Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 1W31
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 ASN 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 2.7 25.3 + - - +
146A LEU 4.4 1.3 + - - -
147A TYR* 3.4 43.6 + - + +
152A ILE* 1.3 71.3 - - - +
154A ARG* 1.3 52.8 + - - +
155A GLU* 3.4 10.4 + - - +
156A ARG* 3.1 39.8 + - + +
157A SER* 2.8 33.9 + - - -
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Residues in contact with ARG 154 (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 TYR* 4.8 2.7 + - - +
152A ILE* 3.7 6.9 + - + +
153A ASN* 1.3 71.0 + - - +
155A GLU* 1.3 68.2 + - - +
157A SER* 4.2 2.0 - - - -
158A VAL* 2.7 64.1 + - - +
182A ILE* 3.4 20.6 - - + -
183A ASP* 2.7 55.2 + - + +
184A GLY* 3.6 16.0 + - - -
187A ARG* 4.5 13.3 - - - +
188A ASP* 3.8 8.1 + - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 5.6 1.1 + - - +
153A ASN* 3.2 8.6 + - - +
154A ARG* 1.3 88.0 - - - +
156A ARG* 1.3 83.7 + - - +
158A VAL* 3.2 9.1 - - + +
159A SER* 3.0 24.6 + - - -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.0 18.7 - - + +
153A ASN* 3.1 31.0 + - - +
155A GLU* 1.3 97.1 + - + +
157A SER* 1.3 61.2 + - - +
159A SER* 3.0 35.4 + - - -
160A ARG* 2.9 30.3 + - - +
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.5 0.6 - - - +
144A GLY* 4.3 1.8 - - - -
145A VAL* 2.8 40.3 + - - +
152A ILE* 3.4 4.2 - - - +
153A ASN 2.8 30.4 + - - -
154A ARG 3.6 2.7 - - - -
156A ARG* 1.3 71.8 - - - +
158A VAL* 1.3 58.5 + - - +
160A ARG* 2.9 6.1 + - - +
161A LEU* 2.8 32.9 + - - +
182A ILE* 3.5 26.2 - - - -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 2.7 58.4 + - - +
155A GLU* 3.2 7.4 - - - +
157A SER* 1.3 74.3 - - - +
159A SER* 1.3 59.5 + - - +
161A LEU* 3.8 8.6 - - - +
162A ALA* 2.9 33.1 + - - +
182A ILE* 3.4 27.4 - - + -
183A ASP 3.9 0.2 - - - +
185A ARG* 3.8 22.2 - - + +
188A ASP* 3.4 26.1 - - - +
189A ILE* 5.6 0.5 - - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 3.0 20.6 + - - -
156A ARG* 3.0 32.7 + - - -
158A VAL* 1.3 79.4 - - - +
160A ARG* 1.3 60.4 + - - +
162A ALA* 3.8 5.8 + - - +
163A ALA* 3.5 17.3 + - - +
188A ASP* 5.8 1.6 - - - -
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Residues in contact with ARG 160 (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 VAL* 2.9 28.3 + - - +
102A GLY 2.8 22.4 + - - -
103A THR* 3.2 12.0 + - - +
105A ALA* 4.0 2.8 - - - +
106A ASP* 2.8 42.4 + - - -
134A LEU* 3.6 26.7 - - + -
145A VAL* 4.6 5.8 - - + -
156A ARG 2.9 14.1 + - - +
157A SER* 3.3 7.9 - - - +
159A SER* 1.3 75.2 - - - +
161A LEU* 1.3 65.3 + - - +
163A ALA* 3.1 25.5 + - - +
164A VAL* 3.1 27.1 + - - +
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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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132A VAL* 3.9 18.9 - - + +
133A CYS* 3.7 31.2 - - - -
134A LEU* 3.8 21.5 - - + +
143A CYS 4.5 1.8 - - - +
157A SER* 2.8 22.2 + - - +
158A VAL* 3.8 8.1 - - - +
160A ARG* 1.3 73.2 - - - +
162A ALA* 1.3 63.3 + - - +
164A VAL* 3.3 6.3 + - + +
165A ALA* 2.9 25.1 + - - +
180A ASP* 3.3 38.6 - - + +
182A ILE* 3.9 16.6 - - + -
185A ARG* 4.5 4.3 - - + -
189A ILE* 4.6 8.3 - - + -
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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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158A VAL 2.9 17.2 + - - +
159A SER* 3.9 6.1 - - - +
160A ARG 3.2 0.2 - - - -
161A LEU* 1.3 77.2 - - - +
163A ALA* 1.3 62.6 + - - +
165A ALA* 3.5 1.4 + - - +
166A VAL* 3.0 31.1 + - - +
188A ASP* 3.7 32.8 - - + +
189A ILE* 3.9 14.6 - - + +
192A GLY* 5.4 4.0 - - - -
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Residues in contact with ALA 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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106A ASP* 4.4 2.0 - - - +
159A SER 3.5 9.6 + - - +
160A ARG* 3.1 25.6 + - - +
162A ALA* 1.3 79.1 - - - +
164A VAL* 1.3 58.3 + - - +
166A VAL* 3.3 6.3 + - - +
167A ASN* 2.9 40.5 + - - +
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Residues in contact with VAL 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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105A ALA* 3.8 26.9 - - + -
106A ASP* 3.7 9.4 - - - +
132A VAL* 4.4 8.7 - - + -
133A CYS 4.9 5.4 - - - +
134A LEU* 3.9 11.9 - - + -
160A ARG* 3.1 32.5 + - - +
161A LEU* 3.5 8.3 - - - +
163A ALA* 1.3 76.6 - - - +
165A ALA* 1.3 62.9 + - - +
167A ASN* 3.2 2.3 + - - +
168A TYR* 2.9 58.6 + - + +
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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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132A VAL* 4.0 25.5 - - + +
161A LEU 2.9 16.1 + - - +
162A ALA 3.8 3.6 - - - +
164A VAL* 1.3 75.9 - - - +
166A VAL* 1.3 63.0 + - - +
168A TYR* 3.2 4.7 + - - +
169A ALA* 3.1 19.6 + - - +
176A VAL* 3.6 15.2 - - + +
189A ILE* 3.9 30.5 - - + -
193A LEU* 4.9 2.5 - - + -
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Residues in contact with VAL 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 ALA 3.0 23.0 + - - +
163A ALA* 3.7 5.4 - - - +
165A ALA* 1.3 75.6 - - + +
167A ASN* 1.3 59.7 + - - +
169A ALA* 3.3 2.9 + - - +
170A LYS* 2.8 45.6 + - + +
189A ILE 4.6 2.0 - - - +
192A GLY* 3.5 34.3 - - - -
193A LEU* 3.7 17.5 - - + +
196A ALA* 3.7 24.9 - - + -
198A LEU* 4.6 1.3 - - + -
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Residues in contact with ASN 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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106A ASP* 2.7 42.9 + - + +
113A ILE* 4.5 7.5 - - + +
163A ALA* 2.9 23.6 + - - +
164A VAL 3.2 4.7 + - - +
166A VAL* 1.3 74.8 - - - +
168A TYR* 1.3 62.3 + - - +
170A LYS* 3.2 24.1 + - - +
171A ALA* 2.8 28.9 + - - +
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Residues in contact with TYR 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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105A ALA 2.9 28.1 + - - -
106A ASP* 4.3 3.1 - - - -
112A VAL* 3.6 30.7 - - + +
113A ILE* 4.0 17.5 - - + -
116A ILE* 3.9 1.9 - - + +
130A CYS* 3.7 17.5 - - + -
131A ASP 3.6 21.9 + - - -
132A VAL* 3.8 15.5 - - + -
133A CYS 5.2 1.4 + - - -
137A TYR* 3.8 18.9 + - - -
164A VAL* 2.9 37.6 + - + +
165A ALA 3.4 7.2 - - - +
167A ASN* 1.3 76.1 - - - +
169A ALA* 1.3 63.6 + - - +
171A ALA* 3.1 9.3 + - - +
172A GLY 3.1 7.3 + - - -
173A ALA* 3.0 29.0 + - + +
176A VAL* 4.2 8.3 - - + -
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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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165A ALA 3.1 9.0 + - - +
166A VAL 3.5 8.3 - - - +
168A TYR* 1.3 81.2 - - - +
170A LYS* 1.3 62.4 + - - +
172A GLY* 3.0 15.1 + - - -
173A ALA* 3.8 13.9 + - - +
176A VAL* 4.8 1.3 - - + +
193A LEU* 3.9 15.3 - - + -
198A LEU* 4.1 16.2 - - + +
202A THR* 3.8 28.5 - - + +
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Residues in contact with LYS 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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117A LYS* 5.3 1.6 + - - -
166A VAL* 2.8 36.4 + - + +
167A ASN* 3.5 24.6 + - - +
168A TYR 3.2 0.2 - - - -
169A ALA* 1.3 77.5 - - - +
171A ALA* 1.3 60.8 + - - +
172A GLY* 3.4 0.9 + - - -
196A ALA* 4.5 12.3 - - - +
198A LEU* 3.7 17.0 - - + -
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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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113A ILE* 3.7 36.6 - - + -
116A ILE* 3.8 14.8 - - + +
117A LYS* 3.3 29.9 + - - +
120A ARG* 5.3 1.4 - - - +
167A ASN 2.8 13.9 + - - +
168A TYR 3.1 11.4 + - - +
170A LYS* 1.3 79.2 - - - +
172A GLY* 1.3 56.2 + - - +
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Residues in contact with GLY 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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116A ILE* 3.7 9.4 - - - -
120A ARG* 3.6 28.2 + - - -
169A ALA 3.0 10.6 + - - -
170A LYS 3.2 1.1 - - - -
171A ALA* 1.3 80.8 - - - +
173A ALA* 1.3 66.3 + - - +
174A HIS* 3.5 6.4 + - - -
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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