Contacts of the helix formed by residues 161 - 180 (chain W) in PDB entry 1XDM
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 LEU 161 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159W SER* 2.9 7.8 + - - +
160W SER* 1.3 77.4 - - - +
162W ALA* 1.3 67.1 + - - +
163W ILE 3.3 0.7 - - - -
164W GLN* 3.5 28.0 - - + -
165W GLU* 3.0 33.0 + - + +
168Z ASN* 5.6 3.8 - - - +
218Z ASP* 4.1 38.8 - - + +
219Z HIS* 3.7 31.9 - - + +
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Residues in contact with ALA 162 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158W PRO* 5.2 2.2 - - + -
159W SER* 2.8 33.4 + - - +
161W LEU* 1.3 79.4 - - - +
163W ILE* 1.3 65.0 + - + +
165W GLU* 3.9 2.4 - - - +
166W ASN* 2.9 27.3 + - - +
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Residues in contact with ILE 163 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158W PRO* 5.2 7.9 - - + -
159W SER 3.1 16.8 + - - +
160W SER* 4.7 4.0 - - - +
162W ALA* 1.3 84.0 - - + +
164W GLN* 1.3 66.5 + - - +
166W ASN* 3.6 8.2 + - - +
167W ALA* 2.9 25.1 + - + +
204W VAL* 6.0 1.8 - - + -
207W LYS* 3.2 42.0 - - + +
208W VAL* 4.1 30.7 - - + +
211W ALA* 3.5 30.7 - - + -
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Residues in contact with GLN 164 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160W SER 3.4 20.1 + - - +
161W LEU* 3.5 27.9 - - + +
162W ALA 3.3 0.2 - - - -
163W ILE* 1.3 82.9 - - - +
165W GLU* 1.3 68.8 + - + +
167W ALA* 3.1 12.2 + - - +
168W ASN* 2.6 47.9 + - - +
211W ALA* 6.1 0.9 - - - -
164Z GLN* 4.2 20.8 + - - -
168Z ASN* 5.3 3.5 - - - +
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Residues in contact with GLU 165 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161W LEU* 3.0 36.3 + - + +
162W ALA* 3.9 2.5 - - - +
164W GLN* 1.3 78.6 - - - +
166W ASN* 1.3 65.2 + - - +
168W ASN* 3.0 16.0 + - - +
169W ALA* 3.0 19.9 + - - +
172W ARG* 4.4 1.9 + - - -
168Z ASN* 3.2 21.3 - - - +
172Z ARG* 2.6 36.6 + - - +
219Z HIS* 3.0 29.9 + - + -
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Residues in contact with ASN 166 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149W PRO* 3.0 39.2 - - + +
162W ALA 2.9 23.1 + - - +
163W ILE* 3.6 9.8 + - - +
165W GLU* 1.3 71.3 - - - +
167W ALA* 1.3 84.0 + - - +
169W ALA* 2.7 25.6 + - - +
170W LEU* 3.1 19.9 + - - +
188W PRO* 5.2 2.2 - - - +
189W GLU* 4.6 8.1 + - - +
208W VAL* 4.8 11.1 - - - +
212W VAL* 4.6 6.9 - - - +
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Residues in contact with ALA 167 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163W ILE 2.9 13.8 + - - +
164W GLN* 3.2 11.2 - - - +
166W ASN* 1.3 83.9 - - - +
168W ASN* 1.3 59.1 + - - +
170W LEU* 2.9 13.4 + - - +
171W ALA* 2.8 26.7 + - - +
211W ALA* 3.6 27.4 - - + +
212W VAL* 4.2 9.1 - - + +
215W ALA* 3.7 12.0 - - + +
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Residues in contact with ASN 168 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164W GLN* 2.6 49.4 + - - +
165W GLU* 3.0 15.6 + - - +
167W ALA* 1.3 76.1 - - - +
169W ALA* 1.3 57.1 + - - +
171W ALA* 3.5 7.7 - - - +
172W ARG* 2.8 51.0 + - - +
215W ALA* 3.9 13.9 - - - +
219W HIS* 4.3 11.9 + - - +
161Z LEU* 5.9 1.6 - - - +
164Z GLN* 5.5 0.6 + - - -
165Z GLU* 4.5 11.0 + - - +
168Z ASN* 5.0 3.4 - - - +
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Residues in contact with ALA 169 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147W TRP* 5.2 11.2 - - + +
149W PRO* 4.8 12.6 - - + -
165W GLU 3.0 9.7 + - - +
166W ASN* 2.7 21.5 + - - +
168W ASN* 1.3 66.7 - - - +
170W LEU* 1.3 70.5 + - - +
172W ARG* 3.0 20.7 + - - +
173W TYR* 2.8 23.1 + - - +
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Residues in contact with LEU 170 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147W TRP* 4.2 19.3 - - + +
149W PRO* 4.1 17.0 - - + -
166W ASN* 3.6 31.0 - - - +
167W ALA* 2.9 4.8 + - - +
169W ALA* 1.3 79.7 - - - +
171W ALA* 1.3 66.7 + - - +
172W ARG 2.7 0.7 + - - -
173W TYR* 2.8 13.9 + - + +
174W ALA* 2.8 24.1 + - - +
186W VAL* 4.5 12.1 - - + -
187W GLU 3.6 33.7 - - - +
188W PRO* 4.3 5.6 - - + -
212W VAL* 4.1 27.1 - - + -
216W LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 171 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ALA 2.8 18.2 + - - +
168W ASN 3.5 2.2 - - - +
170W LEU* 1.3 74.0 - - - +
172W ARG* 1.3 58.0 + - - +
174W ALA* 3.5 2.0 - - - +
175W SER* 3.4 19.6 + - - -
212W VAL* 5.8 0.2 - - - +
215W ALA* 3.8 21.8 - - + -
216W LEU* 3.8 18.5 - - + +
219W HIS* 3.0 35.5 - - + +
221W VAL* 3.7 7.4 - - - +
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Residues in contact with ARG 172 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165W GLU 4.4 2.2 + - - -
168W ASN* 2.8 37.1 + - - +
169W ALA* 3.0 31.9 + - - +
170W LEU 2.7 4.2 + - - -
171W ALA* 1.3 68.7 - - - +
173W TYR* 1.3 64.5 + - - +
174W ALA 3.0 1.6 + - - -
175W SER* 3.4 6.5 + - - -
176W ILE* 3.2 29.1 + - + +
219W HIS* 3.5 20.6 - - + +
165Z GLU* 3.2 23.4 + - - -
172Z ARG* 3.5 32.6 - - - +
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Residues in contact with TYR 173 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108W LEU* 4.4 4.9 - - + -
130W LEU* 4.0 26.5 - - + -
145W GLY 3.0 22.6 + - - -
146W LYS 3.4 9.5 - - - -
147W TRP* 3.3 57.0 - + + -
169W ALA 2.8 12.2 + - - +
170W LEU* 2.8 29.8 + - + -
172W ARG* 1.3 72.8 - - - +
174W ALA* 1.3 67.9 + - + +
176W ILE* 3.3 8.8 - - - +
177W CYS* 3.2 37.5 + - - -
184W PRO* 4.3 6.7 - - + -
185W ILE 3.1 21.8 + - - -
186W VAL* 4.9 6.7 - - + -
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Residues in contact with ALA 174 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170W LEU 2.8 15.8 + - - +
171W ALA 3.5 6.5 - - - +
173W TYR* 1.3 78.0 - - + +
175W SER* 1.3 55.3 - - - +
176W ILE 2.6 14.6 + - - -
177W CYS* 2.7 18.4 + - - +
178W GLN* 3.4 10.1 + - - +
184W PRO* 4.0 23.8 - - + -
186W VAL* 4.8 6.3 - - + -
216W LEU* 4.0 12.1 - - + -
221W VAL* 3.7 18.2 - - + -
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Residues in contact with SER 175 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171W ALA 3.4 10.8 + - - -
172W ARG* 3.7 9.9 - - - -
174W ALA* 1.3 78.4 - - - +
176W ILE* 1.3 62.2 + - - +
178W GLN* 3.5 11.3 + - - +
179W GLN* 3.1 32.7 + - - +
219W HIS* 4.1 16.3 + - - -
220W HIS 5.8 0.2 - - - -
221W VAL* 3.8 14.0 - - - +
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Residues in contact with ILE 176 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130W LEU* 4.0 25.1 - - + -
131W SER* 3.4 45.5 - - - +
134W CYS* 4.6 2.9 - - - -
172W ARG* 3.2 18.8 - - + +
173W TYR* 3.3 8.5 - - - +
174W ALA 2.6 5.3 + - - -
175W SER* 1.3 69.7 - - - +
177W CYS* 1.3 58.5 + - - +
179W GLN* 2.6 37.1 + - + +
180W ASN* 3.0 12.6 + - - +
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Residues in contact with CYS 177 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108W LEU* 4.5 4.0 - - - -
130W LEU* 5.2 0.2 - - - -
134W CYS* 4.4 19.1 - - - -
145W GLY* 5.4 2.2 - - - -
173W TYR* 3.2 45.1 - - - -
174W ALA 2.7 9.8 + - - +
176W ILE* 1.3 76.4 - - - +
178W GLN* 1.3 50.6 + - - +
180W ASN* 2.7 23.0 + - - +
182W LEU* 2.7 47.3 + - + +
184W PRO* 4.0 15.3 - - + -
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Residues in contact with GLN 178 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7W LEU* 3.3 27.6 - - + +
11W GLN* 3.6 4.0 + - - +
15W LEU* 3.6 21.6 - - + +
174W ALA 3.4 6.0 + - - +
175W SER* 3.8 9.3 - - - +
176W ILE 3.2 0.6 - - - -
177W CYS* 1.3 75.0 - - - +
179W GLN* 1.3 61.2 + - - +
181W GLY* 3.4 8.9 + - - -
182W LEU 3.5 6.5 - - - -
184W PRO* 3.8 19.5 - - + +
221W VAL* 3.5 13.0 - - - +
222W TYR* 2.9 45.7 + - - +
225W GLY 2.7 27.2 + - - -
226W THR* 3.0 11.9 + - - -
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Residues in contact with GLN 179 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W ALA* 4.2 21.5 - - - +
7W LEU* 4.2 10.2 + - - +
11W GLN* 3.7 21.4 + - - +
131W SER* 6.0 0.7 - - - +
175W SER* 3.1 29.4 + - - +
176W ILE* 2.6 22.1 + - + +
178W GLN* 1.3 73.4 - - - +
180W ASN* 1.3 62.4 + - - +
181W GLY 3.5 1.1 + - - -
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Residues in contact with ASN 180 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131W SER* 3.0 27.7 + - - +
134W CYS* 3.4 19.8 - - + +
135W ALA* 3.2 38.9 - - - +
138W LYS* 3.3 24.1 - - - +
176W ILE* 3.0 20.6 + - - +
177W CYS 2.7 6.9 + - - +
179W GLN* 1.3 83.6 - - - +
181W GLY* 1.3 60.0 + - - +
182W LEU* 3.0 8.3 + - + +
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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