Contacts of the helix formed by residues 639 - 648 (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 639 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637C GLN* 3.3 25.7 + - - +
638C PRO* 1.3 82.5 + - - +
640C PHE* 1.3 65.2 + - - +
641C VAL 3.2 4.2 - - - +
642C GLU* 3.2 23.3 + - - +
643C GLN* 2.9 48.4 + - + +
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Residues in contact with PHE 640 (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* 3.7 22.4 - - - -
633C MET* 3.7 47.8 - - + +
634C TYR* 3.8 26.2 - + + -
637C GLN* 3.4 17.7 + - + +
639C ASN* 1.3 84.4 - - - +
641C VAL* 1.3 61.3 + - + +
643C GLN* 3.5 7.9 + - + +
644C THR* 2.8 48.2 + - - -
654C VAL* 4.0 14.8 - - + -
655C LEU* 5.3 1.1 - - + -
658C ILE* 3.3 28.0 - - + -
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Residues in contact with VAL 641 (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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634C TYR* 3.9 31.4 - - + -
639C ASN* 3.2 0.8 - - - +
640C PHE* 1.3 77.1 - - + +
642C GLU* 1.3 60.0 + - - +
644C THR* 3.2 5.8 + - - -
645C LEU* 2.8 51.3 + - + +
655C LEU* 4.2 25.6 - - + -
802C VAL* 5.0 13.9 - - + -
805C LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 642 (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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639C ASN* 3.2 26.5 + - + +
641C VAL* 1.3 78.8 - - - +
643C GLN* 1.3 66.3 + - - +
645C LEU* 3.4 11.9 + - + +
646C LYS* 3.0 54.7 + - + +
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Residues in contact with GLN 643 (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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637C GLN* 6.0 1.8 - - - +
639C ASN* 2.9 38.7 + - - +
640C PHE* 3.7 11.0 - - + +
642C GLU* 1.3 80.1 + - - +
644C THR* 1.3 64.5 + - - +
646C LYS* 3.3 26.7 + - - +
647C GLN* 2.9 62.7 + - - +
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Residues in contact with THR 644 (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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640C PHE* 2.8 44.1 + - - -
641C VAL* 3.5 8.1 - - - -
643C GLN* 1.3 76.1 - - - +
645C LEU* 1.3 61.1 + - + +
648C SER* 3.0 47.3 + - - +
651C VAL* 3.6 23.0 - - + +
654C VAL* 3.9 22.5 - - + +
655C LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 645 (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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641C VAL* 2.8 43.0 + - + +
642C GLU* 3.7 10.3 - - + +
644C THR* 1.3 77.6 - - + +
646C LYS* 1.3 62.8 + - + +
648C SER 5.1 1.0 - - - +
651C VAL* 3.7 32.8 - - + +
655C LEU* 4.9 5.4 - - + -
798C ILE* 5.5 4.0 - - + -
802C VAL* 5.4 8.7 - - + -
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Residues in contact with LYS 646 (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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642C GLU* 3.0 46.5 + - + +
643C GLN* 3.6 22.1 - - - +
645C LEU* 1.3 79.4 - - + +
647C GLN* 1.3 73.3 + - + +
648C SER 5.3 0.4 - - - -
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Residues in contact with GLN 647 (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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643C GLN* 2.9 42.6 + - - +
646C LYS* 1.3 94.6 - - + +
648C SER* 1.3 67.9 + - - +
649C GLY* 3.5 2.3 + - - -
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Residues in contact with SER 648 (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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643C GLN 4.2 0.2 + - - -
644C THR* 3.0 34.1 + - - +
645C LEU 5.1 1.7 - - - +
646C LYS 5.3 0.2 - - - -
647C GLN* 1.3 78.9 + - - +
649C GLY* 1.3 62.9 + - - +
650C ASP* 3.1 24.6 + - - +
651C VAL* 3.4 16.8 - - - +
654C VAL* 4.1 9.7 - - - +
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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