Contacts of the helix formed by residues 157 - 173 (chain A) in PDB entry 3I5Y
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 GLY 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.3 1.6 - - - -
133A GLN* 3.0 30.2 + - - +
155A GLY 3.4 2.4 + - - -
156A THR* 1.3 79.8 - - - +
158A LYS* 1.3 65.9 + - - +
159A THR 3.1 4.4 + - - -
160A PHE 3.3 1.4 + - - -
161A ALA 3.2 8.3 + - - -
1000A ANP 3.0 35.7 + - - -
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Residues in contact with LYS 158 (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* 4.2 4.9 - - + -
152A ALA* 2.5 48.7 + - + +
153A LYS 2.8 20.6 + - - -
156A THR* 3.5 1.0 + - - +
157A GLY* 1.3 76.3 - - - +
159A THR* 1.3 64.2 + - - +
161A ALA* 3.0 22.9 + - - +
162A PHE* 3.3 14.6 + - + -
267A ASP* 5.3 2.5 - - - +
268A GLU* 5.7 1.3 - - - -
304A PHE* 4.1 27.9 - - + -
305A SER* 4.0 26.0 - - - +
306A ALA* 4.0 1.7 - - - +
900A MG 4.1 7.2 - - - -
1000A ANP 2.9 42.9 + - - +
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Residues in contact with THR 159 (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 LYS* 1.3 76.1 - - - +
160A PHE* 1.3 61.0 + - + +
162A PHE* 3.0 30.3 + - + -
163A LEU* 3.0 42.3 + - + +
192A LEU* 6.1 0.7 - - - +
195A GLN* 5.0 6.5 + - - +
196A ILE* 4.3 13.8 - - + +
199A GLU* 4.1 22.7 - - + +
267A ASP* 4.9 3.1 + - - -
900A MG 4.0 3.6 - - - -
1000A ANP 2.6 34.6 + - - -
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Residues in contact with PHE 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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121A ILE* 4.7 6.3 - - + -
124A MET* 4.0 19.7 - - + -
126A PHE* 4.1 19.3 - + - -
133A GLN* 3.6 13.7 - - - +
137A ILE* 4.9 0.3 - - - +
157A GLY 3.3 2.8 + - - -
159A THR* 1.3 76.5 - - + +
161A ALA* 1.3 64.3 + - - +
162A PHE 3.0 1.6 - - - -
163A LEU* 4.0 10.1 - - + +
164A ILE* 3.1 42.9 + - + +
199A GLU* 3.2 42.2 - - + -
202A LYS* 5.2 2.0 - - + -
203A ILE* 3.8 35.4 - - + -
1000A ANP 3.7 35.4 - + - -
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Residues in contact with ALA 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* 4.1 8.1 - - + -
133A GLN* 3.8 17.3 - - + +
136A THR* 3.3 27.3 + - - +
137A ILE* 4.4 2.7 - - - +
140A ILE* 3.4 4.5 - - - +
157A GLY 3.2 7.8 + - - +
158A LYS* 3.0 26.2 + - - +
160A PHE* 1.3 77.5 - - - +
162A PHE* 1.3 53.8 + - - +
165A PRO* 3.2 17.9 - - - +
304A PHE* 4.0 12.8 - - + -
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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
----------------------------------------------------------
140A ILE* 4.7 0.2 - - - -
158A LYS 3.3 25.3 + - - -
159A THR* 3.0 27.5 + - + -
161A ALA* 1.3 76.5 - - - +
163A LEU* 1.3 69.5 + - + +
164A ILE 3.3 2.2 - - - -
165A PRO* 3.5 6.3 - - - +
166A ILE* 3.2 29.6 + - + +
185A ILE* 3.7 44.4 - - + -
196A ILE* 4.1 11.7 - - + -
265A VAL* 4.1 24.9 - - + -
267A ASP* 4.1 29.6 - - - -
302A LEU* 4.6 6.0 - - + +
304A PHE* 3.9 32.5 - + + -
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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
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159A THR* 3.0 26.1 + - + +
160A PHE* 3.5 11.2 + - + -
162A PHE* 1.3 82.8 - - + +
164A ILE* 1.3 63.0 + - - +
166A ILE* 3.8 6.8 - - + +
167A PHE* 3.1 33.6 + - + -
185A ILE* 3.6 28.7 - - + -
196A ILE* 4.1 4.5 - - + +
199A GLU* 3.9 16.6 - - + -
200A VAL* 3.3 50.5 - - + +
203A ILE* 4.1 12.6 - - + -
238A ILE* 5.2 3.6 - - + -
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Residues in contact with ILE 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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104A LEU* 5.1 2.5 - - + -
113A LEU* 4.2 19.3 - - + -
117A ILE* 4.3 15.3 - - + +
121A ILE* 3.9 42.4 - - + -
129A LEU* 4.7 9.6 - - + -
133A GLN* 5.2 2.2 - - - -
137A ILE* 4.0 31.4 - - + -
160A PHE* 3.1 33.8 + - + +
163A LEU* 1.3 78.9 - - - +
165A PRO* 1.3 73.3 - - + +
167A PHE* 3.4 3.3 + - - +
168A GLN* 3.2 20.4 + - - +
203A ILE* 5.3 1.1 - - + -
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Residues in contact with PRO 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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137A ILE* 4.0 14.1 - - + +
140A ILE* 3.6 38.1 - - + -
141A LEU* 3.2 33.8 - - + +
160A PHE 3.8 0.4 - - - +
161A ALA 3.2 27.4 - - - +
162A PHE* 3.5 8.7 - - - +
164A ILE* 1.3 100.1 - - + +
166A ILE* 1.3 60.4 + - - +
168A GLN 3.4 0.5 + - - -
169A HIS* 3.1 18.9 + - - +
263A TYR* 5.6 1.2 - - - -
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Residues in contact with ILE 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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140A ILE* 6.1 0.4 - - + -
162A PHE* 3.2 22.5 + - + +
163A LEU* 3.8 7.0 - - + +
164A ILE 3.2 0.4 - - - -
165A PRO* 1.3 76.8 - - + +
167A PHE* 1.3 64.7 + - - +
169A HIS* 3.1 9.3 + - - +
170A LEU* 3.1 23.6 + - + +
183A ALA* 3.6 34.8 - - + -
185A ILE* 4.2 19.1 - - + -
238A ILE* 3.9 24.0 - - + -
263A TYR* 4.9 15.3 - - + -
265A VAL* 3.9 28.0 - - + -
302A LEU* 5.2 4.0 - - + -
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Residues in contact with PHE 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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117A ILE* 3.7 21.5 - - + -
163A LEU* 3.1 27.6 + - + +
164A ILE 3.8 1.1 - - - +
165A PRO 3.4 0.2 - - - -
166A ILE* 1.3 76.5 - - - +
168A GLN* 1.3 61.8 + - - +
170A LEU* 3.0 10.8 + - + +
171A ILE* 3.0 28.1 + - + +
200A VAL* 4.0 20.2 - - + -
203A ILE* 3.8 31.6 - - + -
204A HIS* 3.6 34.8 - + - -
210A LEU* 4.0 20.9 - - + -
213A TYR* 3.9 31.9 - + + -
238A ILE* 4.1 19.1 - - + -
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Residues in contact with GLN 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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111A GLY 5.4 1.6 + - - -
112A VAL 3.2 26.3 + - - +
113A LEU* 3.4 4.4 - - + -
114A ASP* 2.7 42.5 + - - +
117A ILE* 3.4 12.4 - - + +
141A LEU* 3.5 27.8 - - + -
164A ILE 3.2 10.0 + - - +
165A PRO 3.6 3.1 - - - +
166A ILE 3.2 0.2 - - - -
167A PHE* 1.3 77.8 - - - +
169A HIS* 1.3 57.3 + - - +
171A ILE* 3.1 9.2 + - - +
172A ASN* 2.7 61.9 + - - +
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Residues in contact with HIS 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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141A LEU* 3.9 6.5 - - + +
165A PRO 3.1 12.2 + - - +
166A ILE 3.1 9.7 + - - +
168A GLN* 1.3 76.2 - - - +
170A LEU* 1.3 72.4 + - + +
172A ASN* 3.5 13.9 + - - +
173A THR* 2.8 50.8 + - + +
182A LYS* 4.7 5.6 - - + +
262A ASP* 3.2 34.6 + - + +
263A TYR* 3.5 38.7 + + + -
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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 ILE* 3.1 18.5 + - + +
167A PHE* 3.0 12.2 + - + +
169A HIS* 1.3 79.9 - - + +
171A ILE* 1.3 61.2 + - - +
173A THR* 3.6 3.7 - - - -
174A LYS* 3.1 25.3 + - - +
182A LYS* 3.6 41.6 + - + +
183A ALA* 5.3 0.4 - - + -
213A TYR* 3.6 37.6 - - + -
237A ASN* 3.9 16.4 - - + +
238A ILE* 3.5 37.5 - - + -
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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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114A ASP* 3.9 42.4 - - + +
116A GLU* 4.6 2.5 - - + -
117A ILE* 4.3 17.9 - - + +
167A PHE 3.0 20.4 + - - +
168A GLN* 3.5 10.8 - - - +
170A LEU* 1.3 74.3 - - - +
172A ASN* 1.3 67.2 + - - +
173A THR 3.0 1.6 + - - -
174A LYS* 3.0 27.4 + - + +
210A LEU* 3.9 22.2 - - + -
213A TYR* 3.6 30.1 - - + +
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Residues in contact with ASN 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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141A LEU* 4.6 9.7 + - - +
168A GLN* 2.7 55.3 + - - +
169A HIS* 3.6 14.8 + - - +
171A ILE* 1.3 73.4 - - - +
173A THR* 1.3 64.1 - - + +
174A LYS* 3.9 1.2 + - - +
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Residues in contact with THR 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 HIS* 2.8 42.6 + - + +
170A LEU 3.6 0.6 + - - -
172A ASN* 1.3 82.1 - - + +
174A LYS* 1.3 62.1 + - - +
175A PHE 3.3 3.4 - - - -
176A ASP* 3.1 27.8 + - - +
182A LYS* 2.5 51.6 + - - +
262A ASP* 5.6 1.3 - - - +
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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
------------------------------------------------------------
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