Contacts of the helix formed by residues 798 - 805 (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 ILE 798 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645C LEU* 5.5 4.3 - - + -
651C VAL* 3.8 33.4 - - + -
652C LYS* 4.5 18.0 - - + +
655C LEU* 5.0 2.7 - - + -
796C ASP* 4.8 5.6 - - - +
797C GLU* 1.3 77.2 - - - +
799C ASP* 1.3 69.6 + - - +
800C GLN 3.1 0.9 - - - -
801C LEU* 3.4 22.0 - - + +
802C VAL* 2.7 47.9 + - + +
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Residues in contact with ASP 799 (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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796C ASP* 4.4 8.4 - - - +
797C GLU 2.2 20.8 + - - +
798C ILE* 1.3 80.7 - - - +
800C GLN* 1.3 57.2 + - + +
802C VAL* 3.9 6.7 - - - +
803C SER* 2.9 35.9 + - - +
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Residues in contact with GLN 800 (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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796C ASP 4.1 6.3 + - - -
797C GLU* 2.8 42.3 + - + +
799C ASP* 1.3 76.3 - - + +
801C LEU* 1.3 61.9 + - + +
803C SER* 3.8 3.2 - - - -
804C SER* 2.8 33.1 + - - -
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Residues in contact with LEU 801 (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* 3.8 25.8 - - + +
655C LEU* 4.0 26.7 - - + +
656C GLU* 3.6 39.9 - - + +
659C SER* 4.6 9.9 - - - +
797C GLU* 5.5 5.6 - - + +
798C ILE* 3.2 23.8 + - + +
800C GLN* 1.3 81.1 - - + +
802C VAL* 1.3 63.2 + - - +
804C SER* 3.3 19.8 + - - +
805C LEU* 3.4 14.2 - - - +
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Residues in contact with VAL 802 (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* 5.0 15.3 - - + -
645C LEU* 5.4 9.9 - - + -
655C LEU* 3.9 19.7 - - + -
798C ILE* 2.7 30.8 + - + +
799C ASP* 3.9 6.5 - - - +
801C LEU* 1.3 72.7 - - - +
803C SER* 1.3 62.7 + - - +
805C LEU* 3.2 27.8 + - + +
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Residues in contact with SER 803 (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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799C ASP* 2.9 20.0 + - - +
800C GLN* 4.0 3.6 - - - -
802C VAL* 1.3 74.9 - - - +
804C SER* 1.3 66.0 + - - +
805C LEU 3.3 5.5 + - - +
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Residues in contact with SER 804 (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* 3.0 26.8 + - - -
800C GLN 2.8 23.7 + - - -
801C LEU* 3.3 10.9 + - - +
802C VAL 3.3 0.2 - - - -
803C SER* 1.3 73.5 - - - +
805C LEU* 1.3 66.1 + - - +
806C PRO* 3.2 6.8 - - - +
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Residues in contact with LEU 805 (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* 3.5 19.0 + - + +
641C VAL* 4.0 18.8 - - + -
655C LEU* 3.9 31.6 - - + +
658C ILE* 3.7 28.3 - - + -
659C SER* 4.1 19.3 - - - +
801C LEU 3.4 16.1 + - - +
802C VAL* 3.4 17.4 - - + +
803C SER 3.2 7.5 - - - +
804C SER* 1.3 79.7 + - - +
806C PRO* 1.3 72.7 - - + +
807C ASP* 3.5 2.3 + - - -
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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