Contacts of the helix formed by residues 2094 - 2110 (chain B) in PDB entry 6X34
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 SER2094 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1761B HIS* 5.4 12.6 - - - -
2092B LEU* 3.1 7.7 - - - +
2093B GLN* 1.3 79.7 - - - +
2095B LEU* 1.3 64.7 + - - +
2096B GLN* 4.6 1.6 - - - -
2097B GLU* 3.8 24.1 - - - +
2098B LEU* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2095 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1761B HIS* 6.2 1.2 - - - +
1764B PRO* 3.7 37.9 - - + -
1871B VAL* 6.2 3.1 - - + -
1944B LEU* 5.6 4.7 - - + +
1947B PHE* 4.7 19.1 - - + +
1948B CYS* 5.4 9.6 - - + +
1951B GLU* 4.2 23.8 - - - +
2094B SER* 1.3 72.2 - - - +
2096B GLN* 1.3 62.6 + - + +
2098B LEU* 3.3 14.6 - - + +
2099B VAL* 2.9 51.0 + - + +
2128B GLN* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2096 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2094B SER* 3.4 1.7 - - - +
2095B LEU* 1.3 84.6 - - + +
2097B GLU* 1.3 58.1 + - - +
2099B VAL* 3.8 4.2 - - - +
2100B SER* 2.9 31.4 + - - -
2128B GLN* 4.0 30.4 - - + +
2129B TYR* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2097 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092B LEU* 3.9 17.3 - - + -
2094B SER* 3.5 23.6 + - - +
2095B LEU 3.3 0.8 - - - -
2096B GLN* 1.3 78.8 - - - +
2098B LEU* 1.3 57.8 + - - +
2100B SER* 2.9 22.6 + - - -
2101B HIS* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2098 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867B ILE* 6.0 4.7 - - + -
1868B GLU* 5.3 11.0 - - + -
1870B GLU* 5.9 3.6 - - + -
1871B VAL* 4.1 26.0 - - + +
1928B LEU* 6.4 2.9 - - + -
1944B LEU* 5.4 5.6 - - + -
2092B LEU* 4.0 19.2 - - + +
2093B GLN* 5.9 0.4 - - - +
2094B SER 3.1 22.4 + - - +
2095B LEU* 3.3 21.3 - - + +
2097B GLU* 1.3 79.1 - - - +
2099B VAL* 1.3 64.6 + - + +
2101B HIS* 3.3 6.3 + - - +
2102B THR* 2.5 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2099 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1944B LEU* 3.9 30.5 - - + -
2095B LEU* 2.9 40.1 + - + +
2096B GLN* 3.8 5.4 - - - +
2098B LEU* 1.3 87.3 - - + +
2100B SER* 1.3 58.5 + - - +
2102B THR* 2.9 17.5 + - - -
2103B VAL* 2.9 26.7 + - + +
2124B LEU* 3.5 30.5 - - + -
2125B LEU* 6.0 0.7 - - - -
2128B GLN* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2096B GLN 2.9 15.8 + - - -
2097B GLU* 2.9 13.2 + - - -
2099B VAL* 1.3 75.8 - - - +
2101B HIS* 1.3 70.9 + - - +
2103B VAL* 3.0 12.8 - - - +
2104B VAL* 2.9 36.1 + - - +
2125B LEU* 5.2 8.7 - - - +
2128B GLN* 5.7 3.3 - - - +
2129B TYR* 5.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092B LEU* 3.8 29.6 - - + +
2097B GLU* 2.9 21.0 + - + +
2098B LEU* 3.6 6.3 - - - +
2100B SER* 1.3 90.7 + - - +
2102B THR* 1.3 57.2 + - + +
2104B VAL* 3.1 12.5 - - - +
2105B ARG* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1928B LEU* 4.1 41.7 - - + +
1929B GLN* 4.6 8.3 - - - +
1944B LEU* 4.9 6.1 - - - +
2098B LEU* 2.5 30.7 + - + +
2099B VAL* 2.9 15.4 + - - +
2101B HIS* 1.3 74.0 - - + +
2103B VAL* 1.3 57.4 + - - +
2105B ARG* 3.3 5.0 + - + +
2106B TRP* 2.9 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1944B LEU* 5.6 2.9 - - + -
2099B VAL* 2.9 30.8 + - + +
2100B SER* 3.0 26.0 - - - +
2102B THR* 1.3 77.9 - - - +
2104B VAL* 1.3 58.8 + - - +
2106B TRP* 3.3 9.5 + - + -
2107B ALA* 2.9 29.0 + - - +
2121B MET* 3.5 41.6 - - + +
2124B LEU* 5.2 10.3 - - + -
2125B LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2100B SER* 2.9 26.5 + - - +
2101B HIS* 3.1 22.0 - - - +
2103B VAL* 1.3 80.7 - - + +
2105B ARG* 1.3 57.3 + - + +
2107B ALA* 3.7 6.3 - - - +
2108B GLN* 2.9 31.5 + - - +
2125B LEU* 4.5 5.6 - - + -
3672B ASP* 4.6 15.9 - - + +
3673B LEU* 4.1 25.1 - - + +
3693B PRO* 5.2 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101B HIS 2.9 19.0 + - - +
2102B THR* 3.7 7.4 - - + +
2104B VAL* 1.3 79.6 - - - +
2106B TRP* 1.3 62.4 + - + +
2108B GLN* 3.7 4.7 - - - +
2109B GLU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1928B LEU* 3.5 40.1 + - + -
1930B MET 5.6 1.8 + - - -
1937B LYS* 3.5 64.5 - - + +
1940B MET* 4.0 23.6 - - + -
1941B CYS* 4.9 6.5 - - + -
1944B LEU* 5.5 6.7 - - + -
2102B THR* 2.9 29.9 + - - +
2103B VAL* 3.7 12.6 - - + +
2105B ARG* 1.3 82.0 - - + +
2107B ALA* 1.3 62.7 - - - +
2109B GLU* 3.6 14.5 + - + +
2110B ASP 4.0 7.1 - - - +
2112B VAL* 5.4 3.7 - - - +
2121B MET* 3.9 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2103B VAL 2.9 17.0 + - - +
2104B VAL* 3.7 7.9 - - - +
2106B TRP* 1.3 77.9 - - - +
2108B GLN* 1.3 59.8 + - - +
2110B ASP 3.5 13.9 - - - +
2112B VAL* 5.6 6.5 - - - +
2121B MET* 4.2 9.8 - - + +
2122B PHE* 5.5 10.1 - - + -
3673B LEU* 5.6 4.9 - - + -
3691B PRO 5.3 1.9 - - - +
3693B PRO* 4.3 20.4 - - + +
3696B GLN* 4.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2104B VAL 2.9 17.7 + - - +
2105B ARG* 4.1 3.8 - - - +
2107B ALA* 1.3 75.5 - - - +
2109B GLU* 1.3 69.8 + - - +
2110B ASP* 4.6 0.4 - - - -
3676B ALA* 3.2 51.2 + - + +
3691B PRO 6.0 0.9 - - - -
3693B PRO* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937B LYS* 6.3 0.4 - - - +
2105B ARG 2.9 17.1 + - - +
2106B TRP* 3.9 11.2 - - + +
2107B ALA 3.4 0.6 - - - -
2108B GLN* 1.3 83.5 + - - +
2110B ASP* 1.3 65.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2106B TRP 4.0 6.7 + - - +
2107B ALA 3.5 16.5 - - - +
2108B GLN 3.6 0.9 - - - -
2109B GLU* 1.3 83.4 - - + +
2111B PHE* 1.3 70.1 + - - +
2112B VAL* 4.7 3.5 - - - +
3691B PRO* 6.3 0.7 - - - -
3696B GLN* 5.0 2.1 + - - -
----------------------------------------------------------
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