Contacts of the helix formed by residues 160 - 171 (chain A) in PDB entry 1XB2
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 GLN 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 3.4 19.3 + - - +
158A MSE 3.5 12.8 - - + +
159A PRO* 1.3 78.1 - - - +
161A THR* 1.3 60.3 + - - +
162A ARG 2.9 3.1 - - - -
163A GLU* 2.8 38.1 + - + +
164A HIS* 2.9 32.0 + - + +
140B PHE* 4.3 8.1 - - + +
141B VAL* 3.6 31.6 - - + +
144B ASN* 3.7 3.8 - - + +
206B LEU* 2.9 38.8 + - - +
208B GLU* 4.1 3.4 + - - +
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 4.6 25.9 - - + +
151A VAL* 5.2 5.1 - - + +
157A PRO* 3.6 10.5 - - + +
158A MSE 2.8 39.2 + - - +
160A GLN* 1.3 78.1 - - - +
162A ARG* 1.3 61.4 + - - +
164A HIS* 3.1 24.2 + - - +
165A LEU* 3.1 17.7 + - + +
199A ILE* 6.4 0.4 - - + -
202A LEU* 3.7 25.4 - - + -
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MSE 4.3 0.4 + - - -
159A PRO 3.3 14.4 + - - +
161A THR* 1.3 80.1 - - - +
163A GLU* 1.3 71.6 + - - +
165A LEU* 3.3 4.5 + - - +
166A LEU* 3.0 61.8 + - - +
202A LEU* 5.3 6.8 - - + +
205A GLU* 4.7 8.4 + - - -
206A PHE* 3.3 36.0 - - + -
144B ASN* 5.6 1.3 - - - +
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Residues in contact with GLU 163 (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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130A HIS* 4.8 2.1 + - - +
159A PRO 3.1 11.3 - - - +
160A GLN* 2.8 18.3 + - + +
162A ARG* 1.3 91.6 + - - +
164A HIS* 1.3 65.4 + - - +
166A LEU* 3.7 11.5 - - + +
167A LEU* 3.1 24.6 + - - +
140B PHE* 3.1 42.2 - - + +
143B ARG* 3.7 22.6 - - + +
144B ASN* 2.6 36.9 + - + +
145B LEU 5.0 0.3 + - - -
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.0 23.8 - - + +
64A GLY* 3.4 45.8 + - - -
65A HIS* 3.6 5.4 - - + -
149A LEU* 4.7 7.9 - - + +
158A MSE 6.1 0.7 - - + -
160A GLN* 2.9 30.9 + - + +
161A THR* 3.1 22.1 + - - +
163A GLU* 1.3 78.8 - - - +
165A LEU* 1.3 59.9 + - - +
167A LEU* 3.6 5.5 - - - +
168A ALA* 3.3 20.8 + - - +
140B PHE* 3.4 47.7 - + - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.6 11.2 - - + -
149A LEU* 4.3 18.8 - - + -
161A THR* 3.1 19.3 + - + +
162A ARG 3.8 5.6 - - - +
164A HIS* 1.3 77.4 - - + +
166A LEU* 1.3 64.3 + - - +
167A LEU 3.2 1.8 - - - -
168A ALA* 3.7 4.0 - - + +
169A ARG* 3.0 24.1 + - - +
176A VAL* 4.8 7.4 - - + -
202A LEU* 4.1 24.5 - - + -
203A LEU* 4.1 25.6 - - + +
206A PHE* 3.8 37.3 - - + -
208A TYR* 4.3 15.1 + - + -
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Residues in contact with LEU 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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130A HIS* 5.3 3.6 - - + -
162A ARG* 3.0 55.5 + - + +
163A GLU* 3.9 14.8 - - + +
164A HIS 3.4 0.2 - - - -
165A LEU* 1.3 75.8 - - - +
167A LEU* 1.3 58.5 + - - +
169A ARG* 3.3 9.3 + - + +
170A GLN* 2.8 33.0 + - - +
206A PHE* 3.4 24.2 - - + -
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Residues in contact with LEU 167 (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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63A ILE* 4.9 7.2 - - + -
130A HIS* 3.7 48.4 - - + +
133A TYR* 3.8 30.3 - - + -
134A VAL* 4.0 4.3 - - + -
144A LEU* 6.2 0.2 - - + -
163A GLU 3.1 17.5 + - - +
164A HIS 3.6 6.7 - - - +
166A LEU* 1.3 74.4 - - - +
168A ALA* 1.3 71.6 + - - +
170A GLN* 3.0 6.3 + - + +
171A ILE* 3.0 44.7 + - + +
140B PHE* 3.8 17.5 - - + -
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Residues in contact with ALA 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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63A ILE* 4.6 6.1 - - + -
147A CYS* 4.1 22.2 - - + -
164A HIS 3.3 12.1 + - - +
165A LEU* 3.7 11.4 - - + +
166A LEU 3.4 0.2 - - - -
167A LEU* 1.3 86.4 - - + +
169A ARG* 1.3 61.0 + - - +
170A GLN 3.4 0.2 + - - -
171A ILE* 3.5 9.8 + - - +
173A VAL* 3.0 32.2 + - + +
176A VAL* 5.1 1.3 - - + -
208A TYR* 3.3 17.5 - - + +
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Residues in contact with ARG 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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165A LEU 3.0 17.8 + - - +
166A LEU* 3.4 11.7 - - + +
168A ALA* 1.3 76.4 - - - +
170A GLN* 1.3 62.7 + - - +
172A GLY* 3.4 12.5 + - - -
173A VAL 3.6 17.1 + - - -
174A GLU* 3.7 28.1 + - - +
206A PHE* 2.7 40.9 + - + +
207A GLY* 3.0 28.8 + - - -
208A TYR* 3.3 19.0 + - + +
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Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 3.6 32.5 + - - -
134A VAL* 3.7 20.4 - - - +
137A MSE 4.6 7.9 - - + +
166A LEU* 2.8 18.2 + - - +
167A LEU* 3.4 6.1 - - - +
169A ARG* 1.3 78.7 - - - +
171A ILE* 1.3 59.6 + - + +
172A GLY 3.1 4.1 + - - -
355A GLN* 6.3 1.2 - - - -
403A ASP* 5.6 1.2 + - - -
143B ARG* 5.1 3.4 + - - +
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Residues in contact with ILE 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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133A TYR* 4.3 11.0 - - + +
134A VAL* 4.2 27.8 - - + +
137A MSE 3.8 33.2 - - + +
144A LEU* 4.0 36.6 + - + +
147A CYS* 5.3 0.7 - - - -
167A LEU* 3.0 47.8 + - + +
168A ALA* 3.5 10.5 - - - +
170A GLN* 1.3 76.6 - - + +
172A GLY* 1.3 58.1 + - - +
173A VAL* 3.7 14.1 + - + +
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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