Contacts of the helix formed by residues 724 - 742 (chain C) in PDB entry 3CMM
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 ASN 724 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 2.7 29.0 + - - +
146A SER* 3.8 17.8 - - - -
721C ASP* 2.8 16.7 + - + +
723C TYR* 1.3 77.2 - - - +
725C ASN* 1.3 54.7 + - - +
726C ASP* 3.1 14.2 + - - +
727C HIS* 2.8 36.8 + - + +
728C PHE* 2.7 34.0 + - - +
843C GLN* 3.2 23.3 + - - +
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Residues in contact with ASN 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 4.5 0.7 - - - +
121A SER* 6.1 0.3 - - - -
143A PHE* 3.4 20.7 - - + -
146A SER* 3.2 28.6 + - - +
147A SER* 3.3 27.7 + - - +
723C TYR 3.4 4.3 + - - -
724C ASN* 1.3 70.9 + - - +
726C ASP* 1.3 64.4 + - - +
728C PHE* 4.0 5.9 - - - +
729C HIS* 3.0 64.4 + - - +
852C ARG* 5.3 2.6 - - - +
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Residues in contact with ASP 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 4.2 16.1 - - - +
724C ASN* 3.1 1.9 + - - +
725C ASN* 1.3 83.1 + - - +
727C HIS* 1.3 66.2 + - - +
730C PHE* 3.1 16.8 + - - +
835C THR* 5.3 0.7 - - - +
836C ALA* 3.6 15.9 - - - +
839C ASN* 3.3 36.5 + - + +
840C CYS* 3.3 22.6 - - - -
843C GLN* 2.9 29.9 + - - +
849C THR* 4.1 7.6 - - - +
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Residues in contact with HIS 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PHE* 3.8 29.0 - + + -
718C LEU* 4.2 11.9 - - + +
719C GLU 3.8 17.7 - - - -
720C PHE* 3.7 24.3 - - + -
721C ASP* 3.0 37.0 + - + +
724C ASN* 2.8 26.9 + - + +
726C ASP* 1.3 77.4 - - - +
728C PHE* 1.3 64.0 + - - +
730C PHE* 3.1 13.7 + - - +
731C VAL* 3.3 9.2 + - - +
840C CYS* 4.3 3.6 - - - -
843C GLN* 2.7 29.0 + - - -
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Residues in contact with PHE 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.5 34.5 - - + -
143A PHE* 5.6 3.4 - + + -
720C PHE* 4.6 5.4 - - - -
722C ILE* 3.3 50.2 + - + +
723C TYR 5.3 0.2 - - - -
724C ASN 2.7 16.9 + - - +
725C ASN* 4.0 6.1 - - - +
727C HIS* 1.3 73.4 - - - +
729C HIS* 1.3 75.6 + + - +
731C VAL* 3.3 4.9 + - - +
732C VAL* 3.1 52.5 + - + +
753C PRO* 4.1 14.1 - - + -
755C VAL* 4.1 24.5 - - + -
758C TYR* 4.6 9.6 - + + -
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Residues in contact with HIS 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 4.2 16.9 - - + +
725C ASN* 3.0 49.3 + - - +
728C PHE* 1.3 94.1 - + - +
730C PHE* 1.3 66.6 + - - +
732C VAL* 4.3 5.1 - - - +
733C ALA* 2.9 28.4 + - - +
753C PRO* 5.3 6.3 - - + -
832C GLU* 2.9 31.2 + - + +
836C ALA* 3.8 15.8 - - + +
852C ARG* 3.7 24.2 + - - +
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Residues in contact with PHE 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C LEU* 5.2 0.4 - - + -
623C TYR* 4.6 8.1 - + - -
675C TRP* 6.2 1.1 - + - -
676C ALA* 3.4 27.4 - - + -
679C GLU* 4.4 11.4 - - + -
680C PHE* 3.7 26.0 - + + -
683C LYS* 5.2 2.0 - - + -
684C PHE* 3.6 26.2 - + - -
726C ASP 3.1 19.1 + - - +
727C HIS* 3.1 7.4 + - - +
729C HIS* 1.3 78.3 - - - +
731C VAL* 1.3 58.8 + - + +
734C GLY* 2.9 26.4 + - - -
833C PHE* 3.7 34.8 - + - -
836C ALA* 3.4 7.3 - - + +
837C CYS* 3.7 30.7 - - + -
840C CYS* 4.3 4.7 - - - -
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Residues in contact with VAL 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C ILE* 4.0 19.1 - - + +
676C ALA* 3.7 15.7 - - + +
677C ARG* 4.1 20.9 - - - +
680C PHE* 5.0 0.4 - - + -
720C PHE* 3.6 35.0 - - + -
722C ILE* 6.0 1.3 - - + -
727C HIS 3.3 0.9 + - - +
728C PHE* 3.3 8.5 + - + +
730C PHE* 1.3 78.1 - - + +
732C VAL* 1.3 57.8 + - - +
735C ALA* 2.7 37.2 + - - +
758C TYR* 3.7 23.1 - - + -
762C ILE* 4.0 9.4 - - + -
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Residues in contact with VAL 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C PHE* 3.1 47.7 + - + +
729C HIS* 4.1 6.5 - - - +
731C VAL* 1.3 75.0 - - - +
733C ALA* 1.3 58.9 + - - +
735C ALA* 3.8 1.6 - - - +
736C SER* 3.0 31.0 + - - +
748C ASP* 3.7 22.2 - - - +
753C PRO* 4.0 13.5 - - + -
758C TYR* 3.7 27.2 + - + +
829C HIS* 4.8 3.6 - - + +
832C GLU* 3.9 17.0 - - - +
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Residues in contact with ALA 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C HIS 2.9 18.2 + - - +
732C VAL* 1.3 75.4 - - - +
734C GLY* 1.3 65.9 + - - +
736C SER* 3.4 0.5 + - - -
737C LEU* 3.0 29.8 + - - +
829C HIS* 3.8 9.2 - - - +
832C GLU* 3.6 22.9 - - - +
833C PHE* 3.6 35.9 - - + +
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Residues in contact with GLY 734 (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 PHE* 3.9 8.8 - - - -
675C TRP* 3.8 6.2 - - - -
676C ALA* 4.1 12.1 - - - -
730C PHE* 2.9 20.0 + - - -
731C VAL 3.8 0.2 - - - -
733C ALA* 1.3 78.5 - - - +
735C ALA* 1.3 60.7 + - - +
738C ARG* 3.0 26.5 + - - +
833C PHE* 3.9 16.9 - - - -
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Residues in contact with ALA 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C PHE* 3.7 21.8 - - + -
672C CYS* 3.5 33.9 - - - +
673C ILE* 3.9 12.1 - - + +
676C ALA* 3.8 1.2 - - - +
731C VAL 2.7 23.0 + - - +
732C VAL 3.8 2.2 - - - +
734C GLY* 1.3 73.9 - - - +
736C SER* 1.3 56.3 + - - +
738C ARG* 3.4 0.4 + - - -
739C ALA* 2.8 31.0 + - - +
758C TYR* 4.3 1.6 - - + -
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Residues in contact with SER 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C PHE* 3.7 17.0 - - - -
732C VAL 3.0 19.2 + - - -
733C ALA 4.2 0.2 - - - -
735C ALA* 1.3 76.7 - - - +
737C LEU* 1.3 56.6 + - - +
739C ALA* 3.6 3.1 - - - +
740C TYR* 3.0 27.0 + - - +
746C SER* 4.2 10.2 + - - -
748C ASP* 3.5 19.8 + - - -
829C HIS* 3.8 32.8 + - - -
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Residues in contact with LEU 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C PHE* 3.7 17.7 - - + -
624C PHE* 3.5 38.6 - - + -
733C ALA 3.0 22.1 + - - +
736C SER* 1.3 73.5 - - - +
738C ARG* 1.3 61.3 + - - +
740C TYR* 3.2 8.5 + - + +
741C ASN* 2.9 31.9 + - - -
819C VAL* 3.8 24.4 - - + +
828C ASN 3.9 9.4 - - - +
829C HIS* 3.9 12.6 - - + +
830C HIS* 3.8 21.1 - - + +
833C PHE* 3.8 18.2 - - + -
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Residues in contact with ARG 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C TYR 5.8 2.0 + - - -
624C PHE* 3.7 6.6 - - - -
660C ASP 4.9 1.8 + - - -
661C SER* 4.9 6.7 + - - +
664C SER* 2.8 35.0 + - - -
666C PRO* 3.7 11.6 - - + +
672C CYS* 3.9 21.1 - - + -
675C TRP* 3.3 66.9 - - + +
734C GLY 3.0 18.9 + - - +
735C ALA 3.5 4.0 - - - +
737C LEU* 1.3 76.5 - - - +
739C ALA* 1.3 62.9 + - - +
741C ASN* 2.9 20.5 + - - +
742C TYR* 3.1 50.0 + - + -
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Residues in contact with ALA 739 (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 PHE* 3.6 25.6 - - + -
672C CYS* 3.6 14.5 - - - -
735C ALA 2.8 20.9 + - - +
736C SER* 3.6 6.3 - - - +
738C ARG* 1.3 72.5 - - - +
740C TYR* 1.3 60.4 + - - +
742C TYR 3.5 0.9 + - - +
743C GLY 3.2 2.6 + - - -
744C ILE* 2.7 52.5 + - + +
746C SER* 4.9 2.0 - - - -
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Residues in contact with TYR 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736C SER 3.0 13.8 + - - +
737C LEU* 3.3 13.0 - - + +
739C ALA* 1.3 74.9 - - - +
741C ASN* 1.3 67.9 + - - +
742C TYR 3.1 0.7 + - - -
743C GLY* 3.3 11.1 + - - +
744C ILE 4.8 0.9 - - - -
817C GLU* 3.5 48.5 + - + +
818C PRO 4.4 2.4 + - - -
819C VAL* 3.7 33.0 - - + -
820C ASP 5.7 0.9 + - - -
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Residues in contact with ASN 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C TYR 3.6 5.5 - - - +
624C PHE* 3.2 49.7 + - - -
627C SER* 5.6 0.3 - - - -
628C ALA* 4.5 7.2 - - - +
737C LEU 2.9 12.7 + - - +
738C ARG* 2.9 11.3 + - - +
740C TYR* 1.3 74.9 - - - +
742C TYR* 1.3 73.8 + - + +
743C GLY 3.8 0.3 + - - -
815C LYS 4.6 0.5 - - - +
816C LEU* 3.5 14.6 - - + +
817C GLU* 2.5 55.1 + - - +
818C PRO* 4.0 0.6 - - - +
819C VAL* 3.9 8.1 - - - +
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Residues in contact with TYR 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C SER* 2.7 45.9 + - - -
662C LEU* 6.1 0.4 - - + -
665C LYS* 3.8 16.8 - - + -
666C PRO* 3.4 39.3 - - + +
738C ARG* 3.1 47.9 + - + +
739C ALA 3.5 0.2 + - - -
741C ASN* 1.3 88.8 - - + +
743C GLY* 1.3 61.0 + - - +
744C ILE* 3.3 16.5 + - + +
814C PHE* 4.0 22.6 - + + -
815C LYS 5.8 0.9 - - - -
816C LEU* 3.4 27.8 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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