Contacts of the helix formed by residues 656 - 675 (chain C) in PDB entry 1DQA
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 GLY 656 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C NAP 2.6 22.5 + - - -
588C MET* 4.0 5.2 - - - -
651C SER* 4.0 18.8 - - - -
654C ALA* 2.9 4.1 - - - -
655C MET* 1.3 78.2 - - - +
657C MET* 1.3 57.8 + - - +
658C ASN 3.3 0.2 + - - -
659C MET* 3.3 3.3 + - - -
660C ILE* 2.8 34.1 + - - +
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Residues in contact with MET 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C NAP 3.4 48.8 + - + +
588C MET* 4.0 9.4 - - + -
589C THR 3.3 25.8 - - - +
590C ARG* 3.3 31.0 - - - +
655C MET* 3.4 26.3 - - + -
656C GLY* 1.3 75.0 - - - +
658C ASN* 1.3 58.5 + - - +
660C ILE* 4.5 4.9 - - + -
661C SER* 2.8 35.3 + - - +
690C ASP* 3.6 10.5 - - - -
702C ARG* 3.3 16.4 - - - +
770C GLN* 4.0 5.2 - - - +
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Residues in contact with ASN 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C NAP 3.0 65.2 + - - +
657C MET* 1.3 74.7 - - - +
659C MET* 1.3 59.3 + - - +
661C SER* 3.2 6.0 + - - -
662C LYS* 2.9 36.3 + - - +
863D VAL* 5.1 0.3 - - - +
866D HIS* 3.4 23.1 + - - +
867D MET* 3.7 15.0 - - + +
870D ASN* 3.1 34.8 + - - +
871D ARG* 4.3 0.2 - - - -
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Residues in contact with MET 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C NAP 3.0 49.3 + - - +
625C THR* 4.5 3.6 + - - -
626C SER* 3.9 8.3 - - - +
628C PHE* 4.1 5.4 - - + -
629C ALA* 3.7 32.3 - - + +
651C SER* 3.7 32.8 - - - +
654C ALA* 3.4 31.4 - - - -
656C GLY* 3.6 6.3 - - - +
658C ASN* 1.3 76.2 - - - +
660C ILE* 1.3 60.0 + - + +
662C LYS* 3.4 7.8 + - - +
663C GLY* 3.1 23.6 + - - -
871D ARG* 3.8 10.5 - - - +
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Residues in contact with ILE 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C MET* 4.1 17.7 - - + +
589C THR* 3.9 15.9 - - - +
590C ARG* 3.5 26.9 - - + +
622C PHE* 3.7 11.1 - - + -
629C ALA* 4.3 4.9 - - + -
647C PHE* 4.9 2.7 - - + +
649C SER* 3.9 30.3 - - - +
650C ARG 4.0 1.6 - - - +
651C SER* 3.9 26.2 - - - -
656C GLY* 2.8 25.0 + - - +
657C MET* 4.1 3.4 - - + +
659C MET* 1.3 78.4 - - + +
661C SER* 1.3 59.0 + - - +
663C GLY 3.3 0.7 + - - -
664C THR* 2.8 34.9 + - - +
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Residues in contact with SER 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C NAP 3.0 20.2 + - - -
590C ARG* 3.0 21.9 + - - -
657C MET 2.8 24.6 + - - -
658C ASN* 3.7 5.2 - - - -
660C ILE* 1.3 77.2 - - - +
662C LYS* 1.3 57.6 + - - +
664C THR* 3.3 7.3 + - - -
665C GLU* 2.9 30.5 + - - +
683C VAL* 4.1 7.2 - - - +
862D LEU* 5.1 3.4 - - - -
863D VAL* 3.7 19.8 - - - +
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Residues in contact with LYS 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C THR* 3.8 35.2 - - - +
658C ASN 2.9 21.1 + - - +
659C MET* 3.4 9.9 - - - +
660C ILE 3.2 0.2 - - - -
661C SER* 1.3 77.2 - - - +
663C GLY* 1.3 62.7 + - - +
665C GLU* 3.4 8.6 + - - +
666C LYS* 3.2 17.5 + - - +
863D VAL* 3.6 28.5 - - + +
867D MET* 3.4 21.6 - - + +
871D ARG* 3.3 33.4 - - - +
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Residues in contact with GLY 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C PHE* 3.3 31.1 - - - -
625C THR* 3.5 18.6 + - - -
659C MET 3.1 10.0 + - - -
660C ILE 3.3 2.9 + - - -
662C LYS* 1.3 79.3 - - - +
664C THR* 1.3 56.8 + - - +
666C LYS* 3.3 2.4 + - - -
667C ALA* 2.9 28.8 + - - +
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Residues in contact with THR 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C ARG* 3.5 15.6 - - + +
592C PRO* 3.7 34.3 - - + -
622C PHE* 3.5 14.7 - - - -
647C PHE* 3.9 14.9 - - + -
660C ILE* 2.8 23.8 + - - +
661C SER* 3.5 8.5 - - - -
663C GLY* 1.3 74.1 - - - +
665C GLU* 1.3 61.0 + - - +
667C ALA* 3.2 4.1 + - - +
668C LEU* 2.8 43.7 + - + +
683C VAL* 4.0 9.4 - - + -
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Residues in contact with GLU 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C SER 2.9 17.3 + - - +
662C LYS* 3.6 8.7 + - - +
664C THR* 1.3 78.2 - - - +
666C LYS* 1.3 61.9 + - - +
668C LEU* 3.4 7.4 + - - +
669C SER* 3.2 28.6 + - - +
683C VAL* 4.4 10.7 - - + +
860D GLY* 4.2 14.4 - - - +
863D VAL* 3.6 37.1 + - + +
864D LYS* 4.7 15.0 - - - +
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Residues in contact with LYS 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C ALA* 3.4 21.4 + - + +
624C SER* 3.4 29.1 + - - +
625C THR* 3.6 26.9 - - + -
662C LYS 3.2 5.5 + - - +
663C GLY 3.8 2.9 - - - +
664C THR 3.2 0.2 - - - -
665C GLU* 1.3 79.2 - - - +
667C ALA* 1.3 61.7 + - - +
669C SER* 3.3 9.0 + - - -
670C LYS* 3.1 30.7 + - - +
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Residues in contact with ALA 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ILE* 3.7 24.0 - - + +
621C ALA* 4.1 13.6 - - - +
622C PHE* 4.3 4.0 - - + -
647C PHE* 3.5 29.4 - - + -
663C GLY 2.9 17.5 + - - +
664C THR 3.5 4.5 - - - +
666C LYS* 1.3 76.3 - - - +
668C LEU* 1.3 58.2 + - - +
670C LYS* 3.3 4.2 + - - +
671C LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C PRO* 3.8 31.6 - - + -
594C VAL* 4.2 16.8 - - + -
645C ILE* 4.3 11.4 - - + -
647C PHE* 4.2 17.7 - - + -
664C THR* 2.8 32.0 + - + +
665C GLU* 3.8 5.8 - - - +
666C LYS 3.3 0.2 - - - -
667C ALA* 1.3 70.2 - - - +
669C SER* 1.3 66.0 + - - +
671C LEU* 3.3 11.8 + - + +
672C HIS* 3.0 23.2 + - - +
678C MET* 3.6 4.7 - - + +
680C ILE* 3.9 35.1 - - + +
683C VAL* 4.6 8.7 - - + -
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Residues in contact with SER 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665C GLU* 3.2 18.0 + - - +
666C LYS* 3.3 13.1 + - - -
668C LEU* 1.3 75.4 - - - +
670C LYS* 1.3 61.0 + - - +
672C HIS* 3.2 20.8 + - - +
673C GLU* 3.4 15.1 + - - +
680C ILE* 4.5 6.0 - - - +
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Residues in contact with LYS 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C VAL* 4.2 14.4 - - + +
618C ILE* 4.7 7.0 - - + -
621C ALA* 3.8 25.1 - - + -
666C LYS* 3.1 22.2 + - - +
667C ALA 3.4 9.0 - - - +
669C SER* 1.3 73.6 - - - +
671C LEU* 1.3 64.8 + - - +
673C GLU* 3.0 55.5 + - - +
674C TYR* 3.4 28.0 - - + -
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Residues in contact with LEU 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605C VAL* 4.2 11.9 - - + -
608C TRP* 3.6 35.2 - - + -
609C LEU* 4.0 11.4 - - + -
618C ILE* 4.0 8.2 - - + +
645C ILE* 4.0 25.4 - - + -
647C PHE* 6.2 0.9 - - + -
667C ALA 3.0 13.8 + - - +
668C LEU* 3.6 14.8 - - + +
670C LYS* 1.3 75.4 - - - +
672C HIS* 1.3 57.3 + - - +
674C TYR* 3.0 11.9 + - - +
675C PHE* 2.9 39.4 + - + +
678C MET* 3.6 27.4 - - + -
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Residues in contact with HIS 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C LEU 3.0 12.8 + - - +
669C SER* 3.3 15.9 + - - +
670C LYS 3.2 0.2 - - - -
671C LEU* 1.3 77.7 - - - +
673C GLU* 1.3 60.1 + - - +
674C TYR 3.2 0.2 - - - -
675C PHE 3.5 14.1 - - - -
676C PRO* 3.2 44.2 + - + +
678C MET* 3.0 37.6 + - + +
680C ILE* 4.5 9.4 - - + -
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Residues in contact with GLU 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C SER* 3.4 9.6 + - - +
670C LYS* 3.0 53.4 + - - +
672C HIS* 1.3 78.5 - - - +
674C TYR* 1.3 64.1 + - + +
676C PRO* 4.3 6.6 - - - +
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Residues in contact with TYR 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C TRP* 3.4 42.0 - + + -
617C VAL* 3.8 20.4 - - + +
670C LYS* 3.4 34.2 - - + +
671C LEU* 3.0 8.1 + - - +
673C GLU* 1.3 85.6 - - + +
675C PHE* 1.3 81.6 + - + +
676C PRO* 3.6 6.3 - - - +
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Residues in contact with PHE 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C LEU* 4.5 9.9 - - + -
601C ASP 5.6 0.2 - - - -
604C GLU* 3.9 29.2 - - + -
605C VAL* 3.7 30.1 - - + -
608C TRP* 3.9 43.1 - + + -
671C LEU* 2.9 29.0 + - + +
672C HIS* 3.3 10.9 - - - +
674C TYR* 1.3 96.6 - - + +
676C PRO* 1.3 59.8 - - - +
677C GLU* 3.1 5.8 - - + +
678C MET* 3.0 35.6 + - + +
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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