Contacts of the helix formed by residues 608 - 625 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A THR* 5.5 14.4 - - + -
185A MET* 5.0 7.2 - - + -
607A ASN* 1.3 101.9 + - - +
609A ILE* 1.3 59.5 + - - +
610A ASP* 3.9 17.0 - - + +
611A HIS* 3.0 53.8 + - + +
612A THR 3.4 4.0 + - - -
847A ILE* 3.7 13.9 - - - +
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Residues in contact with ILE 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A LYS* 1.3 69.5 - - - +
610A ASP* 1.3 77.1 + - - +
612A THR* 3.2 17.8 + - - +
613A ILE* 3.0 31.5 + - + +
838A SER* 3.9 3.6 - - - +
839A ASN* 3.9 10.8 - - - +
842A ALA* 4.1 9.9 - - + -
847A ILE* 3.7 10.8 - - + +
848A GLU 3.4 22.9 - - - +
850A ALA* 3.7 29.8 - - + +
854A LYS* 4.0 26.5 - - + -
858A ILE* 4.6 3.8 - - + -
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Residues in contact with ASP 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ILE* 4.4 10.5 - - + +
608A LYS* 3.1 19.1 - - + +
609A ILE* 1.3 83.9 - - - +
611A HIS* 1.3 66.7 + - + +
613A ILE* 4.0 7.5 - - - +
614A ALA* 3.2 24.6 + - - +
858A ILE* 3.9 28.2 - - + +
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Residues in contact with HIS 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ILE* 3.7 30.4 - - + +
598A PRO* 5.9 0.9 - - + -
601A THR* 3.8 22.6 - - + +
602A LEU* 3.6 18.6 - - + +
606A PRO* 3.7 17.5 - - + -
607A ASN* 3.1 41.5 + - - -
608A LYS* 3.0 42.6 + - + +
610A ASP* 1.3 80.8 - - + +
612A THR* 1.3 57.4 + - - +
615A TRP* 3.2 26.7 + - - +
841A ARG* 5.9 0.2 - - - -
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Residues in contact with THR 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PRO* 3.9 17.7 - - + -
608A LYS 3.4 1.3 + - - +
609A ILE* 3.2 20.6 + - - +
611A HIS* 1.3 73.3 - - - +
613A ILE* 1.3 59.7 + - - +
615A TRP* 3.7 7.8 - - - +
616A ALA* 2.9 29.1 + - - +
838A SER* 2.7 35.5 + - - -
841A ARG* 3.3 29.4 - - + +
842A ALA* 4.0 9.1 - - - +
847A ILE* 4.0 15.5 - - + -
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A ILE* 3.0 33.3 + - + +
610A ASP 4.0 3.4 - - - +
611A HIS 3.4 0.2 - - - -
612A THR* 1.3 72.9 - - - +
614A ALA* 1.3 55.3 + - - +
616A ALA* 2.9 3.9 + - - +
617A LYS* 2.7 34.5 + - + +
834A ILE* 4.1 7.1 - - + +
838A SER* 3.2 20.6 + - - +
850A ALA* 5.2 0.9 - - + -
854A LYS 5.0 0.4 - - - -
855A THR* 3.9 25.4 - - + +
858A ILE* 3.8 43.7 - - + -
859A ALA* 3.7 31.9 - - + +
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ILE* 4.6 7.6 - - + -
602A LEU* 3.8 22.2 - - + -
610A ASP 3.2 17.2 + - - +
611A HIS 3.8 5.2 - - - +
612A THR 3.5 0.2 - - - -
613A ILE* 1.3 77.3 - - - +
615A TRP* 1.3 58.1 + - - +
617A LYS* 3.2 9.1 + - - +
618A SER* 3.0 29.3 + - - -
858A ILE* 5.7 0.4 - - - +
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Residues in contact with TRP 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 3.4 33.5 - - + +
603A ARG* 4.3 8.3 + - - +
611A HIS 3.2 15.8 + - - +
612A THR* 3.7 7.9 - - - +
613A ILE 3.2 0.4 - - - -
614A ALA* 1.3 78.5 - - - +
616A ALA* 1.3 71.9 + - + +
618A SER* 3.4 9.5 + - - -
619A LEU* 3.0 51.8 + - + +
683A LYS* 4.0 23.3 - - + -
684A PHE* 4.0 23.1 - + - -
687A ASP* 5.7 1.8 - - - -
837A CYS* 3.6 24.0 - - - -
841A ARG* 3.5 45.9 - - + +
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A THR 2.9 19.7 + - - +
613A ILE 3.4 3.8 - - - +
615A TRP* 1.3 83.6 - - + +
617A LYS* 1.3 58.1 + - - +
619A LEU* 3.6 1.8 - - - +
620A PHE* 3.0 28.6 + - - +
833A PHE* 4.1 4.2 - - - -
834A ILE* 3.6 17.7 - - + +
837A CYS* 3.8 14.1 - - + -
838A SER* 3.6 25.8 - - - +
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Residues in contact with LYS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ILE* 2.7 19.5 + - + +
614A ALA* 3.2 8.9 + - - +
616A ALA* 1.3 70.9 - - - +
618A SER* 1.3 62.4 + - - +
620A PHE* 3.6 8.2 + - + +
621A GLN* 3.1 45.3 + - - +
821A PHE* 4.4 19.7 - - + -
834A ILE* 4.3 22.9 - - + +
859A ALA* 3.2 35.1 + - + +
861A ARG* 5.1 9.7 - - - +
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Residues in contact with SER 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ALA 3.0 13.0 + - - -
615A TRP* 3.5 9.9 + - - -
617A LYS* 1.3 74.5 - - - +
619A LEU* 1.3 64.2 + - - +
621A GLN* 3.3 11.2 + - - +
622A GLY* 2.8 25.5 + - - -
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A TRP* 3.0 49.0 + - + +
616A ALA* 3.6 5.8 - - - +
618A SER* 1.3 80.8 + - - +
620A PHE* 1.3 55.6 + - - +
622A GLY* 3.1 3.5 + - - -
623A TYR* 2.8 63.9 + - + +
683A LYS* 3.7 34.1 - - + +
730A PHE* 5.4 0.9 - - + -
833A PHE* 4.9 0.2 - - + -
837A CYS* 3.7 17.0 - - - -
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Residues in contact with PHE 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ALA 3.0 18.2 + - - +
617A LYS* 3.6 9.9 - - + +
619A LEU* 1.3 76.6 - - - +
621A GLN* 1.3 70.4 + - + +
623A TYR 3.2 0.2 + - - -
624A PHE* 3.0 56.1 + + + +
625A THR* 4.0 8.5 + - - -
737A LEU* 4.0 14.4 - - + -
819A VAL* 3.6 28.3 - - + -
821A PHE* 3.8 28.3 - + + -
830A HIS* 3.9 29.8 - + - -
833A PHE* 3.8 27.9 - + + -
834A ILE* 4.2 11.7 - - + -
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A LYS* 3.1 37.9 + - + +
618A SER* 3.7 10.9 - - - +
619A LEU 3.3 0.2 - - - -
620A PHE* 1.3 90.1 - - + +
622A GLY* 1.3 59.0 + - - +
625A THR* 3.1 20.6 + - + +
626A ASP* 2.8 46.3 + - - +
821A PHE* 5.8 4.0 - - + -
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Residues in contact with GLY 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A SER 2.8 18.3 + - - -
619A LEU* 3.4 4.5 - - - -
621A GLN* 1.3 76.9 - - - +
623A TYR* 1.3 54.5 + - - +
626A ASP* 4.2 10.0 + - - +
627A SER* 2.7 34.6 + - - -
657A SER* 5.5 0.5 + - - -
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Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A LEU* 2.8 37.7 + - + +
622A GLY* 1.3 72.2 - - - +
624A PHE* 1.3 84.0 + + + +
627A SER* 3.3 20.9 + - - -
675A TRP* 3.9 24.7 - + + -
679A GLU* 2.4 43.5 + - + +
683A LYS* 3.5 25.8 - - - +
730A PHE* 4.6 8.3 - + - -
738A ARG* 5.6 3.3 + - - -
741A ASN* 3.5 8.8 + - - -
833A PHE* 3.7 32.5 - + - -
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Residues in contact with PHE 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A PHE* 3.0 34.8 + + + +
623A TYR* 1.3 109.4 - + + +
625A THR* 1.3 61.4 + - - +
628A ALA* 4.5 3.0 - - - +
675A TRP* 4.0 15.9 - + - -
734A GLY* 4.0 9.2 - - - -
737A LEU* 3.6 40.8 - - + -
738A ARG* 3.9 9.0 - - + -
741A ASN* 3.1 33.0 - - - +
818A PRO* 3.7 2.8 - - - +
819A VAL* 2.9 42.1 + - + -
833A PHE* 4.0 20.4 - + - -
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Residues in contact with THR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A PHE* 4.6 6.4 - - - -
621A GLN* 3.1 29.6 + - + +
623A TYR 3.8 0.2 - - - -
624A PHE* 1.3 79.6 - - - +
626A ASP* 1.3 73.1 + - - +
627A SER 3.4 0.9 - - - -
628A ALA* 3.4 4.7 + - - +
629A GLU* 3.1 45.3 + - + +
818A PRO* 4.1 4.0 - - + +
819A VAL* 2.9 29.3 + - - +
821A PHE* 5.3 0.9 + - - +
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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
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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