672A GLY 3.2 8.3 + - - -
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Residues in contact with LYS 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ILE* 6.3 2.7 - - + +
641A PHE* 3.4 59.1 - - + +
666A CYS* 4.4 2.9 - - - -
668A ASN* 1.3 70.6 - - - +
670A ARG* 1.3 66.9 + - + +
673A LYS* 3.2 38.2 + - - +
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Residues in contact with ARG 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 3.8 31.6 + - + +
613A SER* 5.8 0.6 + - - -
668A ASN* 2.5 21.0 + - - +
669A LYS* 1.3 82.5 - - + +
671A VAL* 1.3 61.5 + - + +
673A LYS* 4.0 12.7 + - - +
674A GLN* 4.0 17.8 + - - +
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Residues in contact with VAL 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 5.0 19.3 - - + -
666A CYS* 5.4 1.6 - - + -
667A LYS* 5.9 1.3 - - + +
668A ASN* 2.8 32.1 + - - +
670A ARG* 1.3 76.7 - - + +
672A GLY* 1.3 65.8 + - - +
673A LYS 3.1 2.0 - - - -
674A GLN* 3.1 8.5 + - + +
675A LEU* 3.0 46.9 + - + +
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Residues in contact with GLY 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A TYR* 4.1 13.5 - - - -
666A CYS* 3.6 29.0 - - - +
668A ASN 3.2 9.7 + - - -
669A LYS 3.4 1.5 + - - -
671A VAL* 1.3 77.6 - - - +
673A LYS* 1.3 57.4 + - - +
675A LEU* 3.3 7.7 + - - +
676A ALA* 2.8 33.4 + - - +
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Residues in contact with LYS 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A TYR* 3.3 47.3 - - + -
639A ILE* 3.5 34.5 - - + -
655A MET* 4.4 0.9 - - - +
669A LYS* 3.2 31.2 + - - +
670A ARG* 4.0 8.9 - - - +
671A VAL 3.1 0.2 - - - -
672A GLY* 1.3 77.4 - - - +
674A GLN* 1.3 60.8 + - - +
676A ALA* 3.9 5.4 - - - +
677A SER* 2.5 35.4 + - - +
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Residues in contact with GLN 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 3.6 53.3 + - + -
619A SER* 3.3 14.5 + - - -
620A PRO* 3.1 15.4 - - + +
621A TYR* 2.8 40.5 + - - +
670A ARG* 4.0 13.1 + - - +
671A VAL* 3.1 7.0 + - + +
673A LYS* 1.3 82.9 - - - +
675A LEU* 1.3 62.4 + - + +
677A SER* 3.1 4.5 + - - -
678A GLN* 2.8 36.1 + - - +
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Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A SER* 4.7 18.8 - - - +
609A TYR* 5.9 1.6 - - + -
653A TYR* 4.1 11.0 - - - +
665A TRP 4.4 16.2 - - - +
666A CYS* 4.7 3.6 - - + -
671A VAL* 3.0 32.1 - - + +
672A GLY* 3.5 13.5 - - - +
674A GLN* 1.3 77.1 - - + +
676A ALA* 1.3 64.4 + - - +
678A GLN* 2.9 35.5 + - - +
679A LYS* 3.0 20.4 + - - +
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Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ILE* 5.4 1.3 - - + -
653A TYR* 3.6 27.2 + - + -
655A MET* 3.5 30.3 - - + -
662A VAL* 4.2 6.0 - - + +
672A GLY 2.8 21.0 + - - +
673A LYS* 3.9 4.0 - - - +
675A LEU* 1.3 72.1 - - - +
677A SER* 1.3 62.9 + - - +
679A LYS* 3.2 5.5 + - - +
680A ILE* 3.0 26.7 + - - +
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Residues in contact with SER 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A PRO 3.6 7.9 - - - -
621A TYR* 3.3 43.4 - - - -
624A LEU* 4.7 3.7 - - - +
655A MET* 3.7 16.9 - - - +
673A LYS 2.5 23.1 + - - -
674A GLN 3.1 8.3 + - - -
676A ALA* 1.3 74.1 - - - +
678A GLN* 1.3 53.4 + - - +
680A ILE* 3.2 3.8 + - - +
681A LEU* 2.8 39.7 + - - +
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Residues in contact with GLN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 2.8 36.1 - - - +
604A GLU* 3.8 11.4 - - + -
605A ASP 3.2 13.7 + - - +
606A SER* 4.7 1.6 + - - +
608A VAL* 3.1 27.5 - - - +
609A TYR* 4.5 5.3 - - - +
620A PRO* 3.7 17.7 - - + +
674A GLN* 2.8 17.9 + - - +
675A LEU* 3.1 42.5 - - - +
677A SER* 1.3 75.3 - - - +
679A LYS* 1.3 61.1 + - + +
681A LEU* 3.1 12.5 + - - +
682A GLN* 2.9 19.6 + - - +
691A TRP* 4.3 3.1 - - + -
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Residues in contact with LYS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A GLU* 3.6 29.4 - - + +
653A TYR* 3.1 25.1 + - - +
662A VAL* 3.6 33.9 - - + -
663A ARG 3.6 16.3 + - - +
664A GLY* 4.1 4.2 - - - -
675A LEU* 3.0 15.1 + - - +
676A ALA* 3.2 5.4 + - - +
678A GLN* 1.3 74.4 - - + +
680A ILE* 1.3 52.9 + - - +
682A GLN* 3.0 4.0 + - - +
683A LEU* 2.7 44.2 + - + +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 4.4 9.9 - - + -
655A MET* 4.0 39.0 - - + +
657A CYS* 3.9 30.7 - - + +
660A HIS* 4.1 22.7 - - + +
662A VAL* 4.2 12.6 - - + -
676A ALA 3.0 14.6 + - - +
677A SER* 3.5 7.4 - - - +
679A LYS* 1.3 75.1 - - - +
681A LEU* 1.3 53.7 + - - +
683A LEU* 3.1 6.9 + - - +
684A LEU* 2.7 58.7 + - + +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 4.2 9.6 - - + -
620A PRO 3.4 25.8 - - - +
623A ILE* 4.1 9.9 - - + -
624A LEU* 3.8 35.9 - - + +
627A CYS* 4.3 3.8 - - + -
677A SER 2.8 22.6 + - - +
678A GLN 3.1 8.5 + - - +
680A ILE* 1.3 72.2 - - - +
682A GLN* 1.3 58.6 + - - +
684A LEU* 3.1 2.7 + - + -
685A HIS* 2.5 57.8 + - + +
691A TRP* 4.0 20.0 - - + -
694A LEU* 3.8 16.2 - - + -
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Residues in contact with GLN 682 (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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602A SER* 5.6 1.6 - - - -
603A ILE* 3.8 23.2 + - + +
604A GLU* 3.4 31.6 + - + +
678A GLN 2.9 13.3 + - - +
679A LYS 3.3 7.6 - - - +
681A LEU* 1.3 76.7 - - - +
683A LEU* 1.3 66.7 + - + +
685A HIS 3.1 13.0 + - - -
686A PRO* 3.0 31.1 + - + +
688A VAL 2.9 27.7 + - - +
689A LYS* 4.4 5.5 - - - +
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Residues in contact with LEU 683 (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 ASP* 4.9 3.1 - - - +
604A GLU* 5.7 2.0 - - - +
660A HIS* 3.4 46.7 + - + +
662A VAL* 4.6 14.4 - - + -
679A LYS* 2.7 34.1 + - + +
680A ILE* 3.5 10.5 - - - +
682A GLN* 1.3 77.1 - - + +
684A LEU* 1.3 56.6 + - - +
686A PRO* 3.2 21.0 - - + +
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Residues in contact with LEU 684 (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 ILE 4.6 2.6 - - - +
549A ASP* 4.8 2.8 - - - +
551A VAL* 3.3 31.5 - - + +
553A TYR* 4.6 0.3 + - - -
624A LEU* 3.7 29.8 - - + -
627A CYS* 3.8 16.4 - - - -
628A LEU* 4.8 3.1 - - + -
634A MET* 5.1 12.6 - - + +
657A CYS* 4.6 10.5 - - - +
660A HIS* 3.9 24.0 - - + +
680A ILE* 2.7 33.0 + - + +
681A LEU* 3.1 6.9 + - + +
683A LEU* 1.3 69.6 - - - +
685A HIS* 1.3 65.4 + - + +
686A PRO* 3.1 12.3 - - - +
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Residues in contact with HIS 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL* 3.9 12.6 - - + +
553A TYR* 3.4 27.1 - - - +
603A ILE* 5.0 1.3 - - + -
627A CYS* 3.8 8.6 - - - -
681A LEU* 2.5 59.0 + - + +
682A GLN* 3.1 13.3 + - - -
684A LEU* 1.3 87.7 - - + +
686A PRO* 1.3 51.7 - - - +
687A HIS 2.9 17.0 + - - -
688A VAL* 2.9 26.8 + - + +
694A LEU* 4.2 10.3 - - + +
697A MET* 4.1 14.4 - - + -
698A TYR* 2.9 32.7 + + - -
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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