Contacts of the helix formed by residues 664 - 682 (chain C) in PDB entry 3P23
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 GLU 664 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C GLY 5.3 1.4 - - - +
663C LEU* 1.3 83.0 - - + +
665C PRO* 1.3 61.1 - - + +
666C ILE* 3.8 11.2 - - + -
667C THR* 2.6 47.6 + - + +
668C LEU 2.7 21.5 + - - -
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Residues in contact with PRO 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C TYR* 3.2 28.2 - - + +
661C LEU* 4.9 8.1 - - + -
663C LEU 3.5 2.9 - - - +
664C GLU* 1.3 85.2 - - + +
666C ILE* 1.3 62.8 + - + +
668C LEU* 3.1 21.6 - - + +
669C LEU* 3.1 15.6 + - - +
767C VAL* 4.2 19.9 - - + +
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Residues in contact with ILE 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C GLU* 3.8 17.5 - - + -
665C PRO* 1.3 79.8 - - + +
667C THR* 1.3 67.5 + - + +
669C LEU* 3.4 6.8 + - - +
670C GLN* 3.0 20.1 + - - +
831C PHE* 3.3 54.1 - - + +
832C PHE* 3.5 23.7 - - + +
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Residues in contact with THR 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LEU* 4.2 7.3 - - - +
664C GLU* 2.6 52.2 + - + +
666C ILE* 1.3 80.3 - - + +
668C LEU* 1.3 57.5 + - - +
670C GLN* 3.3 20.6 - - - +
671C GLN* 2.7 46.3 + - - +
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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
----------------------------------------------------------
649C LEU* 3.5 28.9 - - + -
652C TYR* 4.3 11.4 - - + -
663C LEU* 3.5 24.2 - - + -
664C GLU 2.7 14.9 + - - +
665C PRO* 3.1 15.7 - - + +
667C THR* 1.3 73.4 + - - +
669C LEU* 1.3 73.2 + - + +
671C GLN* 3.4 6.7 + - - +
672C THR* 3.0 38.6 + - - +
694C ILE* 4.6 3.4 - - + -
696C ILE* 4.1 17.5 - - + -
707C ALA* 3.6 25.3 - - + +
767C VAL* 5.2 1.1 - - + -
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Residues in contact with LEU 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C PRO 3.1 8.7 + - - +
666C ILE* 3.4 10.3 - - - +
668C LEU* 1.3 84.3 - - + +
670C GLN* 1.3 54.3 + - - +
672C THR* 3.3 7.3 + - - -
673C THR* 2.6 38.2 + - - -
763C VAL* 4.7 4.3 - - + +
764C PHE* 3.4 64.3 - - + +
767C VAL* 3.5 40.8 - - + -
768C ILE* 4.2 5.6 - - + -
831C PHE* 3.7 17.9 - - + -
832C PHE* 4.1 2.0 - - + -
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Residues in contact with GLN 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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666C ILE* 3.0 11.3 + - - +
667C THR* 3.1 24.1 + - - +
669C LEU* 1.3 76.2 - - - +
671C GLN* 1.3 66.2 + - - +
673C THR* 3.2 4.4 + - - -
674C SER* 3.0 20.0 + - - -
827C LEU* 3.6 16.3 + - + +
832C PHE* 3.5 50.3 + - + +
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Residues in contact with GLN 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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624C ASN* 3.2 39.6 - - + +
663C LEU* 3.3 23.3 - - - +
667C THR* 2.7 28.7 + - - +
668C LEU* 3.8 3.1 - - - +
670C GLN* 1.3 74.4 - - + +
672C THR* 1.3 64.7 + - - +
674C SER* 3.1 7.6 + - - -
675C GLY 3.1 19.6 + - - -
705C ILE 5.1 0.8 + - - -
706C LYS* 4.2 10.5 - - - +
707C ALA* 3.2 27.5 + - + +
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Residues in contact with THR 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C ASN* 5.2 2.5 - - - -
668C LEU* 3.0 21.7 + - - +
669C LEU* 3.5 11.4 - - - +
671C GLN* 1.3 76.0 - - - +
673C THR* 1.3 64.0 + - - +
675C GLY* 3.6 1.7 + - - -
676C LEU* 3.1 21.9 + - + +
689C LEU* 4.5 12.3 - - + -
694C ILE* 3.6 42.8 - - + +
707C ALA* 4.8 4.4 + - - +
708C MET* 6.4 0.2 - - - +
709C ILE* 3.9 21.1 - - + +
760C ALA* 6.2 1.3 - - + -
763C VAL* 5.7 3.4 - - + -
764C PHE* 5.8 4.3 - - + -
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Residues in contact with THR 673 (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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669C LEU 2.6 21.7 + - - -
670C GLN* 3.6 5.6 - - - -
671C GLN 3.2 0.2 - - - -
672C THR* 1.3 77.3 - - - +
674C SER* 1.3 58.1 + - - +
676C LEU* 3.3 12.1 + - + +
677C ALA* 2.9 26.0 + - - +
760C ALA* 5.9 0.3 - - - +
764C PHE* 3.2 23.6 - - + -
823C ALA* 3.6 27.6 - - + +
826C VAL* 3.6 21.3 - - + -
827C LEU* 3.7 12.3 - - + -
832C PHE* 4.1 1.4 - - - -
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Residues in contact with SER 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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622C HIS* 2.9 27.7 + - - -
624C ASN* 4.8 0.4 - - - -
670C GLN* 3.0 12.8 + - - -
671C GLN* 3.1 11.2 + - - -
673C THR* 1.3 72.9 - - - +
675C GLY* 1.3 59.8 + - - +
676C LEU 3.0 1.1 - - - -
677C ALA* 2.8 6.6 + - - +
678C HIS* 2.8 27.7 + - - +
827C LEU* 3.8 20.2 - - - +
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Residues in contact with GLY 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C HIS* 3.4 13.9 + - - -
624C ASN 4.5 3.8 - - - -
625C VAL* 3.5 19.6 - - - +
671C GLN 3.1 9.3 + - - -
672C THR 4.0 2.9 - - - -
674C SER* 1.3 78.9 - - - +
676C LEU* 1.3 56.0 + - - +
678C HIS* 3.3 3.4 - - - +
679C LEU* 2.9 33.6 + - - +
709C ILE* 3.7 9.4 - - - -
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Residues in contact with LEU 676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C THR* 3.1 14.5 + - + +
673C THR* 3.5 15.0 - - + +
674C SER 3.0 0.8 - - - -
675C GLY* 1.3 75.6 - - - +
677C ALA* 1.3 63.6 + - - +
678C HIS 3.2 0.4 - - - -
679C LEU* 3.4 6.6 + - + +
680C HIS* 3.1 49.7 + - + +
686C HIS* 4.3 11.9 - - + -
689C LEU* 4.4 22.9 - - + -
709C ILE* 3.9 11.0 - - + +
756C ASP* 3.4 44.4 - - + +
757C ILE* 4.6 7.2 - - + -
760C ALA* 4.6 9.2 - - + -
823C ALA* 4.8 4.3 - - + -
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Residues in contact with ALA 677 (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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673C THR 2.9 12.8 + - - +
674C SER* 2.8 10.6 + - - +
676C LEU* 1.3 73.6 - - - +
678C HIS* 1.3 60.0 + - - +
680C HIS* 3.3 3.2 + - - +
681C SER* 2.8 31.6 + - - -
823C ALA* 3.5 21.7 - - + +
824C LYS* 4.0 26.6 - - + +
827C LEU* 4.2 11.0 - - + -
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Residues in contact with HIS 678 (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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616C LEU* 3.7 30.7 + - + +
619C SER* 4.0 21.9 + - - -
620C ASP* 4.9 3.3 - - + -
621C GLU* 4.6 14.7 + - - -
622C HIS* 3.7 41.5 + - + +
625C VAL* 4.1 6.1 - - + -
674C SER 2.8 11.5 + - - +
675C GLY* 3.3 10.5 - - - +
677C ALA* 1.3 75.2 - - - +
679C LEU* 1.3 65.4 + - - +
681C SER* 2.5 27.2 + - - -
682C LEU* 3.3 14.3 + - + +
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Residues in contact with LEU 679 (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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616C LEU* 4.0 21.1 - - + -
625C VAL* 3.9 15.9 - - + -
675C GLY 2.9 26.7 + - - +
676C LEU* 3.6 11.9 - - + +
677C ALA 3.3 0.4 - - - -
678C HIS* 1.3 78.6 - - - +
680C HIS* 1.3 63.3 + - + +
682C LEU* 3.1 11.0 + - - -
684C ILE* 2.8 73.5 + - + +
686C HIS* 5.4 6.3 - - + +
709C ILE* 3.4 24.0 - - + -
712C PHE* 4.7 15.0 - - + -
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Residues in contact with HIS 680 (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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676C LEU* 3.1 43.4 + - + +
677C ALA* 3.8 4.5 - - - +
678C HIS 3.3 0.2 - - - -
679C LEU* 1.3 76.3 - - - +
681C SER* 1.3 58.4 + - - +
683C ASN* 2.8 22.8 + - - +
684C ILE 3.3 21.8 - - - +
685C VAL* 4.6 1.8 - - + -
753C TYR* 3.6 40.0 - - + +
756C ASP* 3.1 27.0 + - + +
757C ILE* 4.3 4.9 - - + -
823C ALA* 3.5 19.2 + - + +
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Residues in contact with SER 681 (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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677C ALA 2.8 13.8 + - - -
678C HIS* 2.5 32.1 + - - -
680C HIS* 1.3 76.6 - - - +
682C LEU* 1.3 68.1 + - - +
683C ASN* 3.2 6.7 + - - -
824C LYS* 6.4 1.3 - - - -
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Residues in contact with LEU 682 (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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615C LEU* 3.8 46.8 - - + +
616C LEU* 3.6 31.6 - - + -
619C SER* 3.8 26.9 - - - +
678C HIS* 3.6 16.6 - - + +
679C LEU 3.1 8.2 + - - +
681C SER* 1.3 85.4 + - - +
683C ASN* 1.3 72.4 + - - +
684C ILE* 3.3 9.8 + - + -
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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