Contacts of the helix formed by residues 120 - 135 (chain W) in PDB entry 5GJQ
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 120 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119W ASP* 1.3 90.0 + - - +
121W GLU* 1.3 54.1 + - - +
122W LYS* 4.3 6.5 - - + +
123W ASP* 3.0 36.1 - - - -
124W LEU* 2.7 36.3 + - - +
152W LYS* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119W ASP 4.2 0.4 + - - -
120W ASN* 1.3 72.2 - - - +
122W LYS* 1.3 55.0 + - + +
124W LEU* 3.1 12.1 - - + +
125W VAL* 2.6 43.9 + - + +
151W GLU 5.7 0.7 - - - -
152W LYS* 4.1 23.8 - - + +
155W ALA* 5.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120W ASN* 3.3 6.0 - - + -
121W GLU* 1.3 74.9 - - + +
123W ASP* 1.3 54.4 - - - +
125W VAL* 2.9 6.1 + - - +
126W LYS* 2.4 47.8 + - + +
129W LYS* 4.4 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87W CYS* 4.3 13.2 - - - -
119W ASP* 3.4 17.3 - - - +
120W ASN* 3.0 28.1 + - - -
122W LYS* 1.3 75.4 - - - +
124W LEU* 1.3 53.5 + - - +
126W LYS* 3.1 11.6 + - - +
127W LEU* 2.7 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119W ASP* 3.5 16.0 + - + +
120W ASN 2.7 17.9 + - - +
121W GLU* 3.1 19.5 - - + +
123W ASP* 1.3 73.3 - - - +
125W VAL* 1.3 67.6 + - + +
127W LEU* 3.0 13.2 - - + +
128W ALA 2.8 20.8 + - - -
152W LYS* 3.3 50.7 - - + +
153W LEU* 4.5 6.5 - - + +
155W ALA* 4.3 4.5 - - + -
156W PHE* 3.2 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121W GLU* 2.6 26.9 + - + +
122W LYS* 3.6 3.8 - - - +
124W LEU* 1.3 82.9 - - + +
126W LYS* 1.3 56.5 + - - +
127W LEU 3.1 0.2 - - - -
128W ALA* 3.2 6.6 - - - +
129W LYS* 2.3 58.0 + - + +
155W ALA* 5.2 4.9 - - + -
159W THR* 3.6 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122W LYS* 2.4 45.0 + - + +
123W ASP* 3.3 11.0 - - - +
125W VAL* 1.3 66.0 - - - +
127W LEU* 1.3 51.6 + - - +
129W LYS* 3.3 23.8 - - + +
130W ARG* 2.5 38.7 + - - +
133W LYS* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86W PHE* 6.2 1.1 - - + -
87W CYS* 3.7 46.7 - - + +
90W ILE* 4.7 10.1 - - + -
91W ARG* 4.0 23.3 - - + +
94W HIS* 5.5 2.9 - - + -
119W ASP* 3.9 3.1 - - - +
123W ASP* 2.7 26.4 + - - +
124W LEU* 3.0 21.3 - - + +
126W LYS* 1.3 71.5 - - - +
128W ALA* 1.3 54.8 + - - +
130W ARG* 2.8 8.7 + - + +
131W LEU* 2.5 43.3 + - + +
156W PHE* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124W LEU 2.8 8.3 + - - -
125W VAL* 2.8 9.6 + - - +
127W LEU* 1.3 69.9 - - - +
129W LYS* 1.3 58.2 + - - +
131W LEU* 3.4 7.8 - - - +
132W LYS* 2.9 31.4 + - - +
156W PHE* 3.4 27.3 - - + -
159W THR* 3.6 16.8 - - - -
160W LEU* 3.4 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122W LYS* 4.4 5.9 + - - +
125W VAL* 2.3 48.1 + - + +
126W LYS* 3.3 30.1 - - + +
128W ALA* 1.3 66.5 - - + +
130W ARG* 1.3 54.0 + - - +
132W LYS* 2.9 9.2 + - - +
133W LYS* 2.4 62.0 + - + +
159W THR* 5.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W ARG* 6.4 2.7 - - + -
94W HIS* 5.1 13.0 - - + -
98W LYS* 5.2 7.6 - - - +
126W LYS 2.5 22.3 + - - +
127W LEU* 2.8 11.7 + - + +
129W LYS* 1.3 70.4 - - - +
131W LEU* 1.3 51.5 + - + +
133W LYS* 3.2 17.5 - - + +
134W GLU* 2.5 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90W ILE* 4.4 4.3 - - + -
94W HIS* 3.6 28.3 - - + -
109W ILE* 4.0 6.3 - - + -
127W LEU* 2.5 22.8 + - + +
128W ALA* 3.4 6.7 - - - +
130W ARG* 1.3 70.5 - - - +
132W LYS* 1.3 52.0 - - - +
134W GLU* 2.8 4.6 + - - -
135W LYS* 2.2 38.1 + - - -
136W VAL* 3.1 34.7 + - + -
138W VAL* 3.6 19.1 - - + -
156W PHE* 3.1 40.6 - - + -
160W LEU* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128W ALA 2.9 14.0 + - - +
129W LYS* 3.4 5.6 - - - +
131W LEU* 1.3 76.4 - - - +
133W LYS* 1.3 65.7 + - - +
135W LYS* 3.0 17.5 + - - +
136W VAL 4.7 1.1 - - - +
159W THR 4.5 5.4 + - - +
160W LEU* 3.1 32.9 - - - +
161W ASN 4.5 2.0 - - - -
162W GLY* 3.8 26.6 - - - +
163W LYS* 6.4 0.4 - - - -
166W THR 5.9 0.2 - - - -
167W GLY* 5.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W LYS* 4.6 4.2 + - - +
129W LYS* 2.4 58.1 + - - +
130W ARG* 3.2 23.4 - - + +
132W LYS* 1.3 71.1 - - + +
134W GLU* 1.3 64.7 - - + +
135W LYS* 3.0 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94W HIS* 5.5 4.7 - - + -
98W LYS* 3.9 32.3 - - + +
100W ARG* 5.6 2.9 + - - -
107W MET* 4.6 9.3 - - + +
130W ARG* 2.5 34.1 + - + +
131W LEU 3.0 3.1 - - - +
133W LYS* 1.3 73.2 - - + +
135W LYS* 1.3 67.0 + - - +
136W VAL* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W LYS* 3.8 16.0 - - + +
107W MET* 3.5 11.3 + - - +
131W LEU 2.2 18.3 + - - -
132W LYS* 3.3 14.1 - - - +
133W LYS 3.0 5.7 - - - +
134W GLU* 1.3 75.7 - - - +
136W VAL* 1.3 59.9 + - - +
163W LYS* 6.3 0.4 - - + -
166W THR* 3.6 29.6 - - - +
----------------------------------------------------------
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