Contacts of the helix formed by residues 685 - 695 (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 685 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680C PHE* 3.9 1.1 + - + -
681C GLU* 3.1 39.7 + - - +
684C PHE* 1.3 79.8 - - - +
686C HIS* 1.3 88.1 + - - +
687C ASP 3.5 1.1 - - - -
688C ILE* 3.4 4.8 + - - +
689C LYS* 3.0 63.0 + - - +
717C PRO* 3.8 9.6 - - - +
718C LEU 3.3 18.2 - - - +
719C GLU* 5.2 2.8 - - - +
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Residues in contact with HIS 686 (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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681C GLU* 2.8 34.0 + - + +
682C LYS* 3.6 21.8 - - + +
685C ASN* 1.3 91.3 + - - +
687C ASP* 1.3 61.1 + - - +
689C LYS 3.0 2.1 + - - -
690C GLN* 2.9 24.3 + - - +
768C PRO* 3.2 32.2 + - - +
769C GLU* 3.4 9.8 + - - -
770C PHE* 3.2 45.4 - + + +
771C THR 5.3 0.7 - - - -
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Residues in contact with ASP 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682C LYS* 2.8 27.9 + - - +
683C LYS* 3.6 34.6 + - - +
686C HIS* 1.3 73.5 - - - +
688C ILE* 1.3 63.6 + - + +
690C GLN* 3.3 9.9 + - - +
691C LEU* 2.9 27.2 + - - +
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Residues in contact with ILE 688 (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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683C LYS 3.9 10.5 - - - +
684C PHE 3.9 8.1 - - - +
685C ASN 3.4 7.3 + - - +
686C HIS 3.3 0.6 - - - -
687C ASP* 1.3 77.2 - - + +
689C LYS* 1.3 59.3 - - - +
691C LEU* 3.4 7.3 + - + +
692C LEU* 3.0 28.2 + - + +
715C PRO* 3.6 25.8 - - + +
716C THR 3.8 1.3 - - - -
717C PRO* 3.7 28.0 - - + -
841C ARG* 4.6 8.1 - - - +
844C ASN* 3.5 26.7 - - - +
845C TYR* 3.8 35.7 - - + +
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Residues in contact with LYS 689 (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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685C ASN* 3.0 49.9 + - - +
686C HIS 3.3 9.0 - - - +
688C ILE* 1.3 75.6 - - - +
690C GLN* 1.3 59.1 + - - +
692C LEU* 3.3 8.6 + - + +
693C PHE* 2.8 26.5 + - - +
717C PRO* 3.6 24.2 - - + -
770C PHE* 3.7 40.5 - - + +
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Residues in contact with GLN 690 (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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686C HIS 2.9 12.3 + - - +
687C ASP* 3.5 15.3 - - - +
689C LYS* 1.3 75.1 - - - +
691C LEU* 1.3 58.9 + - - +
693C PHE* 2.9 23.8 + - - +
694C ASN* 2.8 45.2 + - - +
770C PHE* 3.6 15.8 - - + -
771C THR 4.4 0.5 - - - +
772C PRO* 3.7 0.9 - - - +
773C ASN* 2.9 54.4 + - - +
776C LEU* 3.9 26.3 - - + +
778C ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 691 (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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604C SER* 3.6 23.6 - - - +
605C PHE* 4.5 3.6 - - + -
687C ASP 2.9 16.3 + - - +
688C ILE* 3.6 9.0 - - + +
690C GLN* 1.3 75.6 - - - +
692C LEU* 1.3 57.6 + - - +
694C ASN 3.5 0.3 + - - -
695C PHE* 2.9 48.6 + - + +
708C TRP* 4.1 17.7 - - + -
715C PRO* 4.2 7.9 - - + -
778C ILE* 3.7 31.8 - - + +
841C ARG* 5.8 0.4 - - - +
845C TYR* 3.2 26.9 - - - +
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Residues in contact with LEU 692 (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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688C ILE 3.0 20.2 + - - +
689C LYS* 3.5 7.6 - - + +
690C GLN 3.2 0.4 - - - -
691C LEU* 1.3 72.4 - - - +
693C PHE* 1.3 63.0 + - - +
695C PHE 3.6 15.9 - - - +
696C PRO* 3.2 24.4 - - + +
697C LYS* 3.7 31.9 - - + +
708C TRP* 4.2 4.3 - - + -
715C PRO* 3.5 46.7 - - + +
717C PRO* 4.1 18.6 - - + -
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Residues in contact with PHE 693 (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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689C LYS 2.8 12.8 + - - +
690C GLN* 2.9 33.6 + - - +
692C LEU* 1.3 79.4 - - - +
694C ASN* 1.3 65.4 + - - +
696C PRO* 4.1 8.8 - - - +
770C PHE* 5.0 1.3 - + + -
772C PRO* 3.9 29.6 - - + -
773C ASN 3.7 2.7 - - - -
774C ALA* 3.6 37.5 - - + -
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Residues in contact with ASN 694 (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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690C GLN* 2.8 46.9 + - - +
691C LEU 3.9 4.5 - - - +
693C PHE* 1.3 81.5 - - - +
695C PHE* 1.3 84.9 + - + +
696C PRO* 3.4 7.8 - - - +
776C LEU 2.7 24.9 + - - +
777C LYS* 4.3 0.9 - - - -
778C ILE* 3.9 20.7 + - + +
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Residues in contact with PHE 695 (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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605C PHE* 4.4 2.7 - + - -
691C LEU* 2.9 25.6 + - + +
692C LEU* 3.5 13.1 - - - +
694C ASN* 1.3 91.1 - - + +
696C PRO* 1.3 64.8 - - - +
699C ALA* 4.6 4.0 - - + -
707C PHE* 3.5 48.7 - + + -
708C TRP* 3.0 25.4 + + + +
778C ILE* 3.7 39.3 - - + -
780C VAL* 3.4 27.6 - - + -
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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