Contacts of the helix formed by residues 789 - 809 (chain D) in PDB entry 3IKM
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 PRO 789 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781D ALA 3.9 13.9 - - - +
782D GLY* 4.2 8.1 - - - -
783D PRO* 5.1 0.9 - - + -
785D GLY 4.2 17.9 - - - +
786D ALA* 4.9 1.6 - - - -
787D SER 2.6 17.3 - - - +
788D GLY* 1.3 75.5 - - - -
790D ARG* 1.3 53.1 + - + +
792D LEU* 2.7 15.2 + - + +
793D GLU* 2.5 49.2 + - + +
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Residues in contact with ARG 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786D ALA* 4.4 25.9 - - - +
787D SER* 3.6 14.3 + - - +
788D GLY 2.9 1.4 + - - -
789D PRO* 1.3 76.1 - - + +
791D ALA* 1.3 58.2 + - - +
792D LEU 2.7 10.0 + - - -
793D GLU* 4.3 8.5 - - + +
794D ILE* 3.0 34.4 + - + +
269F SER* 4.4 12.1 - - - -
271F SER* 4.2 25.2 - - - +
272F ASN* 3.8 33.9 + - - +
356F LEU* 5.6 3.4 - - - +
358F GLU* 4.8 6.5 + - - -
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Residues in contact with ALA 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D MET* 3.9 8.1 - - + +
462D SER* 4.2 20.9 - - - +
466D LEU* 5.8 3.4 - - + -
603D MET* 3.9 17.4 - - + +
787D SER* 4.2 2.2 - - - +
788D GLY* 2.2 45.9 + - - +
790D ARG* 1.3 68.3 - - - +
792D LEU* 1.3 53.2 + - - +
794D ILE* 4.3 8.1 - - - -
795D ASN* 2.4 32.4 + - - +
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Residues in contact with LEU 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D MET* 3.7 19.3 - - + -
605D LEU* 4.7 0.4 - - + -
766D PHE* 5.7 0.9 - - + -
775D GLU* 3.5 23.1 - - + +
780D GLN* 4.2 11.4 - - + -
781D ALA* 3.2 47.1 - - + +
788D GLY 2.8 27.1 + - - +
789D PRO* 3.0 12.1 - - + +
790D ARG 2.7 1.2 - - - -
791D ALA* 1.3 85.4 - - - +
793D GLU* 1.3 55.3 + - + +
794D ILE 2.5 3.5 + - - -
795D ASN* 2.4 40.4 + - - +
796D LYS* 2.9 18.9 + - - +
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Residues in contact with GLU 793 (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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776D ASP* 5.4 0.9 - - - +
789D PRO* 2.5 30.1 + - + +
790D ARG* 4.5 7.9 - - + -
792D LEU* 1.3 71.5 - - + +
794D ILE* 1.3 53.3 + - + +
796D LYS* 3.4 35.0 + - - +
797D MET* 2.6 37.5 + - + +
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Residues in contact with ILE 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D LEU* 3.4 37.2 - - + +
458D GLU* 5.3 2.7 - - + -
459D MET* 3.9 39.3 - - + +
790D ARG* 3.0 27.3 + - + +
791D ALA* 4.3 2.9 - - - -
792D LEU 2.5 6.5 + - - -
793D GLU* 1.3 75.0 - - + +
795D ASN* 1.3 72.7 + - - +
796D LYS 3.1 1.1 - - - -
797D MET* 3.3 13.4 + - + -
798D ILE* 2.8 21.6 + - - +
869D ARG* 2.9 10.2 + - - -
271F SER* 5.7 4.7 - - - +
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Residues in contact with ASN 795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D MET* 3.1 22.0 - - + +
594D LEU* 4.4 2.0 - - + +
603D MET* 4.9 0.5 - - - +
766D PHE* 4.3 22.2 - - + -
775D GLU* 4.4 8.7 - - - +
791D ALA 2.4 33.5 + - - +
792D LEU* 2.4 28.6 + - - +
794D ILE* 1.3 69.3 - - - +
796D LYS* 1.3 64.4 + - + +
798D ILE* 2.5 36.1 + - + +
799D SER* 2.9 13.0 + - - +
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Residues in contact with LYS 796 (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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772D PRO* 5.0 8.5 - - + +
775D GLU* 3.3 37.7 - - + +
776D ASP* 2.6 45.2 - - + +
780D GLN* 5.4 1.2 - - - +
792D LEU* 2.9 21.1 + - - +
793D GLU* 3.4 43.6 + - - +
795D ASN* 1.3 80.7 - - + +
797D MET* 1.3 64.5 + - - +
799D SER* 3.4 11.8 + - - -
800D PHE* 3.0 30.2 - - + -
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Residues in contact with MET 797 (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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455D LEU* 3.3 27.6 - - - -
793D GLU* 2.6 20.9 - - + +
794D ILE* 3.4 19.7 - - + -
796D LYS* 1.3 77.1 - - + +
798D ILE* 1.3 62.0 + - - +
799D SER 3.4 0.2 + - - -
800D PHE* 3.7 6.3 + - - +
801D TRP* 3.5 12.3 + - - +
867D PRO 4.3 9.4 - - - +
868D ASP* 3.7 32.4 - - + +
869D ARG* 2.6 41.4 + - + -
1201D SER* 6.3 1.3 - - - +
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Residues in contact with ILE 798 (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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452D TYR 4.6 3.1 - - - +
455D LEU* 3.8 15.7 - - + -
456D GLN* 4.9 5.8 - - + +
459D MET* 3.4 28.0 - - + -
591D LEU* 4.3 8.5 - - + -
794D ILE 2.8 4.4 + - - +
795D ASN* 2.5 49.0 + - + +
797D MET* 1.3 73.1 - - - +
799D SER* 1.3 53.8 + - - +
801D TRP* 3.0 3.2 - - + +
802D ARG* 2.7 59.3 + - - +
869D ARG* 2.4 59.0 - - - +
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Residues in contact with SER 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768D LYS* 5.4 17.4 - - - -
772D PRO* 5.9 4.9 - - - +
795D ASN* 2.9 21.0 + - - +
796D LYS* 3.7 9.0 + - - -
797D MET 3.4 0.2 - - - -
798D ILE* 1.3 75.2 - - - +
800D PHE* 1.3 69.9 + - - +
801D TRP 2.8 1.9 + - - -
802D ARG* 3.3 29.9 + - - +
803D ASN* 3.7 7.3 - - - +
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Residues in contact with PHE 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768D LYS* 6.0 5.8 - - - -
772D PRO* 6.2 4.7 - - + -
773D LYS* 6.3 1.1 - - - -
796D LYS* 3.0 37.5 - - + -
797D MET* 4.0 6.1 - - - +
798D ILE 3.5 0.2 - - - -
799D SER* 1.3 79.5 - - - +
801D TRP* 1.3 64.6 - - - +
803D ASN* 4.3 3.5 + - - +
804D ALA* 4.0 11.4 + - - +
866D ARG* 5.5 2.7 - - - -
867D PRO* 3.2 41.7 - - + -
868D ASP 4.8 4.3 - - - +
1066D THR* 4.3 8.1 - - + -
1068D ASP* 3.6 23.1 - - - -
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Residues in contact with TRP 801 (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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448D ALA 3.4 10.2 + - - -
452D TYR* 2.5 72.1 - + + +
456D GLN* 5.7 0.2 - - - -
797D MET 3.5 9.6 + - - +
798D ILE 3.0 6.5 - - - +
799D SER 2.8 0.8 + - - -
800D PHE* 1.3 77.5 - - - +
802D ARG* 1.3 64.0 + - + +
803D ASN 2.6 4.7 + - - -
804D ALA* 2.4 39.3 + - + +
805D HIS* 2.6 59.0 - + + -
808D ILE* 3.9 0.7 - - + -
869D ARG* 3.0 27.8 - - + +
870D VAL* 2.5 42.2 - - + -
871D GLY* 5.3 2.2 - - - +
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Residues in contact with ARG 802 (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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452D TYR* 5.7 0.7 - - - -
456D GLN* 3.8 21.5 - - - +
589D PRO* 3.6 53.4 + - + +
591D LEU* 3.4 29.2 - - - +
798D ILE* 2.7 34.4 + - - +
799D SER* 3.3 16.4 + - - +
801D TRP* 1.3 87.1 - - + +
803D ASN* 1.3 89.1 + - - +
805D HIS* 3.6 10.1 + - - +
806D LYS* 4.2 3.1 + - - +
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Residues in contact with ASN 803 (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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768D LYS* 6.1 3.4 - - - +
799D SER 3.7 7.9 + - - +
800D PHE 4.6 4.3 - - - +
801D TRP 2.6 4.9 + - - -
802D ARG* 1.3 108.9 - - - +
804D ALA* 1.3 67.5 + - - +
805D HIS 3.2 0.5 + - - -
806D LYS* 3.5 13.3 + - - +
807D ARG* 3.6 14.8 + - + +
1061D LEU 5.5 0.2 + - - -
1062D GLU* 4.1 20.7 + - - +
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Residues in contact with ALA 804 (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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800D PHE 4.0 8.7 + - - +
801D TRP* 2.4 35.4 + - + +
803D ASN* 1.3 71.6 - - - +
805D HIS* 1.3 50.6 + - - +
807D ARG* 3.2 7.1 + - - +
808D ILE* 2.6 56.8 + - + +
858D THR* 5.9 0.7 - - - -
870D VAL* 4.5 2.5 - - + -
871D GLY* 4.9 8.3 - - - -
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Residues in contact with HIS 805 (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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445D LEU* 3.7 19.3 - - + -
448D ALA* 5.0 2.0 - - + -
449D GLN* 2.6 41.7 - - + +
452D TYR* 3.6 18.8 - - - -
589D PRO* 4.9 7.6 - - + -
801D TRP* 2.6 47.2 - + + -
802D ARG 3.8 9.2 - - - +
803D ASN 3.2 1.2 + - - -
804D ALA* 1.3 73.8 - - - +
806D LYS* 1.3 57.6 + - - +
808D ILE* 2.7 7.9 + - - +
809D SER* 2.2 64.9 + - - -
870D VAL* 5.3 1.8 - - + -
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Residues in contact with LYS 806 (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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587D PRO* 3.6 7.9 - - - +
588D GLY* 2.8 53.7 + - - +
589D PRO* 4.3 12.1 - - + +
802D ARG 4.2 3.2 + - - +
803D ASN* 3.5 9.2 + - - +
805D HIS* 1.3 78.8 - - - +
807D ARG* 1.3 69.3 + - + +
809D SER* 2.9 21.8 - - - +
810D SER* 3.8 5.2 + - - -
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Residues in contact with ARG 807 (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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803D ASN* 3.6 16.5 + - - +
804D ALA* 3.6 4.5 - - - +
806D LYS* 1.3 79.0 - - + +
808D ILE* 1.3 66.4 + - - +
809D SER 2.9 0.2 + - - -
810D SER* 3.3 17.5 + - - -
811D GLN* 3.5 3.3 + - - +
857D PRO* 3.2 36.7 - - - +
858D THR* 3.1 30.7 + - + +
1061D LEU* 2.9 30.7 - - - +
1062D GLU* 3.2 27.7 - - - +
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Residues in contact with ILE 808 (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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445D LEU* 3.8 7.9 - - + -
801D TRP* 3.9 10.1 - - + -
804D ALA* 2.6 55.2 + - + +
805D HIS* 2.7 9.5 + - - +
807D ARG* 1.3 71.8 - - - +
809D SER* 1.3 53.3 + - - +
811D GLN* 2.3 71.4 - - - +
858D THR* 4.0 15.3 - - + -
859D TRP* 5.5 2.2 - - + +
870D VAL* 4.2 2.2 - - + -
871D GLY* 5.1 2.7 - - - -
874D LEU* 3.3 40.6 - - + -
878D VAL* 5.5 0.2 - - + -
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Residues in contact with SER 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU* 4.5 9.4 - - - -
449D GLN* 5.5 5.4 - - - -
805D HIS* 2.2 67.3 + - - -
806D LYS* 2.9 17.2 - - - +
808D ILE 1.3 66.3 - - - +
810D SER* 1.3 58.1 + - - +
811D GLN* 4.3 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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