Contacts of the helix formed by residues 994 - 1001 (chain B) in PDB entry 3H44
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 ASN 994 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B TYR* 5.2 2.2 - - - -
992B ILE* 3.6 4.0 - - - +
993B GLN* 1.3 83.7 + - + +
995B MET* 1.3 59.7 + - - +
996B THR* 2.9 18.4 + - - +
997B GLU* 2.9 54.9 + - + +
998B PHE* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 995 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B TYR* 4.3 7.0 - - + +
688B LEU* 3.5 46.4 - - + +
689B LEU* 3.7 30.3 - - + -
696B THR* 5.0 4.7 - - + -
779B TYR* 3.2 37.7 - - + +
992B ILE* 4.6 0.8 - - - +
994B ASN* 1.3 73.7 + - - +
996B THR* 1.3 61.6 + - - +
998B PHE* 3.6 8.3 - - - +
999B LYS* 3.1 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 996 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B GLU* 5.6 2.3 + - - -
994B ASN* 2.9 10.3 + - - +
995B MET* 1.3 77.1 - - - +
997B GLU* 1.3 60.9 + - - +
999B LYS* 3.2 7.9 + - - +
1000B ARG* 2.8 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 997 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B GLN* 5.2 8.3 - - + +
994B ASN* 2.9 37.7 + - + +
996B THR* 1.3 75.2 - - - +
998B PHE* 1.3 64.2 + - - +
1000B ARG* 3.8 25.8 - - - +
1001B GLY* 2.8 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 998 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B LEU* 3.6 37.9 - - + -
690B MET* 3.7 21.3 - - + -
769B VAL* 4.2 9.4 - - + -
771B LEU* 4.1 17.9 - - + -
777B PHE* 3.8 25.6 - + + -
954B VAL* 4.8 0.7 - - + -
990B GLU* 6.1 0.4 - - - -
992B ILE* 3.5 40.8 - - + -
994B ASN 2.8 20.3 + - - +
995B MET* 3.6 6.5 - - - +
997B GLU* 1.3 76.4 - - - +
999B LYS* 1.3 62.9 - - - +
1001B GLY* 3.1 6.9 + - - -
1002B LEU* 3.3 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 999 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B LEU 2.9 16.5 + - - +
689B LEU* 3.6 14.1 - - - +
691B THR 2.8 26.1 + - - +
692B GLU* 3.3 21.3 + - - +
693B VAL* 4.6 0.4 - - - +
694B ALA* 4.2 18.0 + - - +
769B VAL* 3.6 32.2 - - + +
995B MET* 3.1 24.6 + - + +
996B THR* 3.7 5.6 - - - +
998B PHE* 1.3 79.5 - - + +
1000B ARG* 1.3 66.9 + - - +
1002B LEU* 3.2 22.1 + - - +
1004B LEU* 5.4 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1000 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B THR* 2.8 36.1 + - + +
997B GLU* 3.8 38.0 - - - +
999B LYS* 1.3 72.6 - - - +
1001B GLY* 1.3 57.9 + - - +
1002B LEU 3.2 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1001 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU 2.8 15.0 + - - -
998B PHE 3.1 7.4 + - - -
1000B ARG* 1.3 75.8 - - - +
1002B LEU* 1.3 67.3 + - - +
----------------------------------------------------------
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