Contacts of the helix formed by residues 925 - 930 (chain B) in PDB entry 1ED8
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 HIS 925 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 2.9 29.1 + - - -
30A THR* 4.6 4.9 + - - -
538B SER 2.9 16.0 + - - -
539B ASP* 3.3 26.2 + - + -
540B LYS 3.0 28.4 + - - -
541B PRO* 4.2 2.6 - - - +
542B ALA 4.4 0.7 - - - -
863B LEU* 4.5 4.9 - - + +
923B GLY 3.2 0.2 + - - -
924B PRO* 1.3 76.2 - - + +
926B ALA* 1.3 60.5 + - - +
927B ALA* 3.1 7.7 + - - +
928B ASN* 3.1 27.3 + - - +
929B VAL* 5.5 0.5 - - - +
941B THR* 4.4 7.6 - - + +
944B ALA* 4.8 5.8 + - + +
945B ALA* 3.7 38.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 926 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B SER 4.9 0.2 + - - -
580B LEU* 3.5 25.3 - - + +
863B LEU* 4.1 4.0 - - + -
921B ALA* 3.6 34.1 - - + -
922B TYR 3.8 4.0 - - - +
923B GLY 3.2 17.6 + - - +
924B PRO 3.3 1.6 + - - -
925B HIS* 1.3 72.9 - - - +
927B ALA* 1.3 60.4 + - - +
928B ASN 2.9 7.7 + - - -
929B VAL* 3.1 24.9 + - - +
930B VAL* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 927 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 4.0 10.7 - - - +
30A THR* 3.9 35.0 - - - +
33A LEU* 4.1 12.0 - - + +
537B LEU* 3.9 24.6 - - + +
580B LEU* 4.3 3.4 - - - +
925B HIS 3.1 0.8 - - - +
926B ALA* 1.3 78.1 - - - +
928B ASN* 1.3 58.7 + - - +
929B VAL 3.0 6.1 + - - -
930B VAL* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 928 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 12.6 - - + +
27A GLY 4.2 1.4 - - - +
28A ASP* 2.9 27.8 + - - +
29A GLN* 2.8 38.1 + - - +
30A THR* 5.2 0.2 + - - -
925B HIS* 3.3 26.1 + - - +
926B ALA 2.9 0.8 - - - -
927B ALA* 1.3 78.9 - - - +
929B VAL* 1.3 59.8 + - - +
930B VAL 3.5 1.1 - - - -
933B THR* 3.6 19.5 - - - +
937B ASP* 5.7 0.3 - - - +
941B THR* 3.5 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 929 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LEU 3.7 26.0 - - - +
582B GLY* 3.2 19.2 - - - -
865B ILE* 5.0 7.6 - - + -
919B ILE* 3.8 44.5 - - + +
920B ALA 4.4 0.2 - - - -
921B ALA* 3.9 21.8 - - + +
926B ALA* 3.1 18.9 + - - +
927B ALA 3.0 1.4 - - - -
928B ASN* 1.3 83.1 - - + +
930B VAL* 1.3 66.6 + - - +
931B GLY 3.9 2.4 - - - +
933B THR* 4.6 7.5 - - - +
938B LEU* 5.1 6.7 - - + -
941B THR* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 2.9 25.7 + - - -
33A LEU* 3.7 29.5 - - + +
79A PRO 3.3 20.9 - - - +
80A LEU* 4.4 4.9 - - + -
81A THR* 3.8 9.2 - - - +
430A VAL* 5.6 3.1 - - + -
580B LEU* 3.8 31.9 - - + -
581B THR 3.6 18.6 - - - +
926B ALA 4.1 0.2 - - - +
927B ALA 3.1 19.1 + - - +
928B ASN 4.8 0.7 - - - +
929B VAL* 1.3 81.1 - - - +
931B GLY* 1.3 61.4 + - - +
933B THR* 4.3 2.3 - - - +
----------------------------------------------------------
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