Contacts of the helix formed by residues 112 - 127 (chain B) in PDB entry 1XRE
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 THR 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 4.5 2.9 - - - -
107B ASP* 3.3 10.8 - - - -
110B PHE* 3.0 10.5 + - - +
111B ASN* 1.3 84.6 - - + +
113B PHE* 1.3 63.2 + - - +
114B ASP* 3.6 9.5 + - - +
115B ASN* 3.1 23.2 + - - +
116B LEU* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 4.0 19.5 - - - -
97B GLU* 3.7 31.6 - - - +
98B PRO* 3.3 32.1 - - + -
106B ILE* 4.0 10.5 - - + -
107B ASP* 3.5 8.0 + - - +
112B THR* 1.3 72.6 - - - +
114B ASP* 1.3 73.8 + - - +
116B LEU* 3.1 16.1 + - + -
117B LYS* 2.9 52.8 + - + +
187B TRP* 3.9 21.5 - + - -
192B TRP* 3.8 20.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU* 4.8 11.2 + - - +
112B THR* 3.4 8.7 + - - +
113B PHE* 1.3 85.8 - - - +
115B ASN* 1.3 57.1 + - - +
117B LYS* 3.3 19.7 + - - +
118B ASP* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 2.8 31.9 - - - +
111B ASN* 4.8 4.1 - - + +
112B THR* 3.1 14.6 + - - +
113B PHE 3.1 0.6 - - - -
114B ASP* 1.3 74.0 - - - +
116B LEU* 1.3 64.7 + - - +
118B ASP* 3.5 15.8 + - - +
119B GLN* 3.1 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.6 48.0 - - + -
110B PHE* 3.7 41.0 - - + +
112B THR 3.2 3.6 + - - -
113B PHE* 3.1 21.1 + - + +
115B ASN* 1.3 76.7 - - - +
117B LYS* 1.3 65.5 + - - +
119B GLN* 3.0 2.3 + - - -
120B LEU* 2.9 27.0 + - + +
135B LEU* 4.0 19.1 - - + -
144B VAL* 3.7 16.2 - - + -
162B LEU* 5.6 2.0 - - + -
187B TRP* 5.0 8.3 - - + -
192B TRP* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 2.9 40.2 + - + +
114B ASP* 3.5 19.7 + - - +
116B LEU* 1.3 77.3 - - - +
118B ASP* 1.3 57.2 + - - +
121B SER* 2.8 37.8 + - - +
184B THR* 5.1 9.9 + - - +
187B TRP* 3.5 55.7 - - + +
188B HIS* 5.7 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP 3.0 13.5 + - - +
115B ASN* 3.8 19.2 + - - +
116B LEU 3.3 0.4 - - - -
117B LYS* 1.3 75.8 - - - +
119B GLN* 1.3 63.4 + - - +
121B SER* 3.5 4.9 + - - -
122B LYS* 3.0 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.5 33.4 - - + -
115B ASN* 3.1 32.3 + - - +
116B LEU 3.0 4.9 + - - +
118B ASP* 1.3 83.4 - - - +
120B LEU* 1.3 62.6 + - - +
122B LYS* 3.5 6.3 + - - +
123B ALA* 3.1 22.7 + - - +
144B VAL* 3.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 2.9 19.6 + - + +
119B GLN* 1.3 73.7 - - - +
121B SER* 1.3 66.8 + - - +
123B ALA* 3.2 2.4 + - + -
124B ALA* 3.0 21.9 + - - +
133B GLY* 3.8 11.2 - - - +
134B TRP* 3.5 37.2 - - - +
135B LEU* 4.6 14.1 - - + +
144B VAL* 3.8 18.3 - - + +
162B LEU* 4.1 21.1 - - + +
164B ILE* 4.9 7.0 - - + +
186B TRP* 4.6 8.7 - - + -
187B TRP* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 2.8 27.0 + - - +
118B ASP* 3.9 5.2 - - - -
120B LEU* 1.3 78.8 - - - +
122B LYS* 1.3 57.4 + - - +
124B ALA* 3.3 2.4 + - - +
125B ILE* 2.9 42.1 + - - +
183B VAL* 3.5 18.6 - - - +
187B TRP* 3.0 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 3.0 50.9 + - - +
119B GLN* 3.7 6.5 - - + +
121B SER* 1.3 76.3 - - - +
123B ALA* 1.3 55.8 + - - +
125B ILE* 3.3 7.8 + - + +
126B SER* 2.9 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN 3.1 14.0 + - - +
120B LEU* 3.6 10.1 - - + +
122B LYS* 1.3 75.4 - - - +
124B ALA* 1.3 62.0 + - - +
126B SER* 3.5 8.0 + - - -
127B ARG* 3.4 21.8 + - - +
133B GLY* 5.1 0.4 - - - -
144B VAL* 3.6 20.2 - - + -
145B MET* 4.3 17.5 - - - +
146B SER* 3.7 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU 3.0 16.2 + - - +
121B SER* 3.6 5.8 - - - +
123B ALA* 1.3 78.2 - - - +
125B ILE* 1.3 57.8 + - - +
126B SER 3.6 0.2 + - - -
127B ARG* 3.6 5.9 + - - +
133B GLY* 4.5 9.3 - - - +
164B ILE* 3.8 28.5 - - + -
166B VAL* 3.7 21.0 - - + +
179B ARG* 2.9 23.7 + - - -
183B VAL* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER* 2.9 29.4 + - - +
122B LYS* 3.3 7.6 + - + +
124B ALA* 1.3 75.5 - - - +
126B SER* 1.3 60.8 + - - +
127B ARG 4.3 1.0 - - - +
128B PHE* 5.7 0.2 - - - -
179B ARG* 3.4 22.0 + - + +
180B PRO* 3.9 43.7 - - + +
183B VAL* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 2.9 20.4 + - - -
123B ALA* 3.5 11.1 + - - -
125B ILE* 1.3 77.5 - - - +
127B ARG* 1.3 58.4 + - - +
128B PHE* 3.0 13.4 + - - +
146B SER* 5.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA 3.4 16.7 + - - +
124B ALA* 3.7 9.0 - - - +
125B ILE 3.3 1.6 - - - -
126B SER* 1.3 72.5 - - - +
128B PHE* 1.3 70.5 + - - +
129B GLY 3.5 4.0 - - - +
130B SER 3.9 11.4 - - - +
131B GLY* 4.0 14.1 - - - +
132B TYR 4.2 2.2 - - - +
146B SER* 3.1 44.4 + - - +
147B THR* 3.4 26.8 + - - +
148B PRO* 3.4 27.1 - - - +
166B VAL* 4.2 8.5 - - + -
179B ARG* 2.8 25.2 + - - +
----------------------------------------------------------
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