Contacts of the helix formed by residues 169 - 182 (chain A) in PDB entry 1XB4
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 PRO 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.6 24.0 - - + -
45A TYR* 3.6 42.4 - - + +
55A ASP* 5.0 9.0 - - + -
167A ARG 3.6 3.8 - - - +
168A MET* 1.3 96.5 - - + +
170A GLU* 1.3 60.6 + - - +
171A SER* 4.3 2.9 - - - +
172A LEU* 4.1 10.3 - - + -
173A LEU* 2.8 24.1 + - - +
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Residues in contact with GLU 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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151A LEU* 3.6 36.6 + - + +
152A TYR* 3.0 44.9 + - - +
155A SER* 5.1 2.7 - - - +
168A MET 5.0 2.0 - - - +
169A PRO* 1.3 70.5 - - - +
171A SER* 1.3 56.7 + - - +
173A LEU* 2.9 8.8 + - - +
174A TYR* 2.7 35.9 + - - +
195A LYS* 5.0 12.3 + - - -
196A VAL 4.9 4.0 - - - +
197A ILE* 5.1 5.5 - - - +
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Residues in contact with SER 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 2.8 26.0 + - - -
109A SER* 4.5 17.8 + - - -
169A PRO* 4.3 2.1 - - - +
170A GLU* 1.3 79.7 - - - +
172A LEU* 1.3 67.7 + - - +
174A TYR* 3.4 11.7 - - - +
175A TYR* 3.1 24.9 - - - -
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Residues in contact with LEU 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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44A TRP* 4.0 15.9 - - + -
45A TYR* 3.6 29.6 - - + +
106A ILE* 3.7 29.8 - - + -
109A SER 5.1 1.3 - - - +
122A PHE* 3.2 65.6 - - + -
168A MET* 4.1 5.2 - - + -
169A PRO* 3.5 12.0 + - + +
170A GLU 3.1 0.2 - - - -
171A SER* 1.3 89.4 + - - +
173A LEU* 1.3 68.2 + - - +
174A TYR 3.1 1.1 - - - -
175A TYR* 3.1 15.8 + - + +
176A CYS* 3.4 8.8 + - - -
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Residues in contact with LEU 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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135A ILE* 3.5 33.2 - - + -
151A LEU* 3.6 31.0 - - + +
154A LEU* 3.7 20.0 - - + +
155A SER* 4.4 6.3 - - - -
165A PHE* 4.9 7.2 - - + +
168A MET* 3.5 34.3 - - + +
169A PRO 2.8 14.8 + - - +
170A GLU* 2.9 8.7 + - - +
172A LEU* 1.3 77.4 - - - +
174A TYR* 1.3 57.7 + - - +
176A CYS* 2.8 22.2 + - - +
177A LEU* 3.2 26.5 + - + +
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Residues in contact with TYR 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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151A LEU* 4.7 8.7 - - + +
170A GLU 2.7 11.1 + - - +
171A SER* 3.4 13.2 - - - +
173A LEU* 1.3 76.7 - - - +
175A TYR* 1.3 95.2 + + - +
177A LEU* 3.2 11.4 + - - +
178A LYS* 3.1 47.6 + - + +
188A MET* 3.4 37.5 - - + +
196A VAL* 3.7 24.0 - - + -
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Residues in contact with TYR 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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104A LEU* 4.4 16.8 - - + -
106A ILE* 5.1 5.4 - - + -
109A SER 4.8 3.4 - - - -
110A GLY* 3.1 14.1 - - - -
111A ARG* 2.8 53.3 + - + +
122A PHE* 4.8 0.9 - + + -
128A LEU* 4.0 28.0 - - + +
171A SER* 3.1 28.9 - - - -
172A LEU* 3.1 16.3 + - + +
174A TYR* 1.3 100.6 - + - +
176A CYS* 1.3 57.9 + - - +
177A LEU 3.3 0.2 - - - -
178A LYS* 3.8 9.3 - - + +
179A PRO* 3.2 19.4 - - - +
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Residues in contact with CYS 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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122A PHE* 4.3 1.8 - - - -
128A LEU* 3.9 17.5 - - - -
131A TRP* 3.3 43.3 - - + -
132A ALA* 3.0 33.0 - - - +
135A ILE* 3.8 13.4 - - + +
168A MET* 3.7 17.3 - - - -
172A LEU 3.7 12.6 - - - -
173A LEU 2.8 9.2 + - - +
175A TYR* 1.3 77.4 - - - +
177A LEU* 1.3 59.3 + - - +
179A PRO* 3.2 4.5 - - - +
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Residues in contact with LEU 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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135A ILE* 4.0 26.9 - - + -
139A PHE* 4.8 2.2 - - + -
151A LEU* 3.4 33.0 - - + -
154A LEU* 4.1 13.2 - - + -
173A LEU* 3.5 21.8 - - + +
174A TYR* 3.2 8.2 + - - +
176A CYS* 1.3 77.7 - - - +
178A LYS* 1.3 56.2 + - - +
179A PRO* 3.0 3.1 - - - -
180A LEU* 2.5 53.1 + - + +
181A CYS* 3.3 6.5 + - - -
188A MET* 5.0 6.3 - - - -
199A ILE* 3.7 31.4 - - + -
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Residues in contact with LYS 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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174A TYR* 3.1 39.0 + - + +
175A TYR* 3.8 14.4 - - + +
177A LEU* 1.3 74.6 - - - +
179A PRO* 1.3 60.9 - - + +
181A CYS* 2.7 36.2 + - + +
182A ASP* 3.1 36.4 + - - +
188A MET* 4.0 17.2 - - + -
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Residues in contact with PRO 179 (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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128A LEU* 4.3 9.2 - - + +
129A ASP* 3.5 25.8 - - - +
132A ALA* 3.5 20.6 - - + -
175A TYR 3.2 16.2 - - - +
176A CYS 3.2 13.0 - - - +
177A LEU 3.2 4.3 - - - -
178A LYS* 1.3 91.2 - - + +
180A LEU* 1.3 51.4 + - - +
182A ASP* 2.5 37.5 - - + +
183A ARG* 3.4 18.7 - - - +
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Residues in contact with LEU 180 (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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132A ALA* 3.7 33.4 - - + +
133A SER* 4.7 0.7 - - - +
135A ILE* 5.2 0.7 - - + -
136A LEU* 3.9 32.5 - - + +
177A LEU* 2.5 43.7 + - + +
179A PRO* 1.3 71.7 - - + +
181A CYS* 1.3 51.1 + - - +
182A ASP 2.7 17.0 - - - +
183A ARG* 4.2 17.3 - - - +
185A ARG* 2.8 34.5 + - + +
186A ALA* 3.1 18.0 + - + -
201A VAL* 4.4 17.0 - - + -
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Residues in contact with CYS 181 (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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177A LEU 4.3 6.1 - - - -
178A LYS* 2.7 21.1 + - - +
180A LEU* 1.3 68.6 - - - +
182A ASP* 1.3 70.7 + - - +
184A ASN* 3.2 18.2 + - - +
186A ALA* 3.6 24.9 - - - +
187A THR* 4.9 0.4 - - - -
188A MET* 3.3 50.3 - - + -
199A ILE* 5.2 0.7 - - - -
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Residues in contact with ASP 182 (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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178A LYS* 3.1 35.0 + - - +
179A PRO* 2.5 27.4 - - + +
180A LEU 2.7 11.3 - - - +
181A CYS* 1.3 78.1 - - - +
183A ARG* 1.3 66.1 + - + +
184A ASN* 2.9 2.0 - - - -
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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