Contacts of the helix formed by residues 657 - 676 (chain D) in PDB entry 1K0Y
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 657 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D PHE 2.7 32.1 + - - +
647D ASP* 3.4 23.8 + - - +
648D LEU* 3.7 7.5 - - - +
653D ALA 3.0 15.7 + - - +
654D VAL* 3.3 12.8 + - - +
656D GLY* 1.4 73.7 - - - +
658D PRO* 1.3 71.6 - - - +
659D LYS* 2.8 29.3 + - - +
660D VAL* 3.2 18.0 + - + +
661D LYS* 3.1 22.9 + - - +
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Residues in contact with PRO 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D GLY 3.1 11.2 - - - +
657D ASN* 1.3 87.4 - - - +
659D LYS* 1.4 63.3 + - + +
661D LYS* 3.3 11.8 + - + +
662D ALA* 2.9 28.3 + - - +
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Residues in contact with LYS 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D SER 3.5 16.5 + - - +
645D PHE* 3.5 44.3 - - + +
657D ASN* 2.8 14.4 + - - +
658D PRO* 1.4 75.1 - - + +
660D VAL* 1.4 61.5 + - - +
662D ALA* 3.8 6.9 - - + +
663D HIS* 3.0 30.5 + - - +
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Residues in contact with VAL 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D GLY* 4.4 5.5 - - - +
628D LEU* 3.4 12.4 - - + +
629D GLY* 3.9 29.4 - - - +
632D LEU* 4.0 11.4 - - + -
645D PHE* 3.9 17.9 - - + -
648D LEU* 3.8 20.4 - - + -
654D VAL 3.7 15.3 - - - +
655D MET* 5.6 0.9 - - - +
657D ASN* 3.2 31.8 + - + +
659D LYS* 1.4 75.1 - - - +
661D LYS* 1.4 59.7 + - + +
663D HIS 3.4 0.2 + - - -
664D GLY* 2.9 26.5 + - - -
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Residues in contact with LYS 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D ASP 4.7 3.0 - - - +
625D GLY* 4.2 19.9 + - - -
655D MET 3.2 26.2 + - - +
656D GLY* 4.2 15.3 + - - -
657D ASN 3.1 11.0 + - - +
658D PRO* 3.6 13.0 - - + +
659D LYS 3.3 0.2 - - - -
660D VAL* 1.4 78.0 - - + +
662D ALA* 1.4 61.3 + - - +
664D GLY* 3.4 1.2 + - - -
665D LYS* 3.1 23.4 + - - +
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Residues in contact with ALA 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D PRO 2.9 17.7 + - - +
659D LYS* 3.8 8.1 - - + +
661D LYS* 1.4 73.3 - - - +
663D HIS* 1.4 63.2 + - - +
665D LYS* 3.3 14.0 + - - +
666D LYS* 3.2 28.7 + - - +
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Residues in contact with HIS 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D LEU* 3.7 16.8 - - + -
642D PHE* 3.6 22.6 - + - -
645D PHE* 3.8 17.8 - + + -
659D LYS 3.0 17.4 + - - +
662D ALA* 1.4 74.7 - - - +
664D GLY* 1.4 60.2 + - - +
666D LYS* 3.1 21.5 + - + +
667D VAL* 2.9 39.7 + - + +
748D HEM 3.3 72.5 + + + +
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Residues in contact with GLY 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D GLY* 3.4 36.4 - - - -
628D LEU* 3.6 12.2 - - - +
660D VAL 2.9 17.1 + - - -
661D LYS 3.4 1.1 + - - -
663D HIS* 1.4 75.8 - - - +
665D LYS* 1.4 55.3 + - - +
667D VAL* 3.4 5.6 + - - +
668D LEU* 3.0 26.5 + - - +
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Residues in contact with LYS 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D VAL* 3.9 16.3 - - + +
621D ASP* 2.7 56.0 + - + +
624D GLY 4.4 1.0 - - - -
661D LYS 3.1 12.9 + - - +
662D ALA* 3.4 15.5 - - - +
663D HIS 3.2 0.2 - - - -
664D GLY* 1.4 74.6 - - - +
666D LYS* 1.4 57.3 + - + +
669D GLY* 2.9 26.2 + - - -
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Residues in contact with LYS 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D ALA* 3.2 17.2 + - - +
663D HIS* 3.1 26.1 + - + +
665D LYS* 1.4 72.0 - - + +
667D VAL* 1.4 66.3 + - - +
669D GLY* 3.3 2.4 + - - -
670D ALA* 3.0 23.6 + - - +
748D HEM 3.8 52.1 + - + +
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Residues in contact with VAL 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D LEU* 5.4 5.8 - - + -
663D HIS* 2.9 43.7 + - + +
664D GLY* 3.7 7.4 - - - +
666D LYS* 1.4 75.1 - - - +
668D LEU* 1.4 65.4 + - + +
670D ALA 3.1 3.1 + - - -
671D PHE* 2.9 23.7 + - - +
706D LEU* 3.8 18.4 - - + -
748D HEM 3.6 60.9 - - + +
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Residues in contact with LEU 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D TRP* 3.8 25.9 - - + -
618D VAL* 4.8 0.4 - - + -
620D VAL* 3.8 18.4 - - + +
623D VAL* 3.5 33.2 - - + -
624D GLY* 3.7 19.3 - - - +
627D ALA* 4.8 6.3 - - + -
664D GLY 3.0 15.9 + - - +
667D VAL* 1.4 82.6 - - + +
669D GLY* 1.4 55.6 + - - +
671D PHE* 3.2 12.4 - - + +
672D SER* 2.7 35.7 + - - -
706D LEU* 5.8 5.8 - - + -
710D LEU* 4.2 22.2 - - + -
748D HEM 6.0 0.4 - - + -
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Residues in contact with GLY 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D VAL* 3.7 11.1 - - - +
665D LYS 2.9 19.2 + - - -
666D LYS* 3.6 2.2 - - - -
667D VAL 3.2 0.2 - - - -
668D LEU* 1.4 76.6 - - - +
670D ALA* 1.4 60.7 + - - +
672D SER* 3.1 19.6 + - - -
673D ASP* 3.3 13.2 + - - +
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Residues in contact with ALA 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666D LYS 3.0 7.4 + - - +
667D VAL 3.7 6.7 - - - +
669D GLY* 1.4 70.6 - - - +
671D PHE* 1.4 65.8 + - - +
673D ASP* 3.1 25.0 + - - +
674D GLY 3.3 8.3 + - - -
685D PHE* 3.5 12.8 - - + -
688D LEU* 4.0 11.9 - - + -
748D HEM 3.8 40.6 - - + -
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Residues in contact with PHE 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D TRP* 3.6 37.0 - + - -
667D VAL 2.9 14.1 + - - +
668D LEU* 3.2 19.3 + - + +
670D ALA* 1.4 76.3 - - - +
672D SER* 1.4 62.0 + - - +
674D GLY* 3.0 12.5 + - - -
675D LEU* 3.4 23.1 + - + +
685D PHE* 4.4 7.1 - - - -
707D GLY* 6.2 0.4 - - - -
710D LEU* 3.8 24.9 - - + -
730D TYR* 5.3 4.0 - + - -
733D VAL* 4.2 14.1 - - + -
734D VAL* 4.1 18.8 - - + -
737D VAL* 3.9 29.4 - - + +
748D HEM 4.0 24.4 - - + +
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Residues in contact with SER 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D TRP* 3.2 31.1 + - - +
620D VAL* 3.4 16.9 - - - +
668D LEU 2.7 20.7 + - - -
669D GLY* 3.3 11.4 - - - -
671D PHE* 1.4 72.8 - - - +
673D ASP* 1.4 59.6 + - - +
675D LEU* 3.0 26.1 + - - +
676D ALA* 3.6 5.5 + - - +
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Residues in contact with ASP 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D GLY 3.3 13.4 + - - +
670D ALA* 3.1 15.1 + - - +
672D SER* 1.4 75.4 - - - +
674D GLY* 1.4 59.2 + - - +
676D ALA* 3.2 12.5 + - - +
677D HIS* 2.9 31.4 + - + +
684D THR* 4.8 7.6 - - + -
685D PHE* 6.0 0.4 - - + -
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Residues in contact with GLY 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670D ALA 3.3 3.8 + - - -
671D PHE 3.0 10.1 + - - -
673D ASP* 1.4 77.9 - - - +
675D LEU* 1.4 59.7 + - - +
677D HIS* 3.0 26.2 + - - -
678D LEU* 3.3 2.1 + - - +
681D LEU* 3.3 13.4 - - - +
684D THR* 4.3 7.6 - - - -
685D PHE* 3.8 25.5 - - - -
737D VAL* 5.6 1.6 - - - -
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Residues in contact with LEU 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D LYS* 5.5 3.1 + - - -
611D VAL* 4.2 19.1 - - + -
612D THR* 5.5 3.0 + - - -
615D TRP* 3.4 55.0 - - + +
671D PHE* 3.4 22.9 + - + +
672D SER 3.0 9.8 + - - +
674D GLY* 1.4 76.8 - - - +
676D ALA* 1.4 58.4 + - - +
677D HIS 3.2 0.7 - - - -
678D LEU* 3.4 30.7 + - + +
730D TYR* 4.9 1.1 - - + +
733D VAL* 3.5 32.3 - - + -
737D VAL* 5.7 1.3 - - + -
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Residues in contact with ALA 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672D SER 3.6 4.1 + - - +
673D ASP* 3.2 16.3 + - - +
674D GLY 3.2 0.8 - - - -
675D LEU* 1.4 76.0 - - - +
677D HIS* 1.4 75.1 + - + +
678D LEU 3.8 0.7 - - - -
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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