Contacts of the helix formed by residues 685 - 695 (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 ASN 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680A PHE* 4.1 1.5 + - + +
681A GLU* 3.2 36.8 + - - +
683A LYS 3.7 0.2 - - - -
684A PHE* 1.3 80.6 - - - +
686A HIS* 1.3 77.9 + - - +
687A ASP 3.5 1.1 - - - -
688A ILE* 3.4 3.0 + - - +
689A LYS* 3.0 67.8 + - - +
717A PRO* 3.7 9.3 - - - +
718A LEU* 2.9 24.8 - - + +
719A GLU* 4.2 7.6 - - - +
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Residues in contact with HIS 686 (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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681A GLU* 2.8 43.4 + - + +
682A LYS* 3.7 13.9 - - + +
685A ASN* 1.3 84.1 + - - +
687A ASP* 1.3 61.2 + - - +
689A LYS 3.3 1.2 + - - -
690A GLN* 2.9 24.9 + - - +
768A PRO* 3.2 29.6 + - + +
769A GLU* 3.3 11.9 + - - -
770A PHE* 3.1 48.2 - + + +
771A THR 5.2 0.7 - - - -
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Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 5.7 1.4 - - - -
682A LYS* 2.9 30.5 + - - +
683A LYS* 3.7 34.6 + - - +
686A HIS* 1.3 77.1 - - - +
688A ILE* 1.3 62.3 + - + +
690A GLN* 3.6 7.9 + - - +
691A LEU* 3.2 21.1 + - - +
778A ILE* 5.5 1.7 - - - +
841A ARG* 6.1 2.2 - - - +
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Residues in contact with ILE 688 (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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683A LYS 4.1 7.4 - - - +
684A PHE 3.5 25.4 - - - +
685A ASN 3.4 6.9 + - - +
686A HIS 3.2 0.4 - - - -
687A ASP* 1.3 74.8 - - + +
689A LYS* 1.3 61.1 + - - +
691A LEU* 3.1 8.5 + - + +
692A LEU* 2.9 29.4 + - + +
715A PRO* 3.8 24.0 - - + +
716A THR 4.0 1.8 - - - +
717A PRO* 3.7 28.9 - - + -
841A ARG* 4.3 7.6 - - - +
844A ASN* 3.6 24.5 - - + +
845A TYR* 3.8 30.3 - - + +
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Residues in contact with LYS 689 (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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681A GLU* 5.5 0.2 + - - -
685A ASN* 3.0 45.3 + - - +
686A HIS* 3.3 2.6 + - - +
688A ILE* 1.3 75.0 - - - +
690A GLN* 1.3 57.7 + - - +
692A LEU* 3.8 10.3 - - + +
693A PHE* 2.9 26.7 + - - +
717A PRO* 3.6 28.9 - - + -
719A GLU* 5.1 5.1 + - - -
770A PHE* 3.4 43.6 - - + +
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Residues in contact with GLN 690 (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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686A HIS 2.9 16.8 + - - +
687A ASP* 3.8 9.2 - - - +
688A ILE 3.2 0.2 - - - -
689A LYS* 1.3 73.3 - - - +
691A LEU* 1.3 60.8 + - - +
693A PHE* 3.1 12.6 + - - +
694A ASN* 2.8 45.9 + - - +
770A PHE* 3.5 8.8 - - + -
771A THR 4.8 0.3 - - - +
772A PRO* 3.7 6.3 - - - +
773A ASN* 2.7 53.1 + - - +
776A LEU* 4.1 12.5 + - + -
778A ILE* 4.8 7.6 - - + -
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Residues in contact with LEU 691 (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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604A SER* 3.6 27.6 - - - +
605A PHE* 4.6 1.8 - - + -
687A ASP 3.2 11.5 + - - +
688A ILE* 3.1 11.1 + - + +
690A GLN* 1.3 80.2 - - - +
692A LEU* 1.3 51.0 + - + +
694A ASN* 3.2 3.0 + - - +
695A PHE* 2.8 51.2 + - + +
708A TRP* 3.7 24.5 - - + -
715A PRO* 4.3 6.1 - - + -
778A ILE* 3.7 30.5 - - + +
845A TYR* 3.2 28.9 - - + +
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Residues in contact with LEU 692 (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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688A ILE* 2.9 26.9 + - + +
689A LYS* 3.9 8.5 - - + +
691A LEU* 1.3 72.6 - - - +
693A PHE* 1.3 61.6 + - - +
695A PHE 3.6 10.5 - - - +
696A PRO* 3.1 28.8 - - - +
697A LYS* 3.8 36.8 - - + +
708A TRP* 4.2 9.2 - - + +
714A ALA* 4.9 0.2 - - + -
715A PRO* 3.4 42.2 - - + +
717A PRO* 4.5 10.5 - - + -
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Residues in contact with PHE 693 (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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689A LYS 2.9 18.6 + - - +
690A GLN* 3.4 12.8 - - - +
692A LEU* 1.3 78.7 - - - +
694A ASN* 1.3 65.7 + - - +
696A PRO* 3.8 11.2 - - - +
770A PHE* 4.8 2.0 - + + -
772A PRO* 3.8 31.0 - - + -
773A ASN 3.6 26.2 - - - -
774A ALA* 3.9 20.4 - - + -
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Residues in contact with ASN 694 (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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690A GLN* 2.8 19.7 + - - +
691A LEU* 3.3 11.0 - - - +
693A PHE* 1.3 82.1 - - - +
695A PHE* 1.3 85.7 + - + +
696A PRO* 3.7 4.6 - - - +
776A LEU 3.0 26.9 + - - +
777A LYS* 4.2 7.8 - - - +
778A ILE* 3.5 38.8 + - + +
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Residues in contact with PHE 695 (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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605A PHE* 4.6 3.1 - + - -
691A LEU* 2.8 30.8 + - + +
692A LEU* 3.2 14.0 - - - +
694A ASN* 1.3 96.6 - - + +
696A PRO* 1.3 71.4 - - - +
697A LYS 3.5 0.5 + - - -
699A ALA* 5.1 3.1 - - + -
707A PHE* 3.7 42.4 - + + -
708A TRP* 3.0 14.0 + + + +
778A ILE* 3.4 36.8 - - + -
780A VAL* 3.5 26.5 - - + -
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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