Contacts of the helix formed by residues 625 - 637 (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 THR 625 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ASP 626 (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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621C GLN* 2.8 44.5 + - - +
622C GLY* 4.1 11.2 - - - +
625C THR* 1.3 70.8 - - - +
627C SER* 1.3 57.5 + - - +
629C GLU* 3.7 18.7 - - - +
630C ASN* 2.8 51.0 + - - +
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Residues in contact with SER 627 (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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622C GLY 2.9 21.9 + - - -
623C TYR* 3.3 18.7 + - - -
626C ASP* 1.3 78.8 - - - +
628C ALA* 1.3 61.5 + - - -
630C ASN* 3.3 2.5 + - - +
631C VAL* 3.1 28.7 + - - +
657C SER* 4.0 25.2 + - - -
661C SER* 4.1 14.4 + - - -
741C ASN* 5.6 0.4 - - - -
816C LEU* 4.7 2.2 - - - -
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Residues in contact with ALA 628 (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 4.5 0.9 - - - +
625C THR 3.1 11.0 + - - +
627C SER* 1.3 75.9 - - - +
629C GLU* 1.3 62.0 + - - +
631C VAL* 3.1 3.3 + - - +
632C ASN* 3.0 35.4 + - - +
741C ASN* 4.5 8.7 - - - +
816C LEU* 3.9 26.9 - - + -
817C GLU 4.2 2.2 - - - +
818C PRO* 3.6 32.1 - - + -
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Residues in contact with GLU 629 (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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625C THR* 3.0 35.4 + - - +
626C ASP* 3.7 19.8 - - - +
628C ALA* 1.3 76.0 - - - +
630C ASN* 1.3 65.0 + - - +
632C ASN* 4.1 6.8 - - - +
633C MET* 3.1 35.8 + - + +
818C PRO* 4.2 16.4 - - + +
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Residues in contact with ASN 630 (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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626C ASP* 2.8 33.8 + - - +
627C SER 3.6 4.9 - - - +
628C ALA 3.1 0.2 - - - -
629C GLU* 1.3 78.1 - - - +
631C VAL* 1.3 60.3 + - - +
633C MET* 5.4 2.4 - - - +
634C TYR* 3.0 27.5 + - - +
640C PHE* 3.7 17.8 - - + -
653C GLY 5.3 0.2 + - - -
654C VAL* 4.1 27.0 - - - +
657C SER* 3.6 22.4 + - - +
658C ILE* 3.7 15.6 - - + +
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Residues in contact with VAL 631 (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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627C SER 3.1 16.4 + - - +
628C ALA 3.1 8.6 + - - +
630C ASN* 1.3 76.5 - - - +
632C ASN* 1.3 62.8 + - - +
634C TYR* 3.0 7.9 + - - +
635C LEU* 2.8 49.2 + - + +
658C ILE* 4.4 18.4 - - + +
661C SER* 3.7 28.3 - - - -
662C LEU* 3.9 19.5 - - + -
814C PHE* 6.0 0.9 - - + -
816C LEU* 3.8 21.5 - - + +
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Residues in contact with ASN 632 (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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628C ALA 3.0 15.7 + - - +
629C GLU* 4.1 5.9 - - - +
631C VAL* 1.3 76.9 - - - +
633C MET* 1.3 54.0 + - + +
635C LEU* 3.2 6.1 + - - +
636C THR* 2.7 45.6 + - + +
815C LYS* 3.7 25.8 - - + +
816C LEU* 3.2 41.8 + - - +
818C PRO* 4.1 12.9 - - - +
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Residues in contact with MET 633 (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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629C GLU* 3.1 25.1 + - + +
630C ASN* 4.0 3.1 - - - +
632C ASN* 1.3 76.2 - - + +
634C TYR* 1.3 61.4 + - - +
636C THR* 3.8 5.2 - - - +
637C GLN* 2.9 68.0 + - - +
640C PHE* 3.7 32.9 - - + +
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Residues in contact with TYR 634 (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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630C ASN 3.0 16.1 + - - +
631C VAL* 3.0 10.1 + - - +
633C MET* 1.3 76.1 - - - +
635C LEU* 1.3 74.0 + - + +
637C GLN 3.5 12.0 - - - +
640C PHE* 3.8 15.6 - + + -
641C VAL* 3.9 30.3 - - + -
658C ILE* 3.8 27.1 - - + -
662C LEU* 4.1 16.8 - - + -
805C LEU* 3.5 24.8 + - + +
806C PRO* 2.7 31.9 + - + -
807C ASP* 4.5 0.2 - - - -
808C PRO* 3.8 30.9 - - + +
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Residues in contact with LEU 635 (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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631C VAL* 2.8 37.5 + - + +
632C ASN* 3.2 7.1 + - - +
634C TYR* 1.3 92.9 - - + +
636C THR* 1.3 62.1 + - + +
637C GLN 5.3 0.4 - - - -
662C LEU* 4.4 10.8 - - + -
808C PRO* 4.0 36.6 - - + +
811C LEU* 4.1 27.1 - - + +
812C ALA* 6.0 2.7 - - - -
814C PHE* 3.5 31.4 - - + +
815C LYS* 5.2 0.7 - - - -
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Residues in contact with THR 636 (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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632C ASN* 2.7 27.9 + - + +
633C MET* 3.8 4.7 - - - -
635C LEU* 1.3 83.1 - - + +
637C GLN* 1.3 74.2 + - - +
638C PRO* 3.6 9.5 - - - +
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Residues in contact with GLN 637 (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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633C MET* 2.9 66.9 + - - +
634C TYR* 3.5 11.2 - - - +
635C LEU 5.3 0.2 - - - -
636C THR* 1.3 86.6 + - - +
638C PRO* 1.3 65.6 - - + +
639C ASN* 3.3 21.5 + - - +
640C PHE* 3.4 13.7 + - + +
643C GLN* 6.0 1.9 - - - +
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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