Contacts of the helix formed by residues 2051 - 2065 (chain B) in PDB entry 3N00
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 LEU2051 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE* 5.4 0.2 - - + -
443A PHE* 3.4 56.5 - - + -
477A PHE* 3.4 34.8 - - + -
481A MET* 5.9 0.4 - - + -
516A LEU* 4.1 16.6 - - + -
602A HIS 4.3 2.7 - - - +
603A SER 3.5 7.2 + - - +
605A LYS* 2.7 21.4 + - + +
607A LEU* 4.1 17.0 - - + -
2049B ILE 3.7 0.8 + - - -
2050B THR* 1.3 71.9 - - - +
2052B ALA* 1.3 62.6 + - - +
2054B HIS* 3.5 1.1 + - + +
2055B ILE* 3.1 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2052 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A SER* 2.7 35.8 + - - +
604A GLU* 3.8 15.7 - - - +
2050B THR* 4.3 1.1 - - - +
2051B LEU* 1.3 74.4 - - - +
2053B ASP* 1.3 65.5 + - - +
2055B ILE* 3.2 11.5 + - - +
2056B CYS* 3.2 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2053 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A GLU* 5.9 0.4 - - - -
2049B ILE* 3.7 17.3 - - + +
2050B THR* 2.9 30.0 + - - +
2052B ALA* 1.3 79.4 - - - +
2054B HIS* 1.3 62.5 + - - +
2056B CYS* 3.4 8.8 + - - +
2057B GLN* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2054 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A SER 4.2 0.6 + - - -
443A PHE* 3.9 13.7 - - + -
444A THR* 2.8 30.8 + - + -
447A VAL* 5.6 0.2 - - + -
607A LEU* 3.7 28.9 - - + -
609A PHE* 3.5 27.3 - + - -
2047B ARG* 4.9 4.0 + - - -
2049B ILE* 3.9 18.3 - - + +
2050B THR 2.9 15.2 + - - +
2051B LEU* 3.7 5.4 - - + +
2053B ASP* 1.3 78.0 - - - +
2055B ILE* 1.3 57.0 + - + +
2057B GLN* 3.4 8.1 + - - +
2058B ILE* 3.0 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2055 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 3.9 22.4 - - + +
472A LEU 4.3 1.6 - - - +
473A LYS* 4.6 9.4 - - - +
476A THR* 3.8 16.4 - - + -
477A PHE* 3.9 37.0 - - + +
480A LEU* 4.3 9.2 - - + -
2051B LEU* 3.1 35.1 + - + +
2052B ALA* 3.2 11.2 + - - +
2054B HIS* 1.3 76.8 - - + +
2056B CYS* 1.3 63.9 + - - +
2058B ILE* 3.3 2.6 + - - +
2059B ILE* 3.0 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2056 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS* 3.5 46.7 + - + +
2052B ALA* 3.2 17.5 + - - -
2053B ASP* 3.9 10.5 - - - +
2054B HIS 3.4 0.2 - - - -
2055B ILE* 1.3 76.9 - - - +
2057B GLN* 1.3 54.6 + - + +
2059B ILE* 3.4 4.6 + - - +
2060B THR* 2.6 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2057 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2047B ARG* 3.8 16.3 + - - +
2049B ILE* 3.4 29.9 - - - +
2053B ASP* 3.1 20.2 + - + +
2054B HIS* 3.6 9.6 + - - +
2056B CYS* 1.3 76.0 - - + +
2058B ILE* 1.3 58.9 + - + +
2060B THR* 3.2 6.0 + - - -
2061B GLN* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2058 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A THR* 3.4 37.0 - - + +
447A VAL* 3.6 30.3 - - + -
448A ARG* 4.1 19.2 + - + +
451A VAL* 5.8 0.2 - - + -
2054B HIS* 3.0 59.1 + - + +
2055B ILE 3.9 3.6 - - - +
2057B GLN* 1.3 77.2 - - + +
2059B ILE* 1.3 59.1 + - - +
2061B GLN* 3.9 4.9 - - - +
2062B ASP* 2.9 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 4.0 12.3 - - + -
451A VAL* 4.3 9.2 - - + -
469A VAL* 4.0 26.2 - - + +
472A LEU* 3.5 43.3 - - + +
473A LYS* 3.6 11.2 - - + +
476A THR* 3.9 2.5 - - - +
2055B ILE* 3.0 44.8 + - + +
2056B CYS* 3.7 3.6 - - - +
2058B ILE* 1.3 73.2 - - - +
2060B THR* 1.3 61.2 + - - +
2062B ASP* 3.3 4.9 + - - +
2063B PHE* 2.9 44.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 5.7 2.0 - - - -
473A LYS* 2.9 18.3 + - - +
2056B CYS* 2.6 28.8 + - - +
2057B GLN* 3.5 5.8 - - - -
2059B ILE* 1.3 72.2 - - - +
2061B GLN* 1.3 67.5 + - - +
2063B PHE* 3.3 6.4 + - - +
2064B ALA* 3.0 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 6.4 0.4 - - - +
2057B GLN 2.8 21.0 + - - +
2058B ILE* 4.0 5.4 - - - +
2060B THR* 1.3 74.3 - - - +
2062B ASP* 1.3 62.1 + - - +
2064B ALA* 3.3 14.2 + - - +
2065B ARG* 3.4 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 3.7 28.7 - - + +
451A VAL* 4.0 29.0 - - + +
455A LYS* 4.3 5.0 + - - -
2058B ILE* 2.9 23.3 + - + +
2059B ILE* 3.6 6.3 - - - +
2061B GLN* 1.3 76.9 - - - +
2063B PHE* 1.3 62.0 + - + +
2065B ARG* 2.9 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 3.8 20.9 - - + -
455A LYS* 5.0 5.6 - - + -
460A PHE* 5.0 2.2 - + - -
461A ARG* 3.5 16.2 - - - -
465A GLN* 3.4 42.4 + - - +
468A GLN* 3.6 16.8 - - + -
469A VAL* 3.7 23.1 - - + -
472A LEU* 3.7 30.3 - - + -
2059B ILE* 2.9 33.2 + - + +
2060B THR* 3.3 5.1 + - - +
2062B ASP* 1.3 79.9 - - - +
2064B ALA* 1.3 60.9 + - - +
2065B ARG 3.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2060B THR* 3.0 20.0 + - + +
2061B GLN* 3.3 7.8 + - - +
2062B ASP 3.3 0.2 - - - -
2063B PHE* 1.3 76.1 - - - +
2065B ARG* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 5.6 6.3 - - - +
451A VAL* 5.7 0.4 - - - +
452A GLU* 4.6 8.1 + - - -
455A LYS* 4.0 18.3 - - - +
2061B GLN 3.4 8.1 + - - +
2062B ASP* 2.9 57.9 + - - +
2063B PHE 3.3 3.2 - - - -
2064B ALA* 1.3 82.2 - - - +
----------------------------------------------------------
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