Contacts of the helix formed by residues 160 - 174 (chain A) in PDB entry 1Q2U
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 THR 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.7 0.7 - - - +
145A ARG* 3.5 46.9 - - + +
155A SER* 2.7 23.7 + - - -
156A ARG* 3.2 14.8 + - + -
157A GLY 2.9 26.0 + - - +
159A GLY* 1.3 78.0 - - - +
161A SER* 1.3 58.7 + - - +
162A PHE 3.3 2.2 - - - -
163A GLU* 3.2 15.4 + - - +
164A PHE* 2.8 28.2 + - - +
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Residues in contact with SER 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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17A MET 4.4 0.7 - - - -
18A GLU* 3.5 20.1 - - - +
21A ILE* 3.5 29.8 - - - +
22A PRO* 4.9 2.5 - - - +
105A ILE* 3.6 11.8 - - - +
157A GLY 3.2 8.4 + - - -
158A PRO* 3.0 25.5 + - - +
159A GLY 3.5 0.2 - - - -
160A THR* 1.3 79.0 - - - +
162A PHE* 1.3 57.2 - - - +
164A PHE* 3.4 3.6 + - - +
165A ALA* 2.9 29.6 + - - +
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Residues in contact with PHE 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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21A ILE* 3.8 39.7 - - + -
25A VAL* 4.2 11.9 - - + -
158A PRO 5.6 1.6 - - - -
159A GLY 5.3 2.6 + - - +
160A THR 3.3 0.8 - - - -
161A SER* 1.3 74.4 - - - +
163A GLU* 1.3 63.7 + - + +
165A ALA* 3.3 2.3 + - - +
166A LEU* 2.9 37.3 + - - +
185A LEU* 4.1 29.6 - - + -
187A LEU* 3.7 39.9 - - + -
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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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145A ARG* 2.8 57.8 + - - +
146A VAL* 3.6 16.0 - - + +
159A GLY 3.3 10.0 - - - +
160A THR* 3.2 9.7 + - - +
162A PHE* 1.3 78.9 - - + +
164A PHE* 1.3 56.8 + - - +
166A LEU* 3.4 7.2 + - - +
167A ALA* 2.9 30.8 + - - +
189A ASP 6.4 2.2 - - - -
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Residues in contact with PHE 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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22A PRO* 4.6 13.2 - - + -
71A VAL* 4.0 14.4 - - + -
103A ALA* 3.6 26.9 - - + -
104A ALA 3.7 30.7 - - - -
105A ILE* 3.8 26.0 - - + -
146A VAL* 3.8 7.7 - - - +
153A LEU* 3.5 28.9 - - + -
155A SER* 3.5 25.6 - - - -
160A THR 2.8 17.1 + - - +
161A SER* 3.5 6.3 - - - +
163A GLU* 1.3 77.2 - - - +
165A ALA* 1.3 65.3 + - - +
167A ALA* 3.2 6.6 + - - +
168A ILE* 3.1 36.3 + - + +
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Residues in contact with ALA 165 (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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21A ILE* 4.2 0.9 - - + +
22A PRO* 3.7 20.4 - - + +
25A VAL* 3.7 31.4 - - + -
26A MET* 4.9 1.8 - - + +
161A SER 2.9 18.7 + - - +
162A PHE* 3.7 4.3 - - - +
164A PHE* 1.3 78.7 - - - +
166A LEU* 1.3 57.6 + - - +
168A ILE* 3.1 15.1 + - - +
169A VAL* 3.0 29.8 + - - +
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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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25A VAL* 4.1 19.1 - - + -
162A PHE* 2.9 22.5 + - - +
163A GLU* 3.9 6.1 - - - +
165A ALA* 1.3 72.4 - - - +
167A ALA* 1.3 60.5 + - - +
169A VAL* 3.4 5.9 + - + +
170A GLU* 2.9 28.6 + - - +
178A ALA* 3.8 32.7 - - + +
181A VAL* 4.3 6.1 - - + -
182A LYS* 3.9 30.1 - - + +
185A LEU* 4.7 3.6 - - + -
187A LEU* 3.9 27.8 - - + -
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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
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146A VAL* 3.9 24.2 - - + -
148A LYS* 5.6 3.3 - - + +
153A LEU* 4.1 12.8 - - + +
163A GLU 2.9 18.2 + - - +
164A PHE 3.4 5.8 - - - +
165A ALA 3.2 0.2 - - - -
166A LEU* 1.3 74.4 - - - +
168A ILE* 1.3 61.1 + - - +
170A GLU* 3.4 8.3 + - - +
171A ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 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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22A PRO* 5.0 2.9 - - + -
26A MET* 3.8 27.6 - - + -
31A ILE* 5.0 0.2 - - + -
69A VAL* 4.2 20.0 - - + -
71A VAL* 4.1 12.8 - - + -
101A LEU* 4.7 1.6 - - + -
103A ALA* 3.8 31.0 - - + -
153A LEU* 4.1 12.3 - - + -
164A PHE* 3.1 34.5 + - + +
165A ALA* 3.1 11.2 + - - +
167A ALA* 1.3 74.5 - - - +
169A VAL* 1.3 66.6 + - - +
171A ALA* 3.2 5.2 + - - +
172A LEU* 3.0 29.9 + - + +
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Residues in contact with VAL 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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25A VAL* 4.1 20.2 - - + +
26A MET* 4.3 9.4 - - + -
29A ALA* 3.6 35.7 - - + -
31A ILE* 4.3 9.9 - - + -
165A ALA 3.0 17.4 + - - +
166A LEU* 3.6 10.5 - - + +
167A ALA 3.3 0.2 - - - -
168A ILE* 1.3 76.6 - - - +
170A GLU* 1.3 54.6 + - - +
173A ASN* 2.7 34.8 + - + +
174A GLY 3.5 0.5 + - - -
177A VAL* 4.0 7.2 - - + +
178A ALA* 3.8 27.4 - - + +
181A VAL* 4.9 2.9 - - + -
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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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166A LEU 2.9 17.3 + - - +
167A ALA* 3.7 8.2 - - - +
168A ILE 3.3 0.2 - - - -
169A VAL* 1.3 77.3 - - - +
171A ALA* 1.3 61.8 + - - +
174A GLY* 2.9 30.7 + - - -
175A LYS* 3.1 47.2 - - + +
178A ALA* 4.1 10.0 - - + +
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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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101A LEU* 4.0 22.9 - - + -
148A LYS* 4.1 22.4 - - + +
153A LEU* 4.9 0.7 - - + -
167A ALA 3.0 18.0 + - - +
168A ILE 3.2 5.1 + - - +
170A GLU* 1.3 78.6 - - - +
172A LEU* 1.3 62.8 + - - +
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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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4A LYS* 3.5 43.7 - - + +
5A ARG 4.7 0.4 - - - +
31A ILE* 3.9 24.0 - - + -
68A ASP* 3.8 31.0 - - + +
69A VAL* 3.7 25.4 - - + -
101A LEU* 4.2 14.6 - - + -
168A ILE* 3.0 20.5 + - + +
169A VAL 4.2 1.1 - - - +
171A ALA* 1.3 85.5 - - - +
173A ASN* 1.3 68.8 + - - +
174A GLY 3.7 0.4 - - - -
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Residues in contact with ASN 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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4A LYS* 3.3 20.0 + - - +
29A ALA* 3.0 29.9 + - - +
30A GLY 4.8 1.4 + - - -
31A ILE* 3.4 25.6 - - - +
169A VAL* 2.7 17.0 + - + +
172A LEU* 1.3 79.9 - - - +
174A GLY* 1.3 57.9 + - - +
176A GLU* 6.0 0.3 - - - +
177A VAL* 3.5 33.5 + - + +
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Residues in contact with GLY 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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169A VAL 3.5 0.7 + - - +
170A GLU* 2.9 29.7 + - - -
172A LEU 3.7 0.8 - - - -
173A ASN* 1.3 80.0 - - - +
175A LYS* 1.3 65.7 + - - -
176A GLU 3.4 2.5 - - - -
177A VAL* 3.6 0.9 + - - +
178A ALA 3.2 17.2 + - - -
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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