Contacts of the helix formed by residues 160 - 180 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G HIS* 6.6 0.2 - - - -
119H THR* 4.3 4.0 - - - +
122H GLU* 2.6 31.6 + - - -
157H ARG 4.9 5.8 - - - -
158H THR 2.2 17.5 + - - -
159H PRO* 1.3 69.1 - - - +
161H ALA* 1.3 68.6 + - - +
162H LEU* 3.9 8.4 + - - +
163H ALA* 2.8 24.1 + - - +
164H ILE* 2.8 15.4 + - - +
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Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F ALA* 5.3 13.5 - - + -
159H PRO 4.1 0.4 + - - -
160H SER* 1.3 71.2 - - - +
162H LEU* 1.3 53.5 + - - +
164H ILE* 3.3 7.7 + - - +
165H LEU* 2.7 41.7 + - + +
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ASP* 3.8 19.3 - - - +
220G HIS* 3.5 42.6 - - + +
221G HIS* 3.9 31.4 - - + +
116H LEU* 4.0 15.3 - - + -
117H ALA 4.5 5.6 - - - +
119H THR* 3.9 17.0 - - + -
160H SER* 2.9 8.7 + - - +
161H ALA* 1.3 79.5 - - - +
163H ALA* 1.3 55.8 + - - +
165H LEU* 3.1 12.1 + - + +
166H GLU* 2.7 39.7 + - + +
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Residues in contact with ALA 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 3.8 18.3 - - + +
122H GLU* 2.9 34.1 - - + +
123H THR 4.7 0.4 - - - +
152H LEU* 3.8 12.0 - - + +
159H PRO* 4.6 1.1 - - + -
160H SER* 2.8 17.6 + - - +
162H LEU* 1.3 75.9 - - - +
164H ILE* 1.3 53.5 + - - +
166H GLU 2.6 21.0 - - - +
167H ASN* 2.6 24.7 + - - +
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Residues in contact with ILE 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E HIS* 6.3 1.8 - - + -
152H LEU* 4.6 7.0 - - + -
159H PRO* 3.6 35.4 - - + +
160H SER 2.8 21.4 + - - +
161H ALA* 3.8 5.8 - - - +
163H ALA* 1.3 68.3 - - - +
165H LEU* 1.3 58.1 + - - +
166H GLU 2.5 18.7 - - - +
167H ASN* 5.0 0.2 - - - -
168H ALA* 3.0 20.8 + - + +
205H VAL* 6.0 0.4 - - + -
208H LYS* 4.7 9.9 - - + +
209H VAL* 4.4 29.8 - - + +
212H ALA* 3.5 29.4 - - + -
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN* 3.4 27.1 - - - +
219G ASP* 4.0 31.2 - - + +
220G HIS* 4.1 8.3 - - + +
161H ALA* 2.7 24.4 + - + +
162H LEU* 3.4 10.1 - - + +
164H ILE* 1.3 72.0 - - - +
166H GLU* 1.3 86.9 + - + +
168H ALA* 3.6 3.6 - - - +
169H ASN* 3.1 24.5 + - + +
212H ALA* 6.1 0.4 - - - -
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G LEU* 5.2 2.6 - - - +
169G ASN* 3.0 28.8 + - - -
173G ARG* 3.1 30.6 + - - +
220G HIS* 4.1 2.3 - - + -
116H LEU* 4.4 9.0 - - + -
124H THR* 3.0 35.3 + - - +
125H THR 5.4 0.3 - - - +
162H LEU* 2.7 24.7 + - + +
163H ALA 2.6 13.1 - - - +
164H ILE 2.5 20.1 - - - +
165H LEU* 1.3 81.5 - - + +
167H ASN* 1.3 57.8 + - - +
169H ASN* 3.9 4.5 - - - +
170H VAL* 3.3 15.6 - - - +
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Residues in contact with ASN 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 4.7 0.6 - - - +
123H THR 3.0 23.4 + - - +
124H THR* 3.5 17.8 - - - +
150H CYS* 3.3 30.7 - - + +
151H VAL 4.2 2.9 + - - -
152H LEU* 3.5 22.4 - - + +
163H ALA* 2.6 25.8 + - - +
164H ILE* 4.2 0.9 - - - +
166H GLU* 1.3 80.5 + - - +
168H ALA* 1.3 56.1 + - - +
169H ASN 3.0 0.4 - - - -
170H VAL* 3.1 15.3 - - - +
171H LEU* 2.7 42.8 + - + +
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Residues in contact with ALA 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H ILE* 3.0 19.4 + - + +
165H LEU* 3.6 4.3 - - - +
166H GLU 2.8 7.5 + - - -
167H ASN* 1.3 73.8 - - - +
169H ASN* 1.3 61.6 + - - +
171H LEU* 3.7 11.9 - - - +
172H ALA 3.2 16.3 + - - -
212H ALA* 4.1 11.2 - - + +
213H VAL* 4.0 33.2 - - + +
216H ALA* 3.4 17.1 - - + +
217H LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LEU* 3.6 14.9 - - - +
166G GLU* 2.9 26.3 + - - -
169G ASN* 3.5 23.3 - - - +
165H LEU* 3.1 20.0 + - + +
166H GLU* 4.3 8.4 + - - +
167H ASN 3.0 0.2 - - - -
168H ALA* 1.3 77.4 - - - +
170H VAL* 1.3 66.3 + - - +
172H ALA* 3.1 7.4 + - - +
173H ARG* 2.9 25.1 + - - +
216H ALA* 4.5 4.3 - - - +
220H HIS* 2.8 26.0 + - - -
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Residues in contact with VAL 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H THR* 3.5 9.9 - - - +
125H THR 3.5 11.0 - - - +
128H LEU* 4.3 14.1 - - + -
148H TRP* 3.3 38.6 - - + +
150H CYS* 4.6 1.3 - - - -
166H GLU* 3.3 23.6 - - - +
167H ASN* 3.0 27.3 + - - +
169H ASN* 1.3 76.3 - - - +
171H LEU* 1.3 64.5 + - - +
173H ARG* 3.1 7.7 + - - +
174H TYR* 2.9 22.7 + - - +
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Residues in contact with LEU 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H TRP* 3.6 26.9 - - + +
150H CYS* 3.6 23.8 - - + -
167H ASN* 2.7 25.5 + - + +
168H ALA 3.7 3.6 - - - +
170H VAL* 1.3 73.8 - - - +
172H ALA* 1.3 53.1 + - - +
174H TYR* 3.2 9.7 + - + -
175H ALA* 2.8 36.5 + - - +
187H VAL* 3.5 36.1 - - + -
188H GLU 4.0 5.8 - - - +
189H PRO* 3.8 26.7 - - + -
213H VAL* 4.2 14.4 - - + -
217H LEU* 4.8 2.0 - - + -
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Residues in contact with ALA 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H ALA 3.2 11.2 + - - +
169H ASN 3.1 6.6 + - - +
171H LEU* 1.3 79.9 - - - +
173H ARG* 1.3 60.9 + - - +
176H SER* 2.9 26.2 + - - -
216H ALA* 3.8 17.7 - - + +
217H LEU* 3.7 17.2 - - + +
220H HIS* 3.4 35.1 - - + +
222H VAL* 3.6 4.0 - - - +
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Residues in contact with ARG 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 3.9 10.9 - - - +
115G PRO 3.4 23.2 + - - -
116G LEU* 3.9 12.7 - - - +
117G ALA 5.1 2.0 - - - +
124G THR* 3.3 24.7 - - - +
125G THR 5.7 0.6 + - - -
126G GLN* 6.2 0.4 - - - +
166G GLU* 3.2 29.8 + - - +
128H LEU* 3.7 29.2 - - + +
169H ASN* 2.9 18.4 + - - +
170H VAL* 3.1 8.7 + - - +
172H ALA* 1.3 75.3 - - - +
174H TYR* 1.3 63.4 + - - +
176H SER* 3.1 10.2 + - - -
177H ILE* 3.0 61.0 + - - +
220H HIS* 3.8 19.0 + - + -
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Residues in contact with TYR 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H VAL* 3.6 17.0 - - + -
128H LEU* 3.7 9.5 - - + +
131H LEU* 4.0 7.2 - - + -
146H ALA* 3.0 25.5 + - + -
147H LYS* 3.3 1.7 - - - -
148H TRP* 3.3 59.2 - + + -
170H VAL 2.9 12.2 + - - +
171H LEU* 3.4 16.8 - - + +
173H ARG* 1.3 75.7 - - - +
175H ALA* 1.3 71.4 + - - +
177H ILE* 3.2 3.5 + - - +
178H CYS* 3.0 45.6 + - - -
185H PRO* 3.5 15.8 - - + +
186H ILE 2.9 31.8 + - - -
187H VAL* 4.4 6.7 - - + -
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Residues in contact with ALA 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H LEU 2.8 19.9 + - - +
172H ALA 3.7 0.4 - - - +
174H TYR* 1.3 75.2 - - + +
176H SER* 1.3 63.4 + - - +
178H CYS* 3.2 3.1 + - - +
179H GLN* 3.1 28.7 + - - +
185H PRO* 3.8 27.8 - - + -
187H VAL* 4.5 6.1 - - + -
217H LEU* 3.9 10.5 - - + -
222H VAL* 3.6 23.8 - - + -
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Residues in contact with SER 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ALA* 3.2 30.8 + - - +
172H ALA 2.9 18.5 + - - -
173H ARG* 3.4 12.0 + - - -
175H ALA* 1.3 77.0 - - - +
177H ILE* 1.3 64.9 + - - +
179H GLN* 3.5 6.8 + - - +
180H GLN* 3.3 21.9 + - - +
220H HIS* 3.7 23.5 + - - -
221H HIS 5.5 0.5 + - - -
222H VAL* 3.7 8.2 - - - +
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Residues in contact with ILE 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 6.3 0.2 - - + -
128H LEU* 3.9 27.8 - - + +
131H LEU* 4.0 20.0 - - + +
132H SER* 3.5 41.1 - - - +
135H CYS* 4.8 0.4 - - - -
173H ARG* 3.0 45.3 + - - +
174H TYR 3.6 5.4 - - - +
176H SER* 1.3 72.9 - - - +
178H CYS* 1.3 67.2 + - - +
180H GLN* 3.1 26.9 - - - +
181H ASN* 3.1 9.7 + - - +
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Residues in contact with CYS 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H VAL* 5.1 0.4 - - - -
131H LEU* 4.8 1.1 - - - -
135H CYS* 4.0 25.4 - - - -
146H ALA* 4.1 13.0 - - - -
174H TYR* 3.0 47.6 + - - -
175H ALA 3.6 7.0 - - - +
177H ILE* 1.3 76.1 - - - +
179H GLN* 1.3 58.9 + - - +
181H ASN* 2.8 21.0 + - - +
183H ILE* 3.1 34.2 + - + +
185H PRO* 3.8 10.3 - - + -
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Residues in contact with GLN 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 3.5 21.1 - - + +
12H GLN* 5.4 1.7 + - - +
16H LEU* 3.8 20.4 - - + +
175H ALA 3.1 15.0 + - - +
176H SER* 3.9 5.3 - - - +
177H ILE 3.3 0.2 - - - -
178H CYS* 1.3 71.4 - - - +
180H GLN* 1.3 57.8 + - - +
181H ASN 2.9 10.1 + - - -
182H GLY* 3.1 12.5 + - - -
183H ILE 3.8 4.5 - - - +
185H PRO* 3.8 12.3 - - + -
221H HIS 4.8 0.5 - - - +
222H VAL* 3.7 11.9 - - - +
223H TYR* 2.8 59.2 + - - +
226H GLY* 3.0 24.0 + - - -
227H THR* 3.5 4.6 - - - +
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Residues in contact with GLN 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G PRO* 5.0 19.8 - - - +
117G ALA* 3.6 30.0 - - + +
7H ALA 5.3 4.5 - - - +
8H LEU* 4.1 12.1 - - + +
12H GLN* 4.8 10.6 + - - +
132H SER* 3.5 17.5 + - - -
176H SER 3.3 9.3 + - - +
177H ILE* 3.1 28.6 - - - +
179H GLN* 1.3 77.6 - - - +
181H ASN* 1.3 61.6 + - - +
182H 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
------------------------------------------------------------
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