Contacts of the strand formed by residues 905 - 909 (chain A) 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 PHE 905 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 5.9 0.2 - - - -
280A PHE 5.9 0.4 - - - -
283A PHE* 4.4 6.3 - + - -
898A PHE 3.7 17.9 - - - -
899A VAL* 3.3 3.8 - - - -
900A ASN 2.7 40.5 + - - +
903A LEU* 4.0 19.5 - - + -
904A PRO* 1.3 76.4 - - - +
906A PHE* 1.3 82.1 + - - +
907A GLY* 3.8 15.7 - - - -
8B LEU* 3.6 32.8 - - + -
44B ILE* 4.6 1.1 - - + -
68B HIS* 3.3 54.5 - + + -
70B VAL* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 5.3 2.9 - - + -
280A PHE 4.3 10.5 + - - +
281A SER* 3.4 27.9 - - - +
283A PHE* 4.1 10.6 - - - -
365A PHE* 3.9 17.5 - + + -
369A LEU* 3.7 28.0 - - + -
385A LEU* 5.0 1.6 - - + -
389A MET* 3.6 27.8 - - - -
872A LEU* 3.9 14.4 - - + -
898A PHE 3.5 6.1 - - - -
899A VAL* 3.9 14.6 - - + -
901A LEU* 3.6 25.8 - - + -
904A PRO* 4.1 24.5 - - + -
905A PHE* 1.3 92.9 - - - +
907A GLY* 1.3 59.4 + - - +
908A PHE* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER 4.6 0.4 - - - -
282A ASP* 5.5 1.3 - - - -
283A PHE* 5.4 5.6 - - - -
897A GLY* 3.6 0.3 - - - -
898A PHE* 2.8 35.2 + - - -
905A PHE* 3.8 15.8 - - - -
906A PHE* 1.3 76.0 - - - +
908A PHE* 1.3 72.5 + - - -
44B ILE* 4.2 10.3 - - - -
68B HIS* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER 3.5 24.2 - - - -
282A ASP* 3.9 24.9 + - + +
283A PHE 5.9 0.6 - - - +
365A PHE* 5.4 1.6 - + - -
391A PHE* 4.4 16.2 - + - -
575A THR* 6.0 0.7 - - + -
876A LEU* 3.6 40.2 - - + -
880A GLU* 5.8 0.7 - - - -
895A LYS* 3.7 39.3 - - + +
896A ASN 3.2 15.9 - - - +
897A GLY* 3.6 16.4 - - - -
898A PHE* 4.7 1.1 - - - -
899A VAL* 5.8 0.4 - - + -
906A PHE* 4.6 6.5 - - + -
907A GLY* 1.3 80.6 - - - -
909A SER* 1.3 62.5 + - - +
44B ILE* 4.0 11.8 - - - +
47B GLY* 3.4 22.3 + - - -
48B LYS 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LYS* 3.6 3.9 - - - -
896A ASN* 2.7 43.7 + - - +
898A PHE* 3.8 11.1 - - - -
908A PHE* 1.3 77.3 - - - +
910A GLU* 1.3 63.4 + - - +
44B ILE* 3.6 26.0 - - - -
47B GLY 3.2 6.1 - - - -
49B GLN* 3.4 33.4 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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