Contacts of the helix formed by residues 153 - 174 (chain A) in PDB entry 1CXQ
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.1 24.7 - - + +
63A THR 4.1 8.4 + - - -
64A ASP* 4.2 13.7 + - - -
119A LYS* 2.7 31.4 + - + +
120A THR* 3.1 17.1 - - - -
121A ASP* 3.9 20.8 + - - +
152A GLY* 1.3 78.0 - - - +
154A ALA* 1.3 66.3 + - - +
155A MET 3.2 2.6 + - - -
156A VAL* 3.4 20.2 + - + +
157A GLU* 3.2 35.8 + - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 4.6 0.8 - - - +
152A GLY* 3.8 2.1 - - - +
153A GLN* 1.3 77.3 - - - +
155A MET* 1.3 65.4 + - + +
157A GLU* 3.3 11.4 + - - +
158A ARG* 2.9 24.1 + - - +
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Residues in contact with MET 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.3 12.6 + - - +
81A VAL* 3.8 16.0 - - + +
82A ASP 4.4 1.3 - - - +
83A THR* 3.7 47.3 - - - +
86A SER* 3.4 29.6 - - - +
153A GLN 3.2 1.4 - - - -
154A ALA* 1.3 80.1 - - + +
156A VAL* 1.3 57.8 + - - +
158A ARG* 3.3 9.7 + - - +
159A ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 2.9 35.8 + - + +
63A THR 4.6 0.9 - - - -
64A ASP* 3.9 20.0 - - + +
79A VAL* 3.6 37.7 - - + +
81A VAL* 3.6 8.0 - - + +
153A GLN* 3.4 35.4 - - + +
155A MET* 1.3 73.9 - - - +
157A GLU* 1.3 67.1 + - + +
159A ALA* 3.2 2.0 + - - -
160A ASN* 2.8 33.5 + - - +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 4.9 4.3 - - - +
153A GLN* 3.2 29.9 + - + +
154A ALA* 3.7 10.9 - - - +
155A MET 3.3 0.2 - - - -
156A VAL* 1.3 80.0 - - + +
158A ARG* 1.3 62.2 + - - +
160A ASN* 3.3 14.4 + - - +
161A ARG* 3.2 22.9 + - - +
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 5.6 8.9 + - - -
154A ALA 2.9 13.8 + - - +
155A MET* 3.5 10.5 + - - +
157A GLU* 1.3 74.1 - - - +
159A ALA* 1.3 60.7 + - - +
161A ARG* 3.2 31.1 + - - +
162A LEU* 2.9 57.9 + - + +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.1 13.7 - - + -
81A VAL* 4.4 6.5 - - + -
88A ILE* 3.7 35.2 - - + +
155A MET 2.9 14.2 + - - +
156A VAL* 3.5 11.9 - - - +
158A ARG* 1.3 76.4 - - - +
160A ASN* 1.3 58.2 + - - +
162A LEU* 3.3 5.9 + - - +
163A LEU* 2.8 33.7 + - - +
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.1 29.6 + - - +
66A THR* 3.9 29.7 + - + +
79A VAL* 3.5 29.5 - - - +
156A VAL* 2.8 21.7 + - - +
157A GLU* 3.5 14.8 - - - +
158A ARG 3.2 0.2 - - - -
159A ALA* 1.3 77.7 - - - +
161A ARG* 1.3 57.8 + - - +
163A LEU* 3.7 4.6 - - - +
164A LYS* 2.9 39.0 + - - +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU 3.2 9.3 + - - +
158A ARG* 3.2 39.3 + - - +
160A ASN* 1.3 78.3 - - - +
162A LEU* 1.3 81.7 + - - +
164A LYS* 3.4 7.9 + - - +
165A ASP* 2.9 46.6 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 5.4 4.9 - - + -
158A ARG* 2.9 66.3 + - + +
159A ALA* 3.8 7.0 - - - +
161A ARG* 1.3 91.8 - - - +
163A LEU* 1.3 58.6 + - - +
165A ASP* 3.5 8.2 + - + +
166A LYS* 2.9 30.7 + - - +
196A LEU* 4.0 26.6 - - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 5.3 1.3 - - + -
77A LEU* 4.1 12.8 - - + -
79A VAL* 3.8 21.8 - - + -
88A ILE* 5.3 5.6 - - + -
90A VAL* 3.5 44.4 - - + -
159A ALA 2.8 18.5 + - - +
160A ASN* 3.7 3.8 - - - +
162A LEU* 1.3 74.7 - - - +
164A LYS* 1.3 60.6 + - - +
166A LYS* 3.2 1.5 + - - -
167A ILE* 2.9 44.7 + - + +
189A LEU* 4.7 0.4 - - + -
192A ALA* 3.9 26.5 - - + -
193A MET* 4.7 1.1 - - - +
196A LEU* 3.8 17.5 - - + +
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Residues in contact with LYS 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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66A THR* 2.9 36.8 + - + +
67A LEU 4.1 14.9 + - - +
68A GLU* 3.3 33.2 - - + +
70A ARG* 5.3 0.3 + - - -
77A LEU* 4.9 4.5 - - + -
160A ASN* 2.9 28.3 + - - +
161A ARG* 4.2 5.6 - - - +
163A LEU* 1.3 75.7 - - + +
165A ASP* 1.3 66.6 + - - +
167A ILE* 3.4 5.6 + - - +
168A ARG* 3.0 23.2 + - - +
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Residues in contact with ASP 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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161A ARG* 2.9 43.1 + - - +
162A LEU* 3.7 8.8 - - + +
164A LYS* 1.3 80.7 - - - +
166A LYS* 1.3 56.9 + - - +
168A ARG* 3.3 6.8 + - - +
169A VAL* 3.0 34.7 + - + +
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Residues in contact with LYS 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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162A LEU 2.9 19.2 + - - +
163A LEU* 3.8 4.5 - - - +
165A ASP* 1.3 73.1 - - - +
167A ILE* 1.3 66.5 + - - +
169A VAL* 3.2 13.9 + - + +
170A LEU* 2.9 54.1 + - + +
192A ALA* 4.0 18.2 - - + +
195A ALA* 3.9 26.3 + - + +
196A LEU* 4.2 17.3 - - + -
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Residues in contact with ILE 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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68A GLU* 4.5 9.9 - - + -
70A ARG* 4.4 17.3 - - + -
71A MET* 4.0 12.6 - - + -
77A LEU* 3.7 29.2 - - + -
163A LEU* 2.9 32.6 + - + +
164A LYS* 3.8 5.4 - - - +
166A LYS* 1.3 74.5 - - - +
168A ARG* 1.3 57.7 - - - +
170A LEU* 3.4 1.1 + - - +
171A ALA* 2.9 33.1 + - - +
180A ILE* 4.0 24.7 - - + -
188A LEU* 4.0 8.9 - - + +
189A LEU* 3.9 13.5 - - + -
192A ALA* 4.0 16.4 - - + -
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Residues in contact with ARG 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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70A ARG* 2.8 47.5 - - - +
164A LYS 3.0 13.8 + - - +
165A ASP* 3.5 10.5 - - - +
166A LYS 3.2 0.2 - - - -
167A ILE* 1.3 78.0 - - - +
169A VAL* 1.3 59.8 + - + +
171A ALA* 3.7 1.0 - - - +
172A GLU* 2.7 60.6 + - - +
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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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165A ASP* 3.0 22.8 + - + +
166A LYS* 3.2 16.6 + - + +
168A ARG* 1.3 77.6 - - + +
170A LEU* 1.3 67.8 + - + +
172A GLU* 3.5 5.4 + - - +
173A GLY* 2.9 25.3 + - - -
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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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166A LYS* 2.9 35.4 + - + +
167A ILE 4.0 2.5 - - - +
169A VAL* 1.3 79.9 - - + +
171A ALA* 1.3 63.1 + - - +
173A GLY* 3.2 2.7 + - - -
174A ASP* 3.1 27.0 + - - +
188A LEU* 4.0 19.7 - - + +
191A LYS* 3.8 32.1 - - + +
192A ALA* 3.6 38.4 - - + +
195A ALA* 5.3 1.8 - - + -
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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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70A ARG* 5.0 6.5 - - - +
167A ILE 2.9 19.5 + - - +
168A ARG* 3.7 5.2 - - - +
170A LEU* 1.3 77.2 - - - +
172A GLU* 1.3 63.1 + - + +
174A ASP* 3.0 10.6 + - - +
175A GLY 3.2 0.2 + - - -
176A PHE* 2.9 37.7 + - + +
178A LYS 5.4 0.2 - - - +
180A ILE* 3.8 29.6 - - + -
188A LEU* 3.7 10.6 - - - +
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Residues in contact with GLU 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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70A ARG* 4.3 5.8 + - - +
168A ARG* 2.7 63.6 + - + +
169A VAL* 4.0 4.8 - - - +
171A ALA* 1.3 74.4 - - - +
173A GLY* 1.3 63.0 + - - +
175A GLY* 2.9 14.7 + - - -
176A PHE 3.6 11.2 - - - +
177A MET* 3.6 41.3 - - + +
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Residues in contact with GLY 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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169A VAL 2.9 16.8 + - - -
170A LEU* 3.6 5.2 - - - -
171A ALA 3.2 0.4 - - - -
172A GLU* 1.3 77.6 - - - +
174A ASP* 1.4 60.4 + - - +
175A GLY 3.2 1.1 + - - -
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.1 14.2 + - - +
171A ALA 3.0 9.2 + - - +
173A GLY* 1.4 76.8 - - - +
175A GLY* 1.3 60.0 + - - +
176A PHE* 3.4 32.6 + - + -
188A LEU* 4.1 14.6 - - - +
191A LYS* 4.4 17.7 + - - -
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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