Contacts of the strand formed by residues 2188 - 2193 (chain A) in PDB entry 3CMT
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 LEU2188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2040A ILE* 4.9 9.4 - - + -
2056A LEU* 4.0 19.3 - - + -
2057A PRO 3.3 24.0 - - - +
2058A MET* 4.0 16.6 - - - -
2059A GLY 3.7 4.0 - - - +
2060A ARG 3.5 14.4 - - - +
2062A VAL* 3.8 24.5 - - + -
2079A VAL* 4.9 3.4 - - + -
2139A ASP 2.9 12.5 + - - +
2140A VAL* 3.3 13.9 - - + -
2141A ILE 2.8 27.2 + - - +
2186A ASN 3.9 1.2 + - - -
2187A THR* 1.3 75.2 - - - +
2189A LEU* 1.3 61.2 + - - +
2190A ILE* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2060A ARG 3.0 8.4 + - - +
2061A ILE* 3.4 6.2 - - + +
2062A VAL* 2.9 26.7 + - - +
2129A CYS* 4.8 8.3 - - + -
2141A ILE* 3.2 21.8 - - + +
2143A VAL* 3.8 18.2 - - + -
2178A LEU* 3.8 17.7 - - + -
2182A LEU* 3.7 37.5 - - + -
2187A THR 3.7 0.6 + - - -
2188A LEU* 1.3 74.7 - - - +
2190A ILE* 1.3 77.6 + - - +
2191A PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056A LEU* 3.8 23.8 - - + -
2062A VAL* 3.4 19.3 - - + +
2064A ILE* 3.6 29.4 - - + -
2076A THR* 4.0 13.9 - - - +
2079A VAL* 3.9 25.4 - - + -
2140A VAL* 4.8 7.0 - - + -
2141A ILE 2.8 10.1 + - - +
2142A VAL* 3.3 11.5 - - + +
2143A VAL 2.8 28.1 + - - +
2188A LEU* 3.9 18.4 - - + -
2189A LEU* 1.3 80.2 - - - +
2191A PHE* 1.3 66.7 + - - +
2192A ILE* 4.8 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2061A ILE* 3.7 24.9 - - + -
2062A VAL 2.7 12.0 + - - +
2063A GLU* 3.3 3.0 - - - +
2064A ILE 2.9 26.3 + - - +
2126A LEU* 4.1 22.0 - - + -
2129A CYS* 5.7 0.2 - - - -
2143A VAL* 3.8 31.0 - - + -
2146A VAL* 3.8 18.8 - - + -
2149A LEU* 4.5 4.5 - - + -
2171A MET* 4.8 2.7 - - + -
2175A MET* 3.8 30.1 - - + -
2178A LEU* 4.4 1.3 - - + -
2189A LEU* 3.6 32.5 - - + -
2190A ILE* 1.3 73.8 - - - +
2192A ILE* 1.3 63.2 + - - +
2215A LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2064A ILE* 3.4 7.9 - - + +
2072A LYS* 3.6 49.8 - - + +
2073A THR* 3.9 7.6 - - - -
2076A THR* 3.4 30.3 - - + +
2142A VAL* 4.4 3.4 - - + -
2143A VAL 2.9 11.1 + - - +
2144A ASP* 3.4 37.5 - - + +
2145A SER* 3.0 17.9 - - - +
2146A VAL* 2.8 26.9 + - - +
2190A ILE* 4.0 3.6 + - + -
2191A PHE* 1.3 73.7 - - - +
2193A ASN* 1.3 64.2 + - - +
2501A ALF 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2063A GLU* 3.1 20.8 - - - +
2064A ILE 2.8 8.0 + - - +
2065A TYR* 3.3 28.6 - - + -
2066A GLY 3.7 0.3 + - - -
2072A LYS* 3.4 13.2 - - - +
2145A SER* 4.9 0.7 - - - +
2146A VAL* 3.3 20.8 - - + +
2147A ALA 3.9 3.0 - - - +
2191A PHE 3.8 0.2 + - - -
2192A ILE* 1.3 76.9 - - - +
2194A GLN* 1.3 80.8 + - - +
2209A THR* 3.0 14.7 - - - +
2210A THR* 2.9 53.2 + - - +
2215A LEU* 4.5 1.6 - - - +
----------------------------------------------------------
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