Contacts of the helix formed by residues 782 - 794 (chain D) in PDB entry 6KQH
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 SER 782 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684C PHE* 3.5 36.1 - - - -
685C GLU* 4.7 5.2 + - - -
730D PRO 5.4 0.9 + - - -
731D LEU* 5.4 2.5 - - - -
733D CYS* 6.1 0.2 - - - +
734D GLU* 5.0 14.5 + - - +
780D LYS 3.3 5.9 + - - -
781D PRO* 1.3 71.7 - - - +
783D ARG* 1.3 65.3 + - - +
784D ASP 3.4 0.7 - - - -
785D ILE* 3.4 10.8 + - - +
786D ILE* 2.7 38.7 + - - +
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Residues in contact with ARG 783 (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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684C PHE* 5.1 2.0 - - + -
685C GLU* 3.5 35.3 + - - +
874C LEU* 4.0 12.3 - - + -
782D SER* 1.3 80.0 + - - +
784D ASP* 1.3 57.9 + - - +
786D ILE* 4.3 0.4 - - - +
787D LEU* 2.9 26.5 + - - +
1027D GLY 4.6 3.8 + - - +
1028D ALA* 2.3 66.9 + - + +
1029D ARG* 3.4 43.2 - - + +
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Residues in contact with ASP 784 (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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678C PRO* 3.8 14.7 - - - +
681C GLY* 4.6 3.3 + - - -
683C ASN* 4.4 2.4 - - - +
684C PHE* 3.5 25.2 - - + -
685C GLU 4.6 2.3 + - - -
872C ASN* 2.7 33.3 + - - -
874C LEU* 2.7 21.1 - - - +
782D SER* 3.4 1.6 - - - -
783D ARG* 1.3 83.9 - - - +
785D ILE* 1.3 62.1 + - - +
787D LEU* 3.4 10.5 + - - +
788D GLY 3.5 8.3 + - - -
938D GLY 4.1 0.9 - - - +
939D PHE* 3.4 28.1 - - + -
942D SER* 3.8 15.3 + - - -
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Residues in contact with ILE 785 (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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730D PRO* 5.2 2.2 - - + -
731D LEU* 3.4 33.7 - - + -
781D PRO* 3.7 18.4 - - + -
782D SER* 3.4 20.0 + - - +
783D ARG 3.3 0.2 - - - -
784D ASP* 1.3 75.1 - - - +
786D ILE* 1.3 64.0 - - - +
788D GLY 3.4 1.9 + - - -
789D LEU* 3.2 30.0 + - + +
931D LEU 5.6 0.2 - - - +
934D LEU 3.4 26.0 - - - +
935D LYS* 3.8 26.9 - - + +
938D GLY* 3.7 9.4 - - - -
939D PHE* 3.7 21.8 - - + -
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Residues in contact with ILE 786 (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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781D PRO* 3.6 27.4 - - + +
782D SER 2.7 31.0 + - - +
783D ARG* 3.8 4.5 - - - +
785D ILE* 1.3 73.4 - - - +
787D LEU* 1.3 61.3 + - - +
790D TYR* 2.9 29.8 + - - +
906D GLN 4.8 0.2 - - - +
907D GLU* 4.1 7.6 - - - -
908D LYS* 3.6 37.9 - - + +
911D LEU* 4.2 12.1 - - + -
1026D SER* 3.4 36.8 - - - +
1027D GLY 3.8 11.9 - - - +
1028D ALA* 4.3 1.1 - - + +
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Residues in contact with LEU 787 (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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678C PRO* 4.1 17.9 - - + -
874C LEU* 4.2 15.0 - - + -
783D ARG 2.9 16.8 + - - +
784D ASP* 3.5 6.5 - - - +
785D ILE 3.2 0.2 - - - -
786D ILE* 1.3 76.3 - - - +
788D GLY* 1.3 57.9 + - - +
790D TYR* 4.2 4.2 - - - +
791D TYR* 3.1 27.7 + - - +
942D SER* 4.5 6.7 - - - -
947D ILE* 3.7 38.3 - - + +
1022D VAL* 4.3 14.9 - - + +
1023D MET* 3.3 36.8 - - + -
1026D SER* 4.6 1.8 - - - +
1028D ALA* 4.1 11.4 - - + -
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Residues in contact with GLY 788 (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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784D ASP 3.5 4.6 + - - -
785D ILE 3.4 4.0 + - - -
786D ILE 3.2 0.4 - - - -
787D LEU* 1.3 77.2 - - - +
789D LEU* 1.3 65.1 + - - +
791D TYR* 3.1 3.9 + - - +
792D ILE* 3.0 28.8 + - - +
938D GLY 3.5 20.4 - - - -
941D PHE* 4.2 6.3 - - - -
942D SER* 3.6 17.4 - - - -
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Residues in contact with LEU 789 (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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785D ILE* 3.2 28.1 + - + +
786D ILE 4.3 2.0 - - - +
788D GLY* 1.3 75.1 - - - +
790D TYR* 1.3 52.7 + - - +
792D ILE* 3.2 17.0 - - + +
793D THR* 2.6 37.9 + - - +
882D PHE* 4.0 17.7 - - + -
885D ILE* 5.1 2.2 - - + -
906D GLN* 4.3 6.5 - - + -
911D LEU* 3.8 31.4 - - + -
934D LEU* 3.7 31.0 - - + +
937D TYR* 4.4 11.7 - - + +
938D GLY* 4.0 20.4 - - - +
941D PHE* 4.9 0.2 - - + -
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Residues in contact with TYR 790 (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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786D ILE 2.9 20.0 + - - +
787D LEU 4.2 1.6 - - - +
789D LEU* 1.3 76.1 - - - +
791D TYR* 1.3 65.0 + - - +
793D THR* 3.1 2.9 + - - -
794D GLN* 2.9 55.1 + - + +
905D PRO* 4.0 22.4 - - + -
906D GLN 3.1 26.9 + - - +
907D GLU* 4.3 6.1 - - + -
1016D PRO 5.1 2.5 + - - -
1017D PHE* 5.6 1.3 - + - -
1021D TYR* 5.1 5.5 - - - -
1022D VAL* 3.6 40.3 - - + -
1025D GLN* 3.9 23.0 + - + +
1026D SER* 3.7 28.3 - - - -
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Residues in contact with TYR 791 (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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946C ARG* 3.2 12.6 + - - -
984C GLU* 2.7 30.2 + - - +
787D LEU 3.1 22.1 + - - +
788D GLY* 3.1 6.0 + - - +
790D TYR* 1.3 83.4 - - + +
792D ILE* 1.3 73.5 + - + +
794D GLN* 3.9 6.4 + - - +
860D LEU* 6.1 1.3 - - + -
861D GLN* 3.3 38.2 + - - +
941D PHE 4.5 3.8 - - - -
944D THR* 5.8 0.7 - - - -
945D SER* 3.0 49.7 + - - -
947D ILE* 4.7 14.6 - - + -
1017D PHE* 4.9 18.3 - + - -
1022D VAL* 5.7 4.0 - - + -
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Residues in contact with ILE 792 (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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788D GLY 3.0 14.9 + - - +
789D LEU* 3.2 25.4 - - + +
791D TYR* 1.3 85.9 - - + +
793D THR* 1.3 66.9 + - + +
794D GLN 3.4 2.9 + - - +
860D LEU* 4.0 27.8 - - + +
861D GLN* 4.3 6.2 + - - +
876D SER* 4.3 0.5 + - - -
878D GLY* 3.5 36.1 - - - +
879D ARG 4.3 0.2 + - - -
881D LEU* 4.3 8.5 - - + -
882D PHE* 4.6 7.9 - - + -
885D ILE* 4.9 1.1 - - + -
941D PHE* 3.5 50.9 - - + -
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Residues in contact with THR 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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789D LEU 2.6 23.4 + - - +
790D TYR* 3.3 6.2 + - - -
792D ILE* 1.3 85.9 - - + +
794D GLN* 1.3 61.2 + - - +
878D GLY 4.4 3.8 - - - +
879D ARG* 2.9 42.7 + - + -
882D PHE* 3.9 21.8 - - + -
904D VAL 4.7 0.9 - - - -
905D PRO* 3.6 6.8 - - - +
906D GLN* 2.9 45.0 + - + -
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Residues in contact with GLN 794 (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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790D TYR* 2.9 51.3 + - + +
791D TYR* 3.9 2.7 + - - +
792D ILE 3.4 3.4 - - - +
793D THR* 1.3 82.1 - - - +
795D VAL* 1.3 86.1 + - - +
861D GLN* 3.6 24.8 - - - +
876D SER* 4.6 1.0 + - - -
905D PRO* 3.7 23.7 - - + +
1016D PRO* 5.6 6.7 + - + +
1017D PHE* 3.5 35.4 - - + -
1021D TYR* 6.2 1.0 - - - -
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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
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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