Contacts of the helix formed by residues 121 - 130 (chain Y) in PDB entry 2W4V
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 121 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Y GLU* 4.0 3.3 - - - +
119Y ASN* 5.6 0.9 - - - +
120Y PHE* 1.3 77.8 - - - +
122Y LYS* 1.3 53.3 + - - +
123Y ASP* 3.0 18.7 + - - +
124Y GLU* 1.7 61.7 + - - +
125Y MET* 2.6 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Y GLU* 5.2 1.1 + - - -
121Y ASN* 1.3 73.1 - - - +
123Y ASP* 1.3 52.2 + - - +
125Y MET* 2.9 25.1 - - - +
126Y ARG* 2.5 75.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Y ASN* 3.0 14.8 + - - +
122Y LYS* 1.3 74.1 - - - +
124Y GLU* 1.3 61.3 + - - +
125Y MET 2.9 1.1 - - - -
126Y ARG* 3.3 29.4 + - - +
127Y MET* 2.6 80.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C ARG* 4.0 24.3 - - - +
819C LEU* 3.8 24.7 - - + +
820C VAL* 6.0 0.3 - - - +
120Y PHE* 4.0 20.3 - - + -
121Y ASN* 1.7 55.0 + - - +
123Y ASP* 1.3 79.1 - - - +
125Y MET* 1.3 52.5 + - - +
127Y MET* 3.9 2.5 - - - +
128Y THR* 2.2 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110Y LYS* 1.5 57.0 - - + +
114Y GLU* 2.7 40.2 - - - +
120Y PHE* 4.8 1.7 - - - +
121Y ASN 2.6 17.6 + - - +
122Y LYS* 2.9 30.5 - - - +
124Y GLU* 1.3 71.5 - - - +
126Y ARG* 1.3 66.8 + - + +
128Y THR* 2.5 21.7 + - - -
129Y PHE* 3.2 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Y LYS* 2.5 59.2 + - + +
123Y ASP* 3.0 36.4 + - - +
125Y MET* 1.3 77.6 - - + +
127Y MET* 1.3 63.8 + - - +
128Y THR 3.0 1.3 - - - -
129Y PHE* 3.2 3.1 + - - +
130Y LYS* 2.6 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C TRP* 5.9 0.9 - - - -
819C LEU* 3.9 26.5 - - + +
823C ASN* 4.2 27.4 - - - +
123Y ASP* 2.6 59.7 + - - +
124Y GLU* 3.9 5.8 - - - +
126Y ARG* 1.3 73.9 - - + +
128Y THR* 1.3 60.2 + - - +
130Y LYS* 2.8 49.1 + - - +
131Y GLU* 4.3 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815C ILE* 4.1 20.6 - - + -
818C TRP* 5.1 2.9 - - - -
819C LEU* 3.6 23.3 - - + -
113Y LEU* 5.2 15.2 - - + +
120Y PHE* 5.5 3.4 - - + -
124Y GLU* 2.2 32.0 + - + +
125Y MET* 2.5 26.2 + - - -
127Y MET* 1.3 79.2 - - - +
129Y PHE* 1.3 62.4 + - - +
130Y LYS 3.6 0.3 + - - -
131Y GLU* 3.8 3.1 + - - +
132Y ALA* 3.5 16.3 + - - +
144Y PHE* 4.2 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Y ILE* 4.5 17.5 - - + -
110Y LYS* 6.2 1.6 - - + +
125Y MET* 3.2 16.1 + - + +
126Y ARG* 3.2 2.7 + - - +
128Y THR* 1.3 79.6 + - - +
130Y LYS* 1.3 66.2 + - + +
131Y GLU 3.0 4.0 + - - -
132Y ALA* 3.4 23.5 + - + +
134Y VAL* 3.0 50.7 - - + -
139Y PHE* 4.8 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Y ARG* 2.6 28.4 + - + +
127Y MET* 2.8 63.2 - - - +
128Y THR 3.3 0.4 - - - -
129Y PHE* 1.3 80.7 - - + +
131Y GLU* 1.3 70.0 + - + +
132Y ALA 5.2 0.2 - - - +
----------------------------------------------------------
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