Contacts of the helix formed by residues 945 - 951 (chain E) in PDB entry 1NYE
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 CYS 945 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E HIS* 4.4 2.2 - - - -
879E CYS* 3.4 24.9 - - - -
880E PHE* 3.8 19.1 - - - -
883E ALA* 3.5 28.4 - - + +
941E ALA* 3.1 11.5 + - - +
944E GLY* 1.3 77.4 - - - +
946E PRO* 1.3 71.5 - - + +
948E SER* 2.9 40.3 + - - -
949E GLN* 3.1 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 946 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879E CYS* 3.3 14.8 - - - -
883E ALA* 5.5 1.1 - - + -
944E GLY 3.6 2.0 - - - +
945E CYS* 1.3 83.5 - - + +
947E VAL* 1.3 61.4 + - - +
949E GLN* 3.2 10.2 + - + +
950E VAL* 2.9 31.4 + - - +
1059F ARG* 3.5 20.9 - - - +
1069F GLU* 4.3 6.3 - - - +
1106F LEU* 4.1 25.1 - - + -
1113F PHE* 3.9 25.8 - - + +
1114F ALA* 4.5 2.5 - - - -
1115F ILE* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 947 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872E ILE* 4.9 2.9 - - + +
875E ALA* 3.9 3.4 - - + +
876E HIS* 3.7 32.8 - - + +
879E CYS* 3.2 33.3 - - + -
945E CYS 3.3 1.0 + - - -
946E PRO* 1.3 74.7 - - - +
948E SER* 1.3 62.5 + - - +
950E VAL* 3.4 7.4 + - + +
951E LEU* 3.0 41.2 + - + +
1068F PRO* 3.9 11.4 - - + -
1069F GLU* 4.6 4.0 - - - +
1072F ILE* 3.7 32.8 - - + -
1115F ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 948 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E HIS* 2.8 26.9 + - - -
880E PHE* 5.2 0.2 - - - -
920E LEU* 5.1 1.0 - - - +
942E LYS 2.8 29.1 + - - -
943E ALA* 4.1 9.9 - - - -
945E CYS* 2.9 23.3 + - - -
947E VAL* 1.3 77.4 - - - +
949E GLN* 1.3 63.4 + - - +
951E LEU 3.5 16.3 + - - +
955E ILE* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 949 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943E ALA* 3.2 19.2 + - - +
944E GLY* 3.6 15.6 + - - +
945E CYS 3.1 14.1 + - - +
946E PRO* 3.2 11.4 + - + +
948E SER* 1.3 80.2 - - - +
950E VAL* 1.3 59.4 + - + +
1113F PHE 5.1 6.1 + - - +
1114F ALA* 5.2 10.5 - - + -
1152F LYS* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 950 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946E PRO 2.9 18.1 + - - +
947E VAL* 3.4 5.3 + - - +
949E GLN* 1.3 77.3 - - + +
951E LEU* 1.3 60.1 + - + +
1072F ILE* 6.3 0.4 - - + -
1115F ILE* 3.3 47.1 - - + +
1150F VAL 3.2 4.5 - - - +
1151F LEU* 3.5 25.6 - - + -
1152F LYS* 2.9 33.8 + - + +
1153F ALA* 3.9 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 951 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872E ILE* 4.3 14.8 - - + -
876E HIS* 3.6 21.5 - - + +
915E ILE* 6.0 0.2 - - + -
918E ILE* 3.2 34.3 - - + -
947E VAL* 3.0 33.8 + - + +
948E SER* 3.6 13.3 - - - +
949E GLN 3.2 0.8 - - - -
950E VAL* 1.3 78.1 - - + +
952E LYS* 1.3 61.9 + - - +
953E ALA* 3.3 9.7 - - + +
955E ILE* 4.5 7.8 - - + +
1150F VAL* 3.4 22.2 - - + +
1151F LEU* 4.6 14.1 - - + -
1152F LYS* 3.9 10.7 + - - -
----------------------------------------------------------
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