Contacts of the helix formed by residues 120 - 134 (chain B) in PDB entry 1L9W
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 GLY 120 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU 3.8 3.7 + - - -
118B PHE 3.2 4.7 - - - -
119B THR* 1.3 79.0 - - - +
121B ASP* 1.3 68.0 + - - -
122B ALA 3.3 2.7 - - - -
123B ASP* 3.1 9.9 + - - -
124B VAL* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.8 3.8 - - - +
120B GLY* 1.3 71.1 - - - +
122B ALA* 1.4 58.7 + - - +
124B VAL* 3.1 8.4 + - - +
125B LYS* 2.8 34.4 + - - +
160B LYS* 3.0 37.8 + - - -
164B LEU* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 3.3 1.0 - - - -
121B ASP* 1.4 77.6 - - - +
123B ASP* 1.3 63.9 + - - +
125B LYS* 3.5 5.0 + - - +
126B ALA* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 3.9 16.8 - - - +
98B LEU* 3.6 28.1 - - + +
119B THR* 4.3 20.1 - - + +
120B GLY* 3.1 10.8 + - - +
122B ALA* 1.3 75.4 - - - +
124B VAL* 1.4 66.6 + - - +
126B ALA* 3.6 4.0 + - - +
127B THR* 3.0 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 5.8 0.9 - - + -
115B LEU* 3.9 20.4 - - + +
116B GLU 3.6 13.7 - - - +
117B LEU 4.0 7.2 - - - +
119B THR* 3.5 29.4 - - + +
120B GLY 2.9 25.9 + - - +
121B ASP* 3.2 18.4 - - - +
123B ASP* 1.4 72.4 - - - +
125B LYS* 1.4 57.2 + - - +
127B THR* 3.1 2.5 + - - -
128B VAL* 2.9 36.0 + - - +
140B MET* 4.8 11.2 - - + -
164B LEU* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP 2.8 22.7 + - - +
122B ALA* 4.0 4.5 - - - +
124B VAL* 1.4 73.7 - - - +
126B ALA* 1.3 60.7 + - - +
128B VAL* 3.3 6.3 + - - +
129B ASP* 3.1 58.0 + - - +
163B ALA 4.4 4.1 + - - +
164B LEU* 2.6 54.1 + - + +
165B GLY* 3.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 6.5 0.4 - - + -
102B ARG* 4.5 9.0 + - - +
122B ALA 3.1 17.5 + - - +
123B ASP* 4.0 5.2 - - - +
125B LYS* 1.3 75.5 - - - +
127B THR* 1.3 61.0 + - - +
129B ASP* 3.7 5.7 + - - +
130B TYR* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.4 22.3 - - + +
101B ASN* 4.6 9.0 - - + -
102B ARG* 3.9 18.0 + - - +
105B ILE* 4.5 8.7 - - + -
113B ILE* 4.2 12.8 - - + -
115B LEU* 3.7 32.1 - - + -
123B ASP 3.0 15.8 + - - -
124B VAL 3.1 2.0 + - - -
126B ALA* 1.3 73.8 - - - +
128B VAL* 1.3 56.3 + - - +
130B TYR* 3.1 5.0 + - + +
131B ALA* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.9 9.6 - - + -
124B VAL 2.9 22.0 + - - +
125B LYS* 3.6 5.6 - - - +
127B THR* 1.3 75.6 - - - +
129B ASP* 1.3 64.5 + - - +
131B ALA* 3.2 3.5 + - - +
132B HIS* 2.9 55.5 + - + +
138B VAL* 4.1 15.9 - - + -
140B MET* 3.8 28.3 - - + -
164B LEU 3.8 15.9 - - - +
165B GLY* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.1 40.7 + - - +
126B ALA* 4.1 5.8 - - - +
128B VAL* 1.3 77.4 - - - +
130B TYR* 1.3 68.1 + - - +
132B HIS* 3.9 9.0 + - - +
133B ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 3.3 49.8 - - + +
105B ILE* 3.6 23.6 - - + -
106B ASP* 2.5 37.7 + - - -
126B ALA 3.2 18.0 + - - +
127B THR* 3.1 5.5 + - - +
129B ASP* 1.3 77.8 - - - +
131B ALA* 1.4 60.0 + - - +
133B ALA* 3.2 5.9 + - + +
134B HIS* 2.7 48.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.0 23.3 - - + +
113B ILE* 4.5 2.5 - - + -
127B THR 2.7 20.7 + - - +
128B VAL 3.4 5.4 - - - +
130B TYR* 1.4 72.5 - - - +
132B HIS* 1.3 57.1 + - - +
134B HIS* 2.9 17.8 + - - -
136B VAL* 2.9 42.7 + - + +
138B VAL* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 2.9 32.3 + - + +
129B ASP* 3.2 9.3 + - - +
131B ALA* 1.3 76.6 - - - +
133B ALA* 1.3 56.6 + - - +
135B ASN* 3.0 21.6 + - - +
136B VAL 3.5 17.5 - - - +
137B TYR* 4.8 2.9 - + - -
138B VAL* 4.3 3.5 - - + +
165B GLY* 3.3 27.4 - - - -
167B ASP* 2.6 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASP 3.0 15.9 + - - +
130B TYR* 3.2 8.3 + - + +
132B HIS* 1.3 74.7 - - - +
134B HIS* 1.3 72.8 + - + +
135B ASN 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.7 27.4 - - + +
106B ASP* 4.1 12.7 + - - -
130B TYR* 2.7 60.5 + + - -
131B ALA 2.9 4.6 + - - +
133B ALA* 1.3 87.6 + - + +
135B ASN* 1.3 67.9 + - - +
136B VAL* 3.2 8.3 + - + +
----------------------------------------------------------
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