Contacts of the helix formed by residues 629 - 645 (chain D) in PDB entry 1O23
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 629 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D GLN* 3.0 8.1 + - - -
628D PHE* 1.3 77.7 - - - +
630D ARG* 1.3 62.1 + - - +
631D ALA* 3.8 4.0 + - - +
632D LYS* 2.9 25.7 + - - +
633D LEU* 3.1 23.1 + - - +
711D ASN 2.9 27.7 + - - +
713D TYR 3.3 16.4 + - - +
714D TRP* 3.3 34.1 - - + -
715D GLY 5.8 0.4 - - - -
800D ILE* 3.4 18.6 - - + -
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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
----------------------------------------------------------
589D PRO* 4.1 13.8 - - + +
628D PHE* 3.4 24.1 - - + -
629D ASN* 1.3 72.4 + - - +
631D ALA* 1.3 64.0 + - - +
633D LEU* 3.1 7.3 + - - +
634D LEU* 3.0 45.4 + - + +
652D PHE* 4.7 7.9 + - - +
654D ASP* 2.6 29.7 + - - +
692D PHE 5.4 2.2 + - - -
693D GLY* 5.1 0.6 - - - -
694D GLY 3.6 16.2 + - - +
696D SER* 5.4 3.8 + - - -
713D TYR 4.9 1.0 + - - -
715D GLY 5.8 1.0 + - - -
719D GLU* 2.8 46.6 + - + +
720D ASP* 4.4 8.5 - - - +
723D ILE* 5.0 4.6 - - - +
810D UPG 3.0 40.8 + - - +
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Residues in contact with ALA 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D ASN* 3.6 3.6 + - - +
630D ARG* 1.3 78.7 - - - +
632D LYS* 1.3 62.7 + - - +
634D LEU* 3.1 14.9 + - - +
635D ASN* 3.0 24.9 + - - +
709D PHE* 4.1 14.5 - - + +
710D PRO* 3.2 24.5 - - + +
713D TYR* 5.6 2.4 + - + -
719D GLU* 3.9 28.0 - - + +
723D ILE* 4.8 2.9 - - + -
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Residues in contact with LYS 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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629D ASN* 2.9 35.4 + - + +
631D ALA* 1.3 75.7 - - - +
633D LEU* 1.3 63.9 + - - +
635D ASN* 2.9 14.4 + - - +
636D VAL* 3.0 16.1 + - + +
710D PRO 3.8 1.0 + - - -
711D ASN* 3.6 35.8 - - + +
714D TRP* 4.2 8.8 - - + -
780D LEU* 4.2 11.4 - - + -
781D THR* 3.4 32.5 + - - +
800D ILE* 2.4 55.0 + - + +
801D GLY* 4.7 1.0 - - - -
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Residues in contact with LEU 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589D PRO* 4.2 7.6 - - + -
590D PHE 4.1 8.5 - - - +
620D ILE* 3.5 37.1 - - + +
622D GLN* 3.6 35.2 - - + +
628D PHE* 3.4 36.8 - - + -
629D ASN 3.1 15.6 + - - +
630D ARG 3.1 5.7 + - - +
632D LYS* 1.3 75.4 - - - +
634D LEU* 1.3 63.7 + - - +
636D VAL* 3.4 2.6 + - - -
637D GLY 3.0 18.0 + - - -
798D VAL* 3.9 3.8 - - + -
800D ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D ILE* 3.9 18.3 - - + +
589D PRO* 3.5 32.8 - - + -
630D ARG* 3.0 48.0 + - + +
631D ALA* 3.4 11.7 - - - +
632D LYS 3.1 0.2 - - - -
633D LEU* 1.3 76.7 - - - +
635D ASN* 1.3 65.6 + - - +
637D GLY* 3.2 2.3 + - - -
638D PHE* 3.1 20.4 + - - +
652D PHE* 3.8 29.7 - - + -
709D PHE* 3.7 30.1 - - + -
723D ILE* 5.1 1.8 - - + -
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Residues in contact with ASN 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D ALA 3.0 10.3 + - - -
632D LYS 2.9 9.5 + - - +
634D LEU* 1.3 76.0 - - - +
636D VAL* 1.3 63.0 + - - +
638D PHE* 3.0 24.4 + - - +
639D LYS* 3.2 10.0 + - - +
703D PHE* 3.8 11.2 - - - -
708D GLY* 4.4 0.2 - - - -
709D PHE* 2.7 48.3 + - - +
710D PRO 3.9 2.2 + - - -
711D ASN* 2.6 30.6 + - - +
776D GLY 4.1 4.9 + - - -
777D LEU* 4.7 7.1 - - + +
780D LEU* 3.8 17.7 - - + +
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Residues in contact with VAL 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D ILE* 3.7 18.2 - - + -
632D LYS* 3.0 15.5 + - + +
633D LEU* 3.5 7.6 - - - +
635D ASN* 1.3 75.9 - - - +
637D GLY* 1.3 64.4 + - - +
639D LYS* 3.0 4.7 + - - +
640D GLU* 2.9 30.0 + - + +
780D LEU* 4.2 13.7 - - + -
782D TYR* 3.7 50.9 - - + -
796D ILE* 5.5 0.2 - - + -
798D VAL* 3.9 11.7 - - + -
800D ILE* 4.3 12.8 - - + -
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Residues in contact with GLY 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D ILE* 3.3 15.7 - - - +
618D TYR* 5.3 0.9 - - - -
620D ILE* 3.5 29.8 - - - +
633D LEU 3.0 12.1 + - - -
634D LEU 3.2 3.7 + - - -
636D VAL* 1.3 75.8 - - - +
638D PHE* 1.3 62.4 + - - +
640D GLU* 4.5 1.8 - - - -
641D ALA* 3.0 28.2 + - - +
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Residues in contact with PHE 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D ILE* 3.3 10.2 - - + +
634D LEU 3.1 11.4 + - - +
635D ASN 3.0 10.8 + - - +
637D GLY* 1.3 78.3 - - - +
639D LYS* 1.3 64.8 + - + +
641D ALA* 4.0 0.7 - - - +
642D LEU* 2.6 44.6 + - + +
650D PHE* 3.4 46.9 - + - -
652D PHE* 4.9 1.1 - + + -
700D LYS* 4.3 15.7 - - + -
703D PHE* 3.2 48.2 - + + -
704D LEU* 4.0 14.6 - - + -
777D LEU* 3.7 23.3 - - + -
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Residues in contact with LYS 639 (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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635D ASN 3.2 7.4 + - - +
636D VAL 3.0 7.8 + - - +
638D PHE* 1.3 90.2 - - + +
640D GLU* 1.3 67.0 + - - +
641D ALA 3.4 0.2 + - - -
642D LEU* 3.5 8.5 + - - +
643D LYS* 3.5 23.7 + - - +
777D LEU* 4.3 14.8 + - + +
780D LEU* 3.4 35.8 + - + +
782D TYR* 3.9 20.6 - - + +
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Residues in contact with GLU 640 (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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618D TYR* 4.7 2.6 - - + -
636D VAL* 2.9 31.1 + - + +
637D GLY* 4.1 4.3 - - - +
639D LYS* 1.3 75.4 - - - +
641D ALA* 1.3 64.5 + - - +
643D LYS* 3.1 50.7 + - - +
644D ASP* 3.7 5.9 + - - +
782D TYR* 2.6 28.5 + - - +
784D VAL* 3.6 15.5 - - - +
787D VAL* 4.8 6.8 - - - +
796D ILE* 3.3 38.6 - - + +
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Residues in contact with ALA 641 (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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585D ALA* 3.8 28.9 - - + -
587D ILE* 4.9 1.1 - - + -
618D TYR* 3.7 24.1 - - + -
637D GLY 3.0 19.5 + - - +
638D PHE 4.0 2.7 - - - +
640D GLU* 1.3 77.5 - - - +
642D LEU* 1.3 53.8 + - - +
644D ASP* 2.7 32.1 + - - +
645D TYR 3.3 4.7 + - - -
647D TYR* 3.4 10.6 - - + -
650D PHE* 4.6 4.0 - - + -
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Residues in contact with LEU 642 (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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638D PHE* 2.6 43.0 + - + +
639D LYS* 3.7 9.9 - - - +
640D GLU 3.4 0.4 - - - -
641D ALA* 1.3 78.0 - - - +
643D LYS* 1.3 61.7 + - - +
645D TYR 3.0 24.9 + - - +
646D ASP* 4.9 3.1 - - - -
647D TYR* 3.9 24.2 - - + +
650D PHE* 3.2 27.6 - - + -
700D LYS* 4.1 21.1 - - - +
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Residues in contact with LYS 643 (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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639D LYS* 3.5 11.4 + - - +
640D GLU* 3.1 47.5 + - - +
641D ALA 3.0 0.6 + - - -
642D LEU* 1.3 77.2 - - - +
644D ASP* 1.3 63.0 + - - +
782D TYR* 4.3 5.6 + - - -
784D VAL* 5.1 4.9 - - - +
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Residues in contact with ASP 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D ARG* 5.7 3.7 - - - +
618D TYR* 2.9 35.3 + - - +
640D GLU 4.6 3.2 - - - +
641D ALA 2.7 13.3 + - - +
643D LYS* 1.3 79.6 - - - +
645D TYR* 1.3 63.7 + - + +
647D TYR* 4.7 0.2 - - - +
789D ARG* 2.5 48.2 + - - -
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Residues in contact with TYR 645 (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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572D ARG* 3.5 27.3 + - - +
574D THR* 5.2 1.0 + - - +
583D LYS* 3.7 28.3 - - + -
614D ASP* 2.3 35.7 + - - -
641D ALA 3.3 1.4 + - - -
642D LEU* 3.0 21.1 + - - +
644D ASP* 1.3 83.9 - - + +
646D ASP* 1.3 84.5 + - - +
647D TYR* 3.1 50.7 + + + +
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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