Contacts of the helix formed by residues 160 - 180 (chain J) in PDB entry 1XFB
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 SER 160 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J THR* 4.3 3.7 - - - +
122J GLU* 2.6 31.3 + - - -
157J ARG 4.9 5.8 - - - -
158J THR 2.2 17.1 + - - -
159J PRO* 1.3 70.3 - - - +
161J ALA* 1.3 68.6 + - - +
162J LEU* 3.9 7.9 + - - +
163J ALA* 2.8 23.6 + - - +
164J ILE* 2.8 13.9 + - - +
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Residues in contact with ALA 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159J PRO 4.1 0.6 + - - -
160J SER* 1.3 71.9 - - - +
162J LEU* 1.3 53.8 + - - +
164J ILE* 3.3 7.1 + - - +
165J LEU* 2.7 41.3 + - + +
161L ALA* 5.2 14.6 - - + -
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I ASP* 3.9 24.2 - - - +
220I HIS* 3.6 42.2 - - + +
221I HIS* 4.0 18.8 - - + +
116J LEU* 4.0 15.7 - - + -
117J ALA 4.5 5.2 - - - +
119J THR* 3.9 23.1 - - + -
160J SER* 2.9 8.3 + - - +
161J ALA* 1.3 78.8 - - - +
163J ALA* 1.3 56.4 + - - +
165J LEU* 3.1 13.2 + - + +
166J GLU* 2.7 39.2 + - + +
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Residues in contact with ALA 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU* 3.8 18.1 - - + +
122J GLU* 2.9 34.3 - - + +
123J THR 4.7 0.4 - - - +
152J LEU* 3.8 12.3 - - + +
159J PRO* 4.6 1.1 - - + -
160J SER* 2.8 16.9 + - - +
162J LEU* 1.3 75.3 - - - +
164J ILE* 1.3 54.1 + - - +
166J GLU 2.6 20.8 - - - +
167J ASN* 2.6 24.7 + - - +
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Residues in contact with ILE 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J LEU* 4.6 7.0 - - + -
159J PRO* 3.6 35.2 - - + +
160J SER 2.8 20.7 + - - +
161J ALA* 3.8 5.8 - - - +
163J ALA* 1.3 68.0 - - - +
165J LEU* 1.3 58.6 + - - +
166J GLU 2.5 18.7 - - - +
167J ASN* 4.2 0.4 - - - +
168J ALA* 3.0 20.5 + - + +
205J VAL* 6.0 0.4 - - + -
208J LYS* 4.7 10.1 - - + +
209J VAL* 4.4 29.4 - - + +
212J ALA* 3.5 29.4 - - + -
3K HIS* 6.3 1.1 - - + -
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I ASN* 3.5 28.5 - - - +
219I ASP* 4.1 28.7 - - + +
220I HIS* 4.2 5.4 - - - +
161J ALA* 2.7 24.4 + - + +
162J LEU* 3.4 10.5 - - + +
164J ILE* 1.3 72.2 - - - +
166J GLU* 1.3 89.8 + - + +
168J ALA* 3.6 3.4 - - - +
169J ASN* 3.1 24.5 + - + +
212J ALA* 6.1 0.4 - - - -
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Residues in contact with GLU 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I LEU* 5.3 2.4 - - - +
169I ASN* 3.1 26.5 + - - -
173I ARG* 3.2 29.0 + - - +
220I HIS* 4.2 2.5 - - + -
116J LEU* 4.4 11.4 - - + -
124J THR* 3.0 36.5 + - - +
125J THR 5.4 0.3 - - - +
162J LEU* 2.7 25.9 + - + +
163J ALA 2.6 13.5 - - - +
164J ILE 2.5 19.9 - - - +
165J LEU* 1.3 81.8 - - + +
167J ASN* 1.3 57.4 + - - +
168J ALA 3.1 0.4 - - - -
169J ASN* 3.9 4.8 + - - +
170J VAL* 3.3 15.6 - - - +
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Residues in contact with ASN 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU* 4.7 0.6 - - - +
123J THR 3.0 23.6 + - - +
124J THR* 3.5 17.7 - - - +
150J CYS* 3.3 31.1 - - + +
151J VAL 4.2 3.1 + - - -
152J LEU* 3.5 23.0 - - + +
163J ALA* 2.6 24.7 + - - +
164J ILE* 4.2 0.9 - - - +
166J GLU* 1.3 80.7 + - - +
168J ALA* 1.3 56.6 + - - +
169J ASN 3.0 0.4 - - - -
170J VAL* 3.1 15.7 - - - +
171J LEU* 2.7 43.0 + - + +
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Residues in contact with ALA 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J ILE* 3.0 19.2 + - + +
165J LEU* 3.6 4.3 - - - +
166J GLU 2.8 6.9 + - - -
167J ASN* 1.3 74.2 - - - +
169J ASN* 1.3 62.0 + - - +
171J LEU* 3.7 11.7 - - - +
172J ALA 3.2 16.3 + - - -
212J ALA* 4.1 11.0 - - + +
213J VAL* 4.0 33.0 - - + +
216J ALA* 3.4 16.6 - - + +
217J LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I LEU* 3.6 15.3 - - - +
166I GLU* 2.9 26.5 + - - -
169I ASN* 3.6 22.0 - - - +
165J LEU* 3.1 20.2 + - + +
166J GLU* 4.3 8.6 + - - +
167J ASN 3.0 0.2 - - - -
168J ALA* 1.3 76.0 - - - +
170J VAL* 1.3 65.7 + - - +
172J ALA* 3.1 7.6 + - - +
173J ARG* 2.9 24.4 + - - +
216J ALA* 4.5 3.9 - - - +
220J HIS* 2.8 25.8 + - - -
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Residues in contact with VAL 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J THR* 3.5 9.4 - - - +
125J THR 3.5 10.8 - - - +
128J LEU* 4.3 14.4 - - + -
148J TRP* 3.3 38.6 - - + +
150J CYS* 4.6 1.6 - - - -
166J GLU* 3.3 24.0 - - - +
167J ASN* 3.0 28.0 + - - +
169J ASN* 1.3 75.8 - - - +
171J LEU* 1.3 64.0 + - - +
173J ARG* 3.1 7.9 + - - +
174J TYR* 2.9 22.7 + - - +
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Residues in contact with LEU 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J TRP* 3.6 27.6 - - + +
150J CYS* 3.6 22.7 - - + -
167J ASN* 2.7 25.7 + - + +
168J ALA 3.7 3.6 - - - +
170J VAL* 1.3 74.4 - - - +
172J ALA* 1.3 54.0 + - - +
174J TYR* 3.2 9.3 + - + -
175J ALA* 2.8 36.1 + - - +
187J VAL* 3.5 35.7 - - + -
188J GLU 4.0 5.8 - - - +
189J PRO* 3.8 26.5 - - + -
213J VAL* 4.2 15.0 - - + -
217J LEU* 4.8 1.6 - - + -
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Residues in contact with ALA 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J ALA 3.2 11.2 + - - +
169J ASN 3.1 7.1 + - - +
171J LEU* 1.3 80.1 - - - +
173J ARG* 1.3 62.0 + - - +
176J SER* 2.9 25.6 + - - -
216J ALA* 3.8 17.0 - - + +
217J LEU* 3.7 16.3 - - + +
220J HIS* 3.4 35.3 - - + +
222J VAL* 3.6 3.8 - - - +
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Residues in contact with ARG 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I VAL* 3.9 11.3 - - - +
115I PRO 3.5 23.0 + - - -
116I LEU* 4.1 12.2 - - - +
117I ALA 5.3 1.0 - - - +
124I THR* 3.5 23.3 - - - +
125I THR 5.7 0.8 + - - -
126I GLN* 6.1 1.2 - - - +
166I GLU* 3.3 29.2 - - - +
128J LEU* 3.7 29.9 - - + +
169J ASN* 2.9 18.8 + - - +
170J VAL* 3.1 9.2 + - - +
172J ALA* 1.3 74.8 - - - +
174J TYR* 1.3 63.8 + - - +
176J SER* 3.1 11.2 + - - -
177J ILE* 3.0 60.3 + - - +
220J HIS* 3.8 18.8 + - + -
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Residues in contact with TYR 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 3.6 16.6 - - + -
128J LEU* 3.7 9.8 - - + +
131J LEU* 4.0 7.0 - - + -
146J ALA* 3.0 25.3 + - + -
147J LYS* 3.3 1.6 - - - -
148J TRP* 3.3 59.2 - + + -
170J VAL 2.9 12.4 + - - +
171J LEU* 3.4 16.8 - - + +
173J ARG* 1.3 76.8 - - - +
175J ALA* 1.3 71.2 - - - +
177J ILE* 3.2 3.6 + - - +
178J CYS* 3.0 46.4 + - - -
185J PRO* 3.5 15.1 - - + +
186J ILE 2.9 31.5 + - - -
187J VAL* 4.4 6.7 - - + -
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Residues in contact with ALA 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J LEU 2.8 20.1 + - - +
172J ALA 3.7 0.4 - - - +
174J TYR* 1.3 75.2 - - + +
176J SER* 1.3 64.1 + - - +
178J CYS* 3.2 3.5 + - - +
179J GLN* 3.1 28.3 + - - +
185J PRO* 3.8 27.1 - - + -
187J VAL* 4.5 6.1 - - + -
217J LEU* 3.9 11.2 - - + -
222J VAL* 3.6 23.3 - - + -
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Residues in contact with SER 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I ALA* 3.2 32.2 + - - +
172J ALA 2.9 18.1 + - - -
173J ARG* 3.4 13.0 + - - -
175J ALA* 1.3 76.3 - - - +
177J ILE* 1.3 65.3 - - - +
179J GLN* 3.5 6.4 + - - +
180J GLN* 3.3 21.7 + - - +
220J HIS* 3.7 22.5 + - - -
221J HIS 5.5 0.5 + - - -
222J VAL* 3.7 7.7 - - - +
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Residues in contact with ILE 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J LEU* 3.9 28.3 - - + +
131J LEU* 4.0 20.6 - - + +
132J SER* 3.5 41.1 - - - +
135J CYS* 4.8 0.4 - - - -
173J ARG* 3.0 45.2 + - - +
174J TYR 3.6 4.9 - - - +
176J SER* 1.3 73.2 - - - +
178J CYS* 1.3 66.4 + - - +
180J GLN* 3.1 26.7 - - - +
181J ASN* 3.1 9.6 + - - +
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Residues in contact with CYS 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 5.1 0.4 - - - -
131J LEU* 4.8 1.6 - - - -
135J CYS* 4.0 25.4 - - - -
146J ALA* 4.1 13.0 - - - -
174J TYR* 3.0 47.4 + - - -
175J ALA 3.6 7.2 - - - +
177J ILE* 1.3 76.1 - - - +
179J GLN* 1.3 59.6 + - - +
181J ASN* 2.8 20.8 + - - +
183J ILE* 3.1 34.5 + - + +
185J PRO* 3.8 10.8 - - + -
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Residues in contact with GLN 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LEU* 3.5 20.5 - - + +
12J GLN* 5.4 1.7 + - - +
16J LEU* 3.8 20.6 - - + +
175J ALA 3.1 14.5 + - - +
176J SER* 3.9 5.1 - - - +
177J ILE 3.3 0.2 - - - -
178J CYS* 1.3 71.6 - - - +
180J GLN* 1.3 58.8 + - - +
181J ASN 2.9 9.9 + - - -
182J GLY* 3.1 12.3 + - - -
183J ILE 3.8 4.7 - - - +
185J PRO* 3.8 12.6 - - + -
221J HIS 4.8 0.7 - - - +
222J VAL* 3.7 11.5 - - - +
223J TYR* 2.8 59.8 + - - +
226J GLY* 3.0 23.4 + - - -
227J THR* 3.5 4.6 - - - +
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Residues in contact with GLN 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I PRO* 5.1 19.7 - - - +
117I ALA* 4.0 26.4 - - + +
7J ALA 5.3 4.5 - - - +
8J LEU* 4.1 12.7 - - + +
12J GLN* 4.8 10.2 + - - +
132J SER* 3.5 18.2 + - - -
176J SER 3.3 9.8 + - - +
177J ILE* 3.1 28.0 - - - +
179J GLN* 1.3 76.7 - - - +
181J ASN* 1.3 62.5 + - - +
182J GLY 3.5 0.6 + - - -
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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
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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) + - + + + + + -
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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