Contacts of the helix formed by residues 159 - 178 (chain A) 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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A SER* 1.3 58.1 + - - +
161A LEU* 3.1 13.7 + - - +
162A ALA* 2.9 21.4 + - - +
163A ILE* 2.8 44.4 + - - +
191A ILE* 6.1 2.2 - - - +
207A LYS* 5.8 0.9 - - - -
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 1.3 74.0 + - - +
161A LEU* 1.3 62.0 + - - +
163A ILE* 3.6 11.0 + - - +
164A GLN* 3.1 25.3 + - - +
207A LYS* 5.2 10.1 + - - +
160C SER* 3.0 31.9 + - - -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 3.7 11.1 + - - +
160A SER* 1.3 78.2 - - - +
162A ALA* 1.3 68.2 + - - +
164A GLN* 3.3 10.1 + - - +
165A GLU* 3.0 29.4 + - + +
168D ASN* 5.9 1.6 - - - +
218D ASP* 3.4 44.6 - - + +
219D HIS* 4.3 27.8 - - + +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 2.9 25.5 + - - +
161A LEU* 1.3 79.3 - - - +
163A ILE* 1.3 55.7 + - + +
165A GLU* 2.5 39.7 + - - +
166A ASN* 3.4 7.2 + - - +
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 2.8 27.9 + - - +
160A SER* 3.8 8.7 - - - +
162A ALA* 1.3 72.4 - - - +
164A GLN* 1.3 61.6 + - + +
166A ASN* 3.0 25.8 + - - +
167A ALA* 3.3 7.6 - - - +
191A ILE* 5.2 11.2 - - + -
204A VAL* 5.6 3.8 - - + -
207A LYS* 4.0 34.3 - - + +
208A VAL* 4.3 34.1 - - + +
211A ALA* 3.6 25.6 - - + +
212A VAL* 6.1 0.2 - - - +
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER 3.1 14.1 + - - +
161A LEU* 3.7 10.0 - - - +
162A ALA 3.0 1.0 - - - -
163A ILE* 1.3 82.8 - - + +
165A GLU* 1.3 57.1 + - + +
167A ALA* 3.3 5.3 - - + +
168A ASN* 2.5 57.9 + - - +
211A ALA* 5.1 3.1 - - + -
215A ALA* 6.2 0.4 - - + -
214B LYS* 5.5 6.3 - - - +
164D GLN* 4.2 19.3 + - - +
168D ASN* 6.0 0.2 - - - -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.0 33.4 + - + +
162A ALA* 2.5 18.9 + - - +
164A GLN* 1.3 68.5 - - - +
166A ASN* 1.3 60.4 + - - +
167A ALA 2.8 9.9 + - - -
168A ASN* 3.0 19.2 + - - +
169A ALA* 2.9 20.8 + - - +
172A ARG* 4.9 2.8 + - - -
168D ASN* 4.5 9.3 - - - +
172D ARG* 3.3 28.9 + - - -
219D HIS* 3.2 31.6 + - + -
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 3.8 32.7 - - + +
162A ALA 3.4 5.7 + - - +
163A ILE* 3.0 23.9 + - - +
165A GLU* 1.3 77.1 - - - +
167A ALA* 1.3 78.7 + - - +
169A ALA* 3.2 10.2 - - - +
170A LEU* 2.8 46.0 + - - +
188A PRO* 5.3 1.1 - - - +
189A GLU* 4.2 21.5 + - - +
208A VAL* 5.4 8.0 - - - +
212A VAL* 5.6 4.0 - - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE 3.3 19.5 - - - +
164A GLN* 3.3 9.9 - - + +
165A GLU 2.8 0.8 + - - -
166A ASN* 1.3 81.5 - - - +
168A ASN* 1.3 60.6 + - - +
169A ALA 3.0 1.1 - - - -
170A LEU* 3.3 10.6 + - - +
171A ALA* 2.8 29.5 + - - +
211A ALA 3.8 27.4 - - - +
212A VAL* 4.3 6.6 - - + +
215A ALA* 3.7 9.1 - - + +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLN* 2.5 46.2 + - - +
165A GLU* 3.0 15.7 + - - +
167A ALA* 1.3 71.8 - - - +
169A ALA* 1.3 67.8 + - - +
171A ALA* 3.3 9.5 - - - +
172A ARG* 3.0 36.8 + - - +
215A ALA* 3.9 13.7 - - - +
218A ASP* 6.2 0.2 - - - +
219A HIS* 4.0 2.6 + - - +
161D LEU* 5.7 3.4 - - - +
164D GLN* 5.4 2.1 - - - +
165D GLU* 3.2 29.0 + - - +
168D ASN* 5.1 5.5 - - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.1 9.2 - - + +
147A TRP* 5.5 1.3 - - + +
149A PRO* 4.2 14.6 - - + -
165A GLU 2.9 13.1 + - - +
166A ASN* 3.2 16.6 - - - +
168A ASN* 1.3 73.6 - - - +
170A LEU* 1.3 70.4 + - - +
172A ARG* 2.7 33.0 + - - +
173A TYR* 3.0 11.4 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TRP 4.4 0.4 - - - +
149A PRO* 3.8 19.7 - - + +
166A ASN* 2.8 36.0 + - - +
167A ALA* 3.4 7.2 - - - +
169A ALA* 1.3 68.8 - - - +
171A ALA* 1.3 67.1 + - - +
173A TYR* 2.8 24.6 + - + +
174A ALA* 2.7 27.7 + - - +
186A VAL* 3.7 33.4 - - + -
187A GLU 3.8 30.5 - - - +
188A PRO* 4.5 6.3 - - + -
212A VAL* 3.8 19.1 - - + -
216A LEU* 5.2 2.2 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 2.8 16.6 + - - +
168A ASN* 3.3 8.5 - - - +
170A LEU* 1.3 72.9 - - - +
172A ARG* 1.3 55.1 + - - +
174A ALA* 3.6 2.3 + - - +
175A SER* 3.0 28.2 + - - -
215A ALA 3.8 15.7 - - - +
216A LEU* 4.1 17.2 - - + +
219A HIS* 3.0 37.1 - - + +
221A VAL* 3.8 5.5 - - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.5 25.6 - - + +
165A GLU* 4.9 4.0 + - - -
168A ASN* 3.0 31.1 + - - +
169A ALA* 2.7 17.5 + - - +
171A ALA* 1.3 69.6 - - - +
173A TYR* 1.3 59.8 + - - +
175A SER* 3.0 7.6 + - - -
176A ILE* 2.8 39.4 + - + +
219A HIS* 4.1 18.4 - - + +
165D GLU* 2.7 34.1 + - - +
172D ARG* 3.5 26.1 - - - +
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.4 6.1 - - + -
127A LEU* 3.6 23.6 - - + +
130A LEU* 4.2 13.2 - - + +
145A GLY 2.8 24.5 + - - -
147A TRP* 3.4 59.5 + + + +
169A ALA 3.0 6.2 + - - +
170A LEU* 2.8 28.0 + - + +
172A ARG* 1.3 73.8 - - - +
174A ALA* 1.3 64.5 + - + +
176A ILE* 3.2 14.3 + - - +
177A CYS* 3.1 47.8 + - - -
184A PRO* 4.4 4.9 - - + -
185A ILE 3.5 16.3 + - - -
186A VAL* 4.8 4.3 - - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU 2.7 19.5 + - - +
171A ALA 3.8 4.3 - - - +
173A TYR* 1.3 72.6 - - + +
175A SER* 1.3 62.3 + - - +
176A ILE 3.1 0.6 + - - -
177A CYS 3.5 0.5 + - - -
178A GLN* 3.0 30.8 + - - +
184A PRO* 3.6 28.8 - - + +
186A VAL* 4.2 10.1 - - + -
216A LEU* 4.0 22.4 - - + -
221A VAL* 4.1 4.3 - - + -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA 3.0 19.3 + - - -
172A ARG* 3.0 8.0 + - - -
174A ALA* 1.3 77.7 - - - +
176A ILE* 1.3 63.6 + - - +
178A GLN* 3.8 8.5 + - - +
179A GLN* 3.5 23.6 + - - +
219A HIS* 4.2 20.5 + - - -
220A HIS 5.6 0.3 + - - -
221A VAL* 4.6 7.4 - - - +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.3 21.3 - - + +
130A LEU* 4.0 20.4 - - + +
131A SER* 3.5 39.9 - - - +
134A CYS* 4.5 2.7 - - - -
172A ARG* 2.8 31.5 + - + +
173A TYR* 3.4 12.1 - - - +
174A ALA 3.1 0.2 - - - -
175A SER* 1.3 77.3 - - - +
177A CYS* 1.3 69.0 + - - +
179A GLN* 2.8 24.3 + - + +
180A ASN* 3.3 9.4 + - - +
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Residues in contact with CYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.2 15.7 - - - -
134A CYS* 4.6 4.3 - - - -
145A GLY* 5.0 3.4 - - - -
173A TYR* 3.1 55.0 + - - -
174A ALA 3.9 1.3 - - - +
176A ILE* 1.3 75.9 - - - +
178A GLN* 1.3 58.4 + - - +
180A ASN* 2.8 24.8 + - - +
182A LEU* 2.8 38.8 + - + +
184A PRO* 3.7 24.2 - - + -
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.1 34.2 - - + +
11A GLN* 4.3 3.3 + - - +
15A LEU* 3.9 15.2 - - + +
174A ALA 3.0 15.9 + - - +
175A SER* 4.0 7.4 - - - +
176A ILE 3.2 1.0 - - - -
177A CYS* 1.3 73.3 - - - +
179A GLN* 1.3 60.0 + - - +
181A GLY* 4.0 5.7 + - - -
182A LEU 3.5 8.5 + - - +
184A PRO* 3.7 14.9 - - + +
220A HIS 5.0 0.3 - - - +
221A VAL* 3.7 19.3 - - - +
222A TYR* 2.9 45.9 + - - +
225A GLY 2.7 27.8 + - - +
226A THR* 3.7 0.8 + - - -
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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
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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