Contacts of the helix formed by residues 608 - 625 (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 LYS 608 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C THR* 3.3 38.1 + - - +
184C GLY* 6.0 0.4 - - - -
185C MET* 6.1 1.6 - - + -
607C ASN* 1.3 95.0 - - - +
609C ILE* 1.3 62.3 + - - +
610C ASP* 4.0 19.7 - - + +
611C HIS* 2.9 43.1 + - + +
612C THR* 3.3 6.1 + - - -
847C ILE* 4.0 10.3 - - - +
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Residues in contact with ILE 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LYS* 1.3 68.9 - - - +
610C ASP* 1.3 75.5 + - - +
612C THR* 3.2 23.0 + - + +
613C ILE* 3.0 42.8 + - + +
838C SER* 4.1 0.7 - - - +
839C ASN* 4.0 13.9 - - - +
842C ALA* 3.9 15.0 - - + -
847C ILE* 3.8 6.0 - - + +
848C GLU 3.3 26.5 - - - +
850C ALA* 4.0 12.8 - - + +
854C LYS* 4.4 25.4 - - + -
858C ILE* 4.7 3.8 - - + -
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Residues in contact with ASP 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C ILE* 4.2 9.1 - - + +
608C LYS* 4.0 20.3 - - + +
609C ILE* 1.3 84.7 - - - +
611C HIS* 1.3 68.7 + - + +
613C ILE* 4.0 1.4 - - - +
614C ALA* 3.2 24.9 + - - +
858C ILE* 3.5 37.1 - - + +
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Residues in contact with HIS 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C ILE* 3.6 31.5 - - + +
601C THR* 4.3 12.6 + - - +
602C LEU* 3.9 18.8 - - + +
606C PRO* 3.8 20.0 - - + -
607C ASN* 3.0 44.4 + - - -
608C LYS* 2.9 31.1 + - + +
610C ASP* 1.3 79.2 - - + +
612C THR* 1.3 63.2 + - - +
614C ALA* 3.6 3.3 + - - +
615C TRP* 3.3 21.5 + - - +
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Residues in contact with THR 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C PRO* 4.8 2.3 - - - +
608C LYS 3.3 7.6 + - - -
609C ILE* 3.2 28.6 + - + +
611C HIS* 1.3 78.1 - - - +
613C ILE* 1.3 59.6 - - - +
615C TRP* 3.4 10.1 - - - +
616C ALA* 3.0 26.7 + - - +
838C SER* 2.8 47.2 + - - +
841C ARG* 3.2 28.2 - - - +
842C ALA* 3.5 9.2 + - + -
847C ILE* 4.4 7.9 - - - +
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Residues in contact with ILE 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ILE* 3.0 35.1 + - + +
610C ASP 4.0 2.7 - - - +
612C THR* 1.3 72.3 - - - +
614C ALA* 1.3 56.3 + - - +
615C TRP 3.1 1.1 - - - -
616C ALA* 3.1 2.2 + - - +
617C LYS* 2.7 34.5 + - - +
834C ILE* 4.4 1.7 - - + +
838C SER* 3.2 25.6 - - - +
850C ALA* 5.1 1.3 - - + -
854C LYS* 4.9 1.3 - - + -
855C THR* 3.8 37.5 - - + +
858C ILE* 4.1 25.4 - - + -
859C ALA* 3.9 36.1 - - + +
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Residues in contact with ALA 614 (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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597C ILE* 4.2 17.5 - - + -
602C LEU* 4.4 13.5 - - + -
610C ASP 3.2 16.1 + - - +
611C HIS 3.8 4.0 - - - +
613C ILE* 1.3 79.2 - - - +
615C TRP* 1.3 64.4 + - - +
617C LYS* 3.2 8.2 + - - +
618C SER* 2.9 25.3 + - - -
858C ILE* 5.7 0.8 - - + +
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Residues in contact with TRP 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU* 3.6 32.9 - - + +
603C ARG* 4.7 6.2 + - - +
611C HIS 3.3 11.6 + - - +
612C THR 3.4 9.6 - - - +
613C ILE 3.1 0.4 - - - -
614C ALA* 1.3 78.7 - - - +
616C ALA* 1.3 78.9 + - + +
618C SER* 3.3 7.8 + - - -
619C LEU* 3.0 41.0 + - + +
683C LYS* 4.0 26.2 - - + -
684C PHE* 3.8 26.0 - + - -
837C CYS* 3.5 23.1 - - - -
841C ARG* 3.3 47.3 - - + +
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Residues in contact with ALA 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C THR 3.0 14.1 + - - +
613C ILE 3.1 4.2 + - - +
615C TRP* 1.3 78.7 - - + +
617C LYS* 1.3 56.4 + - - +
619C LEU* 3.2 3.1 + - - +
620C PHE* 3.0 29.2 + - - +
833C PHE* 4.4 3.6 - - - -
834C ILE* 3.6 16.8 - - + +
837C CYS* 3.6 20.2 - - + -
838C SER* 3.5 30.5 - - - +
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Residues in contact with LYS 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ILE 2.7 20.9 + - - +
614C ALA* 3.5 8.3 - - - +
616C ALA* 1.3 71.8 - - - +
618C SER* 1.3 59.2 + - - +
620C PHE* 3.1 10.2 + - + +
621C GLN* 2.9 37.6 + - + +
821C PHE* 4.7 16.0 - - + -
834C ILE* 4.4 13.2 - - + +
859C ALA* 2.9 45.1 + - + +
861C ARG* 4.2 18.6 - - - +
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Residues in contact with SER 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU* 6.0 3.8 - - - -
614C ALA 2.9 16.2 + - - -
615C TRP* 3.4 9.2 - - - -
617C LYS* 1.3 76.6 - - - +
619C LEU* 1.3 57.1 + - - +
621C GLN* 3.4 9.7 - - - +
622C GLY* 3.2 21.7 + - - -
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Residues in contact with LEU 619 (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 TRP* 3.0 39.9 + - + +
616C ALA 3.5 5.8 - - - +
617C LYS 3.1 0.2 - - - -
618C SER* 1.3 75.2 - - - +
620C PHE* 1.3 60.5 + - - +
622C GLY* 3.5 1.4 + - - +
623C TYR* 2.9 67.2 + - + +
683C LYS* 4.1 26.9 - - + +
730C PHE* 5.2 1.6 - - + -
833C PHE* 4.8 1.1 - - + -
837C CYS* 3.7 25.6 - - - -
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Residues in contact with PHE 620 (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 ALA 3.0 11.9 + - - +
617C LYS* 3.4 11.0 - - + +
619C LEU* 1.3 74.0 - - - +
621C GLN* 1.3 73.9 + - + +
624C PHE* 3.1 50.1 + + - +
625C THR* 4.0 5.1 + - - -
737C LEU* 3.7 20.9 - - + -
819C VAL* 3.6 26.0 - - + -
821C PHE* 3.4 40.6 - + + -
830C HIS* 3.8 19.3 - + + -
833C PHE* 3.8 25.3 - + + -
834C ILE* 4.0 19.3 - - + -
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Residues in contact with GLN 621 (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 LYS* 2.9 22.4 + - + +
618C SER* 3.4 14.1 - - - +
620C PHE* 1.3 84.4 - - + +
622C GLY* 1.3 54.8 + - - +
625C THR* 2.8 42.5 + - - +
626C ASP* 2.8 48.4 + - - +
821C PHE* 6.1 1.8 - - + +
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Residues in contact with GLY 622 (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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618C SER 3.2 10.1 + - - -
619C LEU* 3.9 2.5 - - - -
620C PHE 3.2 0.8 - - - -
621C GLN* 1.3 79.0 - - - +
623C TYR* 1.3 64.8 + - - +
626C ASP* 4.1 14.5 + - - +
627C SER* 2.9 27.2 + - - -
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Residues in contact with TYR 623 (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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619C LEU* 2.9 47.1 + - + +
622C GLY* 1.3 73.8 - - - +
624C PHE* 1.3 83.7 - + + +
625C THR 3.7 0.2 - - - -
627C SER* 3.3 21.1 + - - -
675C TRP* 3.6 26.7 - + + -
679C GLU* 2.6 42.0 + - + +
683C LYS* 3.6 21.6 - - + +
730C PHE* 4.6 5.9 - + - -
738C ARG* 5.8 1.9 + - - -
741C ASN* 3.6 7.3 - - - +
833C PHE* 3.8 26.9 - + - -
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Residues in contact with PHE 624 (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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620C PHE* 3.1 34.7 + + + +
623C TYR* 1.3 108.7 - + + +
625C THR* 1.3 61.6 + - - +
628C ALA* 5.0 2.0 - - - -
675C TRP* 3.8 23.3 - + - -
734C GLY* 4.1 3.4 - - - -
737C LEU* 3.5 40.6 - - + -
738C ARG* 3.7 12.1 - - - -
741C ASN* 3.2 26.8 + - - +
818C PRO* 3.7 1.6 - - - +
819C VAL* 2.8 43.2 + - + -
833C PHE* 3.9 23.3 - + - -
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Residues in contact with THR 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C PHE* 4.9 4.9 + - - -
621C GLN* 2.8 32.3 + - - +
624C PHE* 1.3 80.5 - - - +
626C ASP* 1.3 66.1 + - - +
627C SER 3.3 1.6 - - - -
628C ALA* 3.1 5.9 + - - +
629C GLU* 3.0 51.8 + - - +
818C PRO* 3.9 5.2 - - + +
819C VAL* 2.5 33.3 + - - +
821C PHE* 5.1 1.4 + - - +
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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