Contacts of the helix formed by residues 685 - 703 (chain D) in PDB entry 3JW0
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 ASP 685 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D TYR* 5.4 2.0 - - - +
683D ASN* 3.0 11.6 + - - +
684D GLU* 1.3 90.2 - - - +
686D HIS* 1.3 65.1 + - - +
687D LEU 3.2 2.7 - - - -
688D SER* 2.9 28.8 + - - +
689D TYR* 3.3 13.9 + - + -
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Residues in contact with HIS 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D LEU* 4.3 2.9 - - + -
679D SER* 2.9 40.6 + - - +
680D GLY* 3.1 23.8 + - - -
683D ASN* 3.2 19.3 + - + +
684D GLU 4.5 5.6 - - - -
685D ASP* 1.3 77.0 - - - +
687D LEU* 1.3 93.7 + - + +
689D TYR* 3.0 8.2 + - - +
690D PHE* 2.6 46.7 + + + -
802D LYS* 5.5 6.2 + - + +
803D GLN* 4.2 10.9 - - - +
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Residues in contact with LEU 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685D ASP 3.2 0.8 - - - -
686D HIS* 1.3 114.6 - - + +
688D SER* 1.3 61.4 + - - +
690D PHE* 4.1 3.6 - - + -
691D THR* 3.0 20.4 + - - -
802D LYS* 3.5 48.9 - - + +
803D GLN* 3.9 9.2 - - + +
806D ALA* 3.5 14.0 - - + +
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Residues in contact with SER 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D TYR* 2.8 26.5 + - - -
616D MET* 3.6 18.7 - - - +
685D ASP* 2.9 20.9 + - - -
687D LEU* 1.3 75.2 - - - +
689D TYR* 1.3 66.5 + - - +
691D THR* 2.8 17.3 + - - -
692D PHE* 3.0 11.4 + - - +
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Residues in contact with TYR 689 (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 PHE* 3.9 22.7 - + + -
609D GLU* 3.1 32.2 + - - -
612D TYR* 3.6 45.5 - + - -
662D LEU* 3.7 20.9 - - + -
683D ASN* 3.0 37.5 - - - -
685D ASP* 3.3 24.3 + - + -
686D HIS* 3.0 6.6 + - - +
688D SER* 1.3 78.2 - - - +
690D PHE* 1.3 57.8 + - - +
692D PHE* 2.9 9.4 + + - +
693D ILE* 2.8 33.2 + - - +
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Residues in contact with PHE 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D LEU* 3.2 39.7 - - + -
663D PHE* 3.9 26.5 - + - -
675D ILE* 3.5 25.8 - - + -
679D SER* 3.4 18.4 - - - -
686D HIS* 2.6 32.8 + - + +
687D LEU* 3.7 5.6 - - - +
688D SER 3.0 0.2 - - - -
689D TYR* 1.3 70.0 - - - +
691D THR* 1.3 59.2 + - - +
692D PHE 3.0 5.4 - - - -
693D ILE* 3.5 8.3 + - + +
694D GLY 3.2 17.3 + - - -
803D GLN* 3.4 37.5 - - + +
806D ALA* 3.9 13.2 - - + -
807D PHE* 3.3 20.1 - + + +
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Residues in contact with THR 691 (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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616D MET* 4.0 17.0 - - + -
687D LEU 3.0 9.2 + - - -
688D SER* 2.8 10.3 + - - -
690D PHE* 1.3 74.8 - - - +
692D PHE* 1.3 56.2 + - - +
694D GLY 3.9 1.8 - - - -
695D ARG* 3.2 31.4 + - - +
806D ALA* 2.5 33.4 + - - +
807D PHE* 4.4 0.7 - - - +
809D GLU* 3.3 22.2 + - - +
810D GLY* 3.6 19.2 - - - +
813D GLU* 4.6 3.4 - - - +
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Residues in contact with PHE 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D PHE* 3.7 30.1 - + - -
611D SER* 3.3 25.8 - - - -
612D TYR* 3.8 34.3 - + + -
615D ILE* 3.9 27.6 - - + -
616D MET* 4.0 14.8 - - + -
651D LEU* 4.0 4.0 - - + -
655D MET* 4.6 7.2 - - + -
688D SER 3.0 9.4 + - - +
689D TYR* 3.0 18.2 - + - +
691D THR* 1.3 78.4 - - - +
693D ILE* 1.3 69.1 + - + +
694D GLY 3.0 1.1 - - - -
695D ARG* 2.9 5.1 + - - +
696D VAL* 2.8 49.0 + - + +
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Residues in contact with ILE 693 (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 PHE* 4.6 1.3 - - + -
655D MET* 3.4 53.7 - - + +
656D PHE* 3.9 20.4 - - + -
662D LEU* 4.2 17.5 - - + -
663D PHE* 4.2 20.6 - - + -
689D TYR 2.8 23.6 + - - +
690D PHE* 3.8 9.2 - - + +
692D PHE* 1.3 82.9 - - + +
694D GLY* 1.3 57.9 + - - +
696D VAL* 3.3 2.1 + - - +
697D ALA* 2.8 29.8 + - + +
711D PHE* 5.9 0.4 - - + -
807D PHE* 4.2 11.9 - - + -
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Residues in contact with GLY 694 (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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690D PHE 3.2 8.2 + - - -
691D THR 4.2 0.4 - - - -
692D PHE 3.0 0.6 - - - -
693D ILE* 1.3 78.2 - - - +
695D ARG* 1.3 64.6 + - - +
697D ALA* 3.1 1.7 + - - +
698D GLY 2.8 20.3 + - - -
807D PHE* 3.6 40.3 - - - -
810D GLY 3.6 7.2 - - - -
811D PHE* 3.4 8.6 - - - -
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Residues in contact with ARG 695 (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 ILE* 3.9 22.6 + - + -
616D MET* 3.5 43.8 + - - +
618D VAL* 3.5 23.4 + - - +
621D PRO* 3.8 9.1 - - - +
624D LEU* 3.9 14.9 - - + +
691D THR* 3.2 23.2 + - - +
692D PHE* 2.9 12.2 + - - +
694D GLY* 1.3 75.4 - - - +
696D VAL* 1.3 57.4 + - - +
698D GLY* 3.3 0.9 + - - -
699D LEU* 2.9 31.7 + - + +
810D GLY* 3.2 15.3 + - - +
813D GLU* 3.3 45.4 + - + +
814D LEU* 4.0 5.3 - - + +
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Residues in contact with VAL 696 (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 ILE* 5.3 2.7 - - + -
647D TRP* 4.7 8.1 - - + -
648D PHE* 4.0 18.9 - - + -
651D LEU* 4.0 21.3 - - + -
655D MET* 4.2 20.2 - - + -
692D PHE* 2.8 50.6 + - + +
693D ILE 3.5 7.0 - - - +
695D ARG* 1.3 74.3 - - + +
697D ALA* 1.3 59.9 + - - +
699D LEU* 3.1 11.9 + - + +
700D ALA* 2.8 27.4 + - - +
707D LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 697 (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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693D ILE 2.8 21.0 + - - +
694D GLY 3.6 3.8 - - - +
696D VAL* 1.3 72.8 - - - +
698D GLY* 1.3 63.0 + - - +
700D ALA* 3.3 6.1 - - - +
701D VAL* 3.3 23.0 + - - +
707D LEU* 3.6 31.2 - - + +
807D PHE* 4.0 22.9 - - + -
811D PHE* 4.0 8.1 - - + -
832D MET* 4.2 7.0 - - + +
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Residues in contact with GLY 698 (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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694D GLY 2.8 15.3 + - - -
695D ARG 3.7 1.8 - - - -
697D ALA* 1.3 73.8 - - - +
699D LEU* 1.3 53.6 + - - +
700D ALA 3.1 1.6 - - - -
701D VAL* 3.2 2.3 + - - -
702D PHE* 2.7 35.3 + - - +
811D PHE* 3.8 22.8 - - - -
814D LEU* 4.1 3.8 - - - -
815D LEU* 3.5 19.5 - - - +
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Residues in contact with LEU 699 (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 ILE* 4.0 28.0 - - + -
624D LEU* 3.2 39.0 - - + +
628D LEU* 4.2 20.9 - - + -
647D TRP* 4.5 9.2 - - + -
648D PHE* 4.2 9.1 - - + -
695D ARG 2.9 14.8 + - - +
696D VAL* 3.3 12.3 - - - +
698D GLY* 1.3 75.1 - - - +
700D ALA* 1.3 62.1 + - - +
702D PHE* 3.3 0.6 + - - -
703D HIS* 3.0 49.2 + - + +
814D LEU* 3.4 19.5 - - + +
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Residues in contact with ALA 700 (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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648D PHE* 3.7 26.2 - - + -
696D VAL 2.8 12.1 + - - +
697D ALA 3.3 11.7 - - - +
699D LEU* 1.3 78.4 - - - +
701D VAL* 1.3 59.1 + - + +
703D HIS 3.3 0.7 + - - -
704D GLY 2.9 9.0 + - - -
705D LYS* 2.8 42.8 + - - +
706D LEU 4.7 0.2 - - - -
707D LEU* 4.2 17.5 - - + +
832D MET* 5.5 0.9 - - - +
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Residues in contact with VAL 701 (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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581D TYR* 4.8 3.3 + - - -
584D PHE* 3.6 30.0 - - + -
585D ARG* 5.0 1.2 - - - -
588D LEU* 4.7 0.2 - - - +
697D ALA 3.3 8.4 + - - +
698D GLY 3.2 6.3 + - - +
700D ALA* 1.3 76.3 - - + +
702D PHE* 1.3 66.5 + - - +
704D GLY* 3.3 11.4 + - - +
705D LYS 4.5 2.2 - - - +
811D PHE* 5.1 3.6 - - + -
815D LEU* 3.4 29.6 - - + -
820D ILE* 4.5 2.2 - - + -
831D LEU* 3.6 40.5 - - + +
832D MET* 3.9 21.3 - - + -
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Residues in contact with PHE 702 (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 ARG* 2.7 31.0 + - - -
588D LEU* 3.7 40.3 - - + +
589D LYS 4.3 10.1 - - - -
590D LYS* 4.5 12.3 - - + -
625D LYS* 3.3 58.8 - - + -
698D GLY 2.7 21.1 + - - +
699D LEU* 3.6 9.4 - - + +
700D ALA 3.2 0.2 - - - -
701D VAL* 1.3 75.8 - - - +
703D HIS* 1.3 71.5 + + - +
814D LEU* 4.1 20.0 - - + -
815D LEU* 4.3 7.4 - - + -
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Residues in contact with HIS 703 (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 ARG* 3.5 16.9 + - - +
624D LEU 3.6 7.9 - - - -
625D LYS 3.7 7.2 + - - -
626D ALA 3.1 20.5 + - - -
627D ARG* 4.6 5.2 - - + -
628D LEU* 4.2 27.9 + - + +
648D PHE* 5.5 0.2 - - + -
699D LEU* 3.0 47.5 + - + +
700D ALA* 4.3 0.9 - - - +
702D PHE* 1.3 97.5 - + - +
704D GLY* 1.3 63.9 + - - +
705D LYS* 2.9 26.6 - - + -
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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