Contacts of the helix formed by residues 650 - 664 (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 ASP 650 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648C SER* 3.1 13.4 + - - +
649C GLY* 1.3 72.9 - - - +
651C VAL* 1.3 64.9 + - - +
652C LYS* 3.9 6.4 + - - +
653C GLY* 3.0 33.9 + - - -
654C VAL* 3.5 16.6 + - + +
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Residues in contact with VAL 651 (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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644C THR* 3.6 27.4 - - + +
645C LEU* 3.7 33.2 - - + +
648C SER* 3.4 23.8 - - - +
649C GLY 3.4 4.7 + - - +
650C ASP* 1.3 70.8 - - - +
652C LYS* 1.3 69.2 + - - +
654C VAL* 3.2 3.1 + - - +
655C LEU* 3.2 28.5 + - + +
798C ILE* 3.8 20.9 - - + -
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Residues in contact with LYS 652 (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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650C ASP* 3.4 6.5 + - - +
651C VAL* 1.3 79.4 - - - +
653C GLY* 1.3 57.8 + - - +
656C GLU* 2.8 60.4 + - - +
794C GLY* 4.1 4.9 - - - -
795C SER* 4.0 14.5 - - - +
797C GLU* 3.2 42.8 + - - +
798C ILE* 4.5 15.5 - - + +
801C LEU* 3.8 15.2 - - + +
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Residues in contact with GLY 653 (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* 5.3 0.2 + - - -
650C ASP* 3.0 30.9 + - - -
651C VAL 3.3 0.2 - - - -
652C LYS* 1.3 76.0 - - - +
654C VAL* 1.3 62.0 + - - +
656C GLU* 4.1 11.2 - - - +
657C SER* 3.4 22.6 + - - -
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Residues in contact with VAL 654 (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* 4.1 20.4 - - - +
640C PHE* 4.0 29.4 - - + -
644C THR* 3.9 21.8 - - + +
648C SER* 4.1 9.9 - - - +
650C ASP* 3.5 19.2 + - + +
651C VAL 3.2 3.9 + - - +
652C LYS 3.2 0.8 - - - -
653C GLY* 1.3 77.9 - - - +
655C LEU* 1.3 61.5 + - + +
657C SER* 3.0 20.4 + - - -
658C ILE* 3.1 16.4 + - + +
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Residues in contact with LEU 655 (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* 5.3 0.9 - - + -
641C VAL* 4.2 26.5 - - + -
644C THR* 5.0 7.2 - - + -
645C LEU* 4.9 2.5 - - + -
651C VAL* 3.2 30.3 + - + +
654C VAL* 1.3 77.9 - - + +
656C GLU* 1.3 66.4 + - - +
658C ILE* 3.9 15.3 - - + +
659C SER* 3.2 25.1 + - - -
798C ILE* 5.0 3.1 - - + -
801C LEU* 4.0 23.8 - - + +
802C VAL* 3.9 27.8 - - + -
805C LEU* 3.9 28.2 - - + +
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Residues in contact with GLU 656 (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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652C LYS* 2.8 55.6 + - - +
653C GLY* 4.1 8.8 - - - +
655C LEU* 1.3 72.7 - - - +
657C SER* 1.3 57.0 + - - +
659C SER* 3.8 1.2 - - - -
660C ASP* 2.8 43.3 + - - +
797C GLU* 5.2 0.2 - - - +
801C LEU* 3.6 21.8 - - + +
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Residues in contact with SER 657 (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* 4.0 20.0 + - - -
630C ASN* 3.6 23.7 + - - +
631C VAL* 5.5 0.2 - - - -
653C GLY 3.4 14.5 + - - -
654C VAL 3.0 11.6 + - - -
655C LEU 3.3 0.4 - - - -
656C GLU* 1.3 79.4 - - - +
658C ILE* 1.3 66.5 + - - +
660C ASP* 3.3 10.2 + - - +
661C SER* 2.9 28.4 + - - -
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Residues in contact with ILE 658 (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 27.1 - - + +
631C VAL* 4.4 10.1 - - + +
634C TYR* 3.8 30.3 - - + -
640C PHE* 3.3 36.1 - - + -
654C VAL* 3.1 16.9 + - + +
655C LEU* 3.9 16.4 - - + +
657C SER* 1.3 81.5 + - - +
659C SER* 1.3 57.6 + - - +
661C SER* 3.2 4.2 + - - -
662C LEU* 3.1 34.7 + - + +
805C LEU* 3.7 19.3 - - + -
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Residues in contact with SER 659 (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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655C LEU 3.2 16.6 + - - -
656C GLU 3.8 2.2 - - - -
658C ILE* 1.3 75.7 - - - +
660C ASP* 1.3 64.3 + - - +
662C LEU* 5.0 2.5 - - - -
663C SER* 2.6 39.7 + - - -
801C LEU* 4.6 10.7 - - - +
804C SER* 3.0 26.1 + - - -
805C LEU* 4.1 11.1 - - - -
806C PRO* 5.5 2.7 - - - -
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Residues in contact with ASP 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C GLU* 2.8 28.3 + - - +
657C SER* 3.3 13.3 - - - +
659C SER* 1.3 74.6 - - - +
661C SER* 1.3 62.7 + - - +
663C SER* 4.7 0.2 - - - -
664C SER* 3.1 38.9 + - - +
682C LYS* 5.7 3.9 + - - -
738C ARG* 4.9 2.3 + - - -
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Residues in contact with SER 661 (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* 4.1 19.1 + - - -
631C VAL* 3.7 23.4 - - - +
657C SER 2.9 17.7 + - - -
658C ILE 3.6 4.5 - - - -
659C SER 3.2 0.4 - - - -
660C ASP* 1.3 80.7 - - - +
662C LEU* 1.3 61.9 + - - +
664C SER 4.3 0.3 - - - -
665C LYS* 4.0 8.0 + - - +
738C ARG* 4.9 6.4 + - - +
742C TYR* 2.7 39.3 + - - -
816C LEU* 4.5 4.8 - - - +
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Residues in contact with LEU 662 (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* 3.9 26.0 - - + -
634C TYR* 4.1 25.4 - - + -
635C LEU* 4.4 8.1 - - + -
658C ILE* 3.1 20.8 + - + +
659C SER 4.6 1.6 - - - +
661C SER* 1.3 81.0 - - - +
663C SER* 1.3 60.3 + - - +
665C LYS* 3.2 26.4 + - - +
806C PRO* 3.6 34.6 - - + +
811C LEU* 3.8 32.7 - - + +
814C PHE* 4.9 10.5 - - + -
816C LEU* 5.7 1.8 - - + -
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Residues in contact with SER 663 (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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659C SER* 2.6 29.0 + - - -
660C ASP* 4.4 0.5 + - - -
662C LEU* 1.3 76.7 - - - +
664C SER* 1.3 62.2 + - - +
665C LYS* 3.1 8.3 + - - +
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Residues in contact with SER 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C ASP* 3.1 26.4 + - - -
661C SER 4.3 1.1 - - - -
663C SER* 1.3 79.7 + - - +
665C LYS* 1.3 60.4 + - - +
666C PRO* 3.3 0.5 - - - +
675C TRP* 5.7 3.8 - - - -
738C ARG* 2.8 35.8 + - - -
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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