Contacts of the helix formed by residues 619 - 635 (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 619 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617D LYS 3.6 4.0 + - - +
618D VAL* 1.4 69.8 - - - +
620D VAL* 1.4 64.1 + - - +
621D ASP* 3.2 16.6 + - - +
622D GLU* 3.0 44.6 + - + +
623D VAL* 3.0 27.5 + - + +
717D HIS* 6.1 2.6 + - + -
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Residues in contact with VAL 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D TRP* 4.4 16.4 - - + +
618D VAL* 3.3 14.5 + - + +
619D ASN* 1.4 70.4 + - - +
621D ASP* 1.4 64.2 + - - +
624D GLY* 2.8 29.1 + - - -
665D LYS* 3.9 10.4 - - + +
668D LEU* 3.8 10.2 - - + +
669D GLY* 3.7 31.2 - - - +
672D SER* 3.4 22.7 - - - +
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Residues in contact with ASP 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D ASN* 3.2 12.6 + - - +
620D VAL* 1.4 82.1 - - - +
622D GLU* 1.4 63.2 + - + +
624D GLY* 4.1 0.5 - - - -
625D GLY* 3.3 15.9 + - - -
661D LYS* 4.7 2.9 - - - +
665D LYS* 2.7 57.4 + - + +
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Residues in contact with GLU 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D ASN* 3.0 28.7 + - + +
621D ASP* 1.4 76.8 - - + +
623D VAL* 1.4 66.8 + - + +
625D GLY* 3.4 2.2 + - - +
626D GLU* 3.1 27.0 + - + +
717D HIS* 5.6 6.5 - - + -
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Residues in contact with VAL 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D VAL* 3.7 25.8 - - + -
619D ASN* 3.0 23.8 + - + +
622D GLU* 1.4 76.3 - - + +
624D GLY* 1.4 56.7 + - - +
626D GLU* 3.3 7.8 + - - +
627D ALA* 2.9 28.1 + - - +
668D LEU* 3.5 20.4 - - + -
710D LEU* 3.9 16.8 - - + -
713D VAL* 4.1 15.7 - - + +
714D LEU* 4.4 9.0 - - + -
717D HIS* 5.0 22.4 - - + +
718D PHE* 5.7 0.2 - - + -
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Residues in contact with GLY 624 (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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620D VAL 2.8 20.3 + - - -
623D VAL* 1.4 77.4 - - - +
625D GLY* 1.4 60.1 + - - +
627D ALA* 4.0 1.4 - - - +
628D LEU* 3.0 19.9 + - - +
664D GLY* 3.4 32.5 - - - -
668D LEU* 3.7 17.0 - - - +
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Residues in contact with GLY 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D ASP 3.3 14.7 + - - -
622D GLU* 3.4 2.9 + - - -
623D VAL 3.4 0.2 - - - -
624D GLY* 1.4 73.8 - - - +
626D GLU* 1.4 56.4 + - - +
628D LEU* 4.2 1.1 - - - +
629D GLY* 3.0 27.0 + - - -
655D MET* 4.5 3.3 - - - +
660D VAL* 4.4 5.1 - - - +
661D LYS* 4.2 31.3 - - - +
664D GLY* 4.2 4.2 - - - -
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Residues in contact with GLU 626 (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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519C PRO* 5.1 1.6 - - - +
622D GLU* 3.1 16.5 + - + +
623D VAL* 3.5 8.7 - - - +
625D GLY* 1.4 75.1 - - - +
627D ALA* 1.4 58.2 + - - +
629D GLY* 3.4 1.0 + - - -
630D ARG* 2.9 72.6 + - - +
655D MET* 3.3 24.2 - - - +
713D VAL* 3.9 20.3 - - + +
716D HIS* 4.5 6.3 + - - -
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Residues in contact with ALA 627 (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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623D VAL 2.9 17.4 + - - +
624D GLY* 4.0 4.5 - - - +
626D GLU* 1.4 77.1 - - - +
628D LEU* 1.4 61.4 + - - +
631D LEU* 3.0 21.5 + - - +
668D LEU* 4.8 4.0 - - + -
706D LEU* 4.1 16.6 - - + +
709D VAL* 3.4 10.4 - - + +
710D LEU* 4.2 27.8 - - + -
713D VAL* 3.9 16.1 - - + +
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Residues in contact with LEU 628 (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 3.0 18.1 + - - +
625D GLY 4.2 1.6 - - - +
627D ALA* 1.4 74.2 - - - +
629D GLY* 1.4 63.3 + - - +
631D LEU* 3.2 25.0 + - + +
632D LEU* 3.1 33.3 + - + +
642D PHE* 4.4 16.2 - - + -
645D PHE* 4.8 3.1 - - + -
660D VAL* 3.4 30.1 - - + +
663D HIS* 3.7 24.7 - - + -
664D GLY* 3.6 17.5 - - - +
667D VAL* 5.4 5.8 - - + -
706D LEU* 4.5 13.8 - - + +
748D HEM 5.5 3.4 - - + -
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Residues in contact with GLY 629 (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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625D GLY 3.0 18.5 + - - -
628D LEU* 1.4 76.0 - - - +
630D ARG* 1.4 60.5 + - - +
632D LEU 3.3 1.9 + - - -
633D VAL* 3.0 26.3 + - - +
654D VAL* 3.4 17.0 - - - +
655D MET* 3.6 19.3 - - - -
660D VAL* 3.9 8.7 - - - +
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Residues in contact with ARG 630 (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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517C PHE* 2.9 39.7 + - - -
518C THR* 3.6 3.6 + - - +
519C PRO* 3.8 33.8 - - + +
522C HIS* 3.2 41.0 + - + +
626D GLU* 2.9 40.8 + - - +
629D GLY* 1.4 71.3 - - - +
631D LEU* 1.4 65.6 + - - +
633D VAL* 4.4 6.1 - - - -
634D VAL* 2.8 29.8 + - + +
655D MET* 4.3 2.5 - - + -
709D VAL* 3.8 14.8 - - + -
712D CYS* 6.1 0.2 - - - -
713D VAL* 3.8 22.6 - - - +
716D HIS* 3.5 22.3 - - - -
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Residues in contact with LEU 631 (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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627D ALA 3.0 14.8 + - - +
628D LEU* 3.2 25.1 + - + +
630D ARG* 1.4 74.9 - - - +
632D LEU* 1.4 58.7 + - + +
635D TYR* 2.9 42.9 + - + +
638D THR* 3.4 18.8 + - + +
702D ASN 4.6 1.1 - - - +
705D LEU* 3.7 33.0 - - + +
706D LEU* 3.7 20.4 - - + +
709D VAL* 3.9 10.4 - - + +
748D HEM 3.9 37.9 - - + -
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Residues in contact with LEU 632 (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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628D LEU* 3.1 23.1 + - + +
629D GLY 3.3 6.7 + - - +
631D LEU* 1.4 85.3 - - + +
633D VAL* 1.4 58.4 - - - +
636D PRO* 3.4 10.2 - - - +
638D THR* 3.4 21.5 - - - +
639D GLN* 2.8 43.2 + - + +
642D PHE* 3.9 35.9 - - + -
645D PHE* 5.5 0.2 - - + -
648D LEU* 4.7 7.0 - - + -
654D VAL* 3.9 13.9 - - + -
660D VAL* 4.0 30.7 - - + -
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Residues in contact with VAL 633 (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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519C PRO* 4.0 26.0 - - + +
520C ALA* 4.9 0.4 - - - -
523C ALA* 4.3 11.4 - - + +
629D GLY 3.0 18.0 + - - +
630D ARG* 3.2 5.8 + - - +
632D LEU* 1.4 76.9 - - - +
634D VAL* 1.4 63.7 + - + +
636D PRO* 3.6 16.5 - - - +
639D GLN* 4.9 1.1 - - - +
650D THR 5.5 0.2 - - - -
651D PRO* 4.0 35.7 - - + +
654D VAL* 3.9 25.6 - - + -
655D MET* 4.5 7.0 - - - -
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Residues in contact with VAL 634 (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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141A ARG* 3.0 38.6 + - - +
519C PRO 4.2 5.4 - - - +
522C HIS* 3.7 39.5 - - + +
523C ALA* 3.9 21.2 - - + +
526C ASP* 3.8 13.9 - - + +
630D ARG* 2.8 25.0 + - + +
633D VAL* 1.4 75.0 - - + +
635D TYR* 1.4 85.3 + - + +
636D PRO* 3.4 7.1 - - - +
709D VAL* 5.3 0.2 - - + -
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Residues in contact with TYR 635 (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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141A ARG* 3.5 6.3 - - - -
506C LEU* 5.2 2.3 - - - +
522C HIS* 5.4 1.6 + - - -
526C ASP* 2.8 34.1 + - - -
631D LEU* 2.9 29.2 + - + +
632D LEU 4.0 0.2 - - - -
634D VAL* 1.4 93.1 - - + +
636D PRO* 1.3 62.9 - - - +
637D TRP* 3.3 37.0 - + + -
638D THR* 2.7 42.1 + - + -
705D LEU* 4.2 16.2 - - + -
708D ASN* 6.0 3.1 - - + +
709D VAL* 3.8 20.9 - - + -
802D CNO 3.3 33.3 + + + +
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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