Contacts of the strand formed by residues 156 - 171 (chain A) in PDB entry 1P01
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLY 6.2 0.4 - - - -
138A ARG* 3.3 12.8 + - - +
139A SER* 3.5 2.9 - - - -
140A GLY 3.0 35.7 + - - -
141A ARG 4.6 0.6 - - - -
142A THR 3.5 2.4 - - - -
143A THR* 1.3 76.4 - - - +
157A TYR* 1.3 60.7 + - - -
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Residues in contact with TYR 157 (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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118A VAL* 4.5 3.1 - - + -
119A ALA 3.3 20.2 - - - +
120A GLY* 3.4 46.5 - - + +
122A VAL* 3.3 34.7 - - + +
137A CYS* 3.4 25.8 - - + +
138A ARG 3.2 13.5 - - - -
139A SER* 3.9 4.3 - - - +
143A THR 3.7 0.8 + - - -
156A GLY* 1.3 70.1 - - - -
158A GLN* 1.3 68.2 + - - +
159A CYS* 3.6 22.6 - - - -
200A ILE* 4.5 13.6 - - + +
202A SER* 5.0 8.1 - - - -
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Residues in contact with GLN 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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137A CYS* 3.1 1.0 - - - -
138A ARG* 2.7 55.1 + - - +
143A THR* 3.0 28.3 + - - +
157A TYR* 1.3 81.4 + - - +
159A CYS* 1.3 64.4 + - - +
190A ALA* 3.9 1.5 - - + +
191A CYS* 3.6 47.2 - - - +
220A CYS* 5.0 0.8 - - - -
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Residues in contact with CYS 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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135A ALA* 6.4 0.7 - - + -
136A VAL 3.3 5.2 - - - +
137A CYS* 2.0 45.5 - - - -
157A TYR* 3.6 16.4 - - - -
158A GLN* 1.3 79.1 + - - +
160A GLY* 1.3 59.2 + - - +
184A ASN 5.0 0.2 - - - +
190A ALA* 3.7 13.9 - - - -
191A CYS 5.1 0.2 + - - -
224A ARG* 5.4 2.6 + - - -
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Residues in contact with GLY 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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135A ALA* 3.2 9.0 - - - +
136A VAL* 2.8 29.5 + - - -
159A CYS* 1.3 77.2 - - - +
161A THR* 1.3 69.5 - - - +
184A ASN* 3.3 11.4 - - - -
190A ALA* 3.8 8.3 - - - +
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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
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133A GLY* 4.1 12.7 - - - +
134A ALA 3.2 14.4 - - - +
135A ALA* 4.4 7.2 - - + -
136A VAL* 4.2 3.8 - - - +
160A GLY* 1.3 82.7 - - - +
162A ILE* 1.3 69.0 + - - +
163A THR* 3.6 5.4 + - - +
183A GLY* 3.1 3.4 - - - -
184A ASN* 2.8 45.1 + - - +
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Residues in contact with ILE 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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130A ALA* 3.8 33.9 - - + +
131A ALA 4.0 9.9 - - - +
132A VAL* 3.8 19.7 - - + +
133A GLY* 2.9 27.7 + - - -
134A ALA* 3.0 13.1 + - + +
136A VAL* 3.7 25.8 - - + -
161A THR* 1.3 75.4 + - - +
163A THR* 1.3 62.4 + - - +
164A ALA 4.1 5.8 - - - +
165A LYS* 4.6 3.4 - - - -
181A THR* 3.5 28.9 - - + -
182A GLN 3.4 4.7 - - - +
183A GLY* 4.0 1.3 - - - -
210A GLN* 4.5 4.7 - - - +
228A PHE* 4.4 18.4 - - + -
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Residues in contact with THR 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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132A VAL* 3.8 15.3 - - - +
161A THR* 3.8 15.9 - - - +
162A ILE* 1.3 78.1 - - - +
164A ALA* 1.3 60.6 - - - +
182A GLN* 2.6 51.1 + - - +
183A GLY* 4.0 1.0 + - - -
184A ASN* 3.8 25.3 - - + +
224A ARG 5.5 0.5 + - - -
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Residues in contact with ALA 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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132A VAL* 4.0 9.4 - - - +
162A ILE 3.7 1.2 - - - -
163A THR* 1.3 81.9 - - - +
165A LYS* 1.3 62.7 - - - +
167A VAL* 4.0 15.0 - - + -
181A THR* 3.4 6.9 - - - +
182A GLN* 2.6 50.0 + - - +
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Residues in contact with LYS 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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129A GLU* 3.0 27.5 + - - +
130A ALA 2.7 31.2 + - - -
131A ALA* 3.9 13.3 - - - +
132A VAL* 4.1 18.8 - - + +
162A ILE* 4.6 2.2 - - - -
164A ALA* 1.3 79.1 - - - +
166A ASN* 1.3 76.5 + - + +
167A VAL* 3.3 7.1 + - - +
180A LEU 3.9 3.8 - - - -
181A THR* 3.8 24.5 - - + +
230A ARG* 5.9 2.0 - - - -
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Residues in contact with ASN 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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165A LYS* 1.3 81.7 - - + +
167A VAL* 1.3 62.1 + - - +
168A THR* 4.0 1.9 + - - -
178A ARG* 5.7 0.2 - - - +
179A GLY* 3.2 29.8 + - - +
180A LEU 3.0 8.8 + - - -
181A THR* 4.8 0.8 + - - -
230A ARG* 6.2 1.0 - - - +
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Residues in contact with VAL 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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164A ALA* 4.0 20.6 - - + -
165A LYS 3.8 11.7 - - - +
166A ASN* 1.3 75.8 - - - +
168A THR* 1.3 73.3 + - - +
178A ARG 3.7 0.7 - - - -
179A GLY 3.2 4.5 + - - -
180A LEU* 2.6 49.6 + - - +
182A GLN* 4.2 16.8 - - + +
225A SER* 5.6 0.7 - - - +
227A LEU* 4.1 23.6 - - + -
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Residues in contact with THR 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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166A ASN 4.0 2.7 + - - -
167A VAL* 1.3 83.5 - - - +
169A ALA* 1.3 65.8 + - - +
170A ASN* 3.8 18.4 + - - +
176A ALA* 3.7 26.5 - - + -
177A VAL 3.3 10.8 - - - +
178A ARG* 3.6 30.7 + - + +
179A GLY 4.8 0.7 + - - -
180A LEU* 5.1 0.2 - - - -
227A LEU* 5.4 0.3 - - - +
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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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4A 0EG 3.9 7.9 - - + -
167A VAL 4.1 1.0 + - - -
168A THR* 1.3 72.1 - - - +
170A ASN* 1.3 61.0 + - - +
171A TYR* 3.4 38.1 + - + -
176A ALA* 3.2 4.0 - - - -
177A VAL* 2.7 31.8 + - - +
180A LEU* 3.7 17.7 - - + +
227A LEU* 3.7 13.9 - - + -
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Residues in contact with ASN 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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4A 0EG 4.4 17.7 - - + +
168A THR* 3.8 15.6 + - - +
169A ALA* 1.3 71.6 - - - +
171A TYR* 1.3 64.9 - - - +
175A GLY 5.0 0.2 - - - -
176A ALA* 3.6 24.1 + - - +
178A ARG* 5.2 1.0 + - - -
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Residues in contact with TYR 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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4A 0EG 3.3 61.9 - - + -
94A PHE* 3.8 17.3 - + + -
102A ASP* 4.4 0.9 - - - -
169A ALA* 3.4 29.7 + - + +
170A ASN* 1.3 76.9 - - - +
172A ALA* 1.3 67.2 + - - +
174A GLU* 3.1 13.5 - - - +
175A GLY* 2.9 23.4 + - - +
177A VAL* 3.8 30.5 - - + -
180A LEU* 4.2 2.6 - - - +
214A SER* 2.7 30.2 + - - -
215A GLY* 3.1 22.2 + - - -
216A GLY 4.7 0.2 - - - -
227A LEU* 4.5 0.3 - - - +
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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
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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