Contacts of the helix formed by residues 151 - 167 (chain A) in PDB entry 1PEA
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 ILE 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A SER* 3.6 23.8 - - - -
86A HIS* 3.9 19.0 - - + +
89A LYS* 4.1 26.2 - - + -
109A GLU* 4.6 3.5 - - + +
150A TYR* 1.3 80.6 - - + +
152A TYR* 1.3 65.8 + - - +
154A ARG* 4.6 5.2 - - + +
155A GLU* 3.0 45.4 + - + +
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Residues in contact with TYR 152 (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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85A SER* 3.7 6.3 - - - +
107A PRO* 4.4 3.0 - - + +
108A TYR* 4.2 15.0 - - - -
109A GLU* 3.7 18.8 - - - +
150A TYR* 3.5 19.3 - - + -
151A ILE* 1.3 82.5 - - - +
153A PRO* 1.4 69.2 - - + +
155A GLU* 4.1 1.0 - - - +
156A SER* 2.6 64.2 + - - -
204A THR* 4.0 20.9 - - + +
206A VAL* 4.0 7.6 - - + -
232A LEU* 3.2 31.2 + - + +
233A THR* 3.6 33.4 + - + +
386A ACM 3.2 33.0 - - + +
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Residues in contact with PRO 153 (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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148A SER 3.0 27.1 - - - +
150A TYR* 3.2 30.1 - - + +
152A TYR* 1.4 93.5 - - + +
154A ARG* 1.3 52.3 + - - +
156A SER* 3.2 1.0 + - - -
157A ASN* 2.7 41.0 + - - -
176A TYR* 3.7 9.6 - - + -
204A THR* 3.0 47.8 - - + +
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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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149A ASP* 2.9 34.1 + - - -
150A TYR* 3.5 20.6 + - - +
151A ILE* 4.0 5.6 - - + +
152A TYR 3.4 0.4 - - - -
153A PRO* 1.3 75.0 - - - +
155A GLU* 1.3 64.7 + - + +
157A ASN* 3.5 2.3 + - - +
158A HIS* 3.1 25.5 + - - +
174A GLU* 5.0 2.0 + - - +
176A TYR* 3.3 50.3 + - + +
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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
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109A GLU* 3.3 29.1 - - + +
111A PHE* 5.4 6.8 - - + -
151A ILE* 3.0 42.8 + - + +
154A ARG* 1.3 75.5 - - + +
156A SER* 1.3 64.8 + - - +
158A HIS* 3.2 38.2 + - - +
159A VAL* 3.3 13.7 + - - +
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Residues in contact with SER 156 (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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108A TYR 4.9 0.2 - - - -
109A GLU* 4.0 10.9 - - - +
124A PRO* 6.0 2.5 - - - -
128A SER* 5.2 3.8 + - - -
152A TYR* 2.6 52.2 + - - -
153A PRO 3.6 3.4 - - - -
155A GLU* 1.3 75.0 - - - +
157A ASN* 1.3 59.2 + - - +
159A VAL* 3.4 6.8 + - - +
160A MET* 3.0 27.1 + - - +
202A PHE* 4.9 1.5 - - - -
204A THR* 4.0 15.9 - - - -
232A LEU* 4.5 10.5 - - - +
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Residues in contact with ASN 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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145A PHE* 3.6 36.0 - - + +
146A ILE 4.9 0.2 - - - +
147A GLY 4.8 2.6 - - - +
153A PRO 2.7 20.1 + - - +
154A ARG 4.0 0.7 - - - +
156A SER* 1.3 71.0 - - - +
158A HIS* 1.3 64.4 + - - +
160A MET* 3.7 4.7 - - - -
161A ARG* 3.0 23.9 + - - +
174A GLU* 4.2 7.8 - - - +
176A TYR* 3.1 31.3 + - - +
202A PHE* 3.3 31.0 - - - +
204A THR* 3.6 16.3 + - - +
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Residues in contact with HIS 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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111A PHE* 4.7 13.4 - + - -
154A ARG 3.1 14.2 + - - +
155A GLU* 3.2 28.3 - - - +
157A ASN* 1.3 75.7 - - - +
159A VAL* 1.3 73.6 + - + +
161A ARG* 2.9 31.4 - - - +
162A HIS* 3.3 42.7 + + - -
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Residues in contact with VAL 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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109A GLU 4.9 0.9 - - - +
111A PHE* 3.8 30.5 - - + -
124A PRO* 3.9 30.3 - - + -
128A SER* 5.1 1.8 - - - -
155A GLU 3.3 11.3 + - - +
156A SER 3.8 7.4 - - - +
158A HIS* 1.3 87.1 - - + +
160A MET* 1.3 56.1 + - - +
161A ARG 3.0 0.2 - - - -
162A HIS* 3.2 14.9 + - + +
163A LEU* 3.0 37.5 + - + +
367A VAL* 4.1 21.3 - - + +
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Residues in contact with MET 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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128A SER* 4.0 22.4 - - - +
131A LEU* 4.1 13.9 - - + -
132A ALA* 3.9 19.5 - - + +
135A LEU* 4.8 2.5 - - + -
145A PHE* 3.6 29.5 - - + -
156A SER 3.0 16.6 + - - +
157A ASN* 4.0 4.7 - - - +
158A HIS 3.3 0.2 - - - -
159A VAL* 1.3 74.5 - - - +
161A ARG* 1.3 65.9 + - - +
163A LEU* 3.7 21.3 - - - -
164A TYR* 3.0 34.3 + - + +
202A PHE* 3.9 38.4 - - + -
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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
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145A PHE* 4.3 6.7 - - - -
157A ASN 3.0 12.1 + - - +
158A HIS* 2.9 20.6 - - - +
160A MET* 1.3 81.3 - - - +
162A HIS* 1.3 68.6 + - + +
164A TYR* 3.1 9.0 + - - +
165A ARG* 3.1 35.5 + - + +
171A VAL* 3.7 42.7 + - + +
173A GLU 5.5 0.2 - - - -
174A GLU* 3.0 33.7 + - - +
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Residues in contact with HIS 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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111A PHE* 6.2 0.9 - + - -
158A HIS* 3.3 52.7 + + - -
159A VAL* 3.2 15.6 + - + +
161A ARG* 1.3 91.1 - - + +
163A LEU* 1.3 55.7 + - - +
165A ARG* 3.5 5.9 + - - +
166A GLN* 3.1 27.5 + - - +
367A VAL 4.9 9.8 + - - -
369A VAL* 3.9 30.1 + - + +
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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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124A PRO 5.0 0.7 - - - +
128A SER* 3.6 42.8 - - - +
129A ALA* 3.8 7.6 - - + +
132A ALA* 4.1 16.8 - - + -
159A VAL* 3.0 25.8 + - + +
160A MET* 3.7 14.4 - - - +
162A HIS* 1.3 73.3 - - - +
164A TYR* 1.3 70.4 + - - +
166A GLN* 3.4 8.5 + - - +
167A HIS* 3.4 26.8 + - + -
367A VAL* 5.2 0.4 - - + -
369A VAL* 3.5 26.9 - - + -
372A LEU* 3.7 22.2 - - + -
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Residues in contact with TYR 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 ALA* 4.3 15.3 - - + -
135A LEU* 3.6 27.9 - - + +
136A ILE* 4.1 20.6 - - + +
140A GLY 4.7 1.0 + - - -
141A GLU* 3.5 28.9 - - - -
143A VAL* 3.5 42.0 - - + +
145A PHE* 4.8 0.2 - + - -
160A MET* 3.0 47.6 + - + +
161A ARG 3.7 3.4 - - - +
163A LEU* 1.3 76.3 - - - +
165A ARG* 1.3 62.9 + - - +
167A HIS* 3.0 9.9 + - - +
169A GLY* 2.8 37.2 + - - -
170A THR 4.0 2.5 - - - -
171A VAL* 4.1 11.7 - - + -
200A VAL* 4.3 5.7 - - - +
202A PHE* 6.0 0.4 - - + -
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Residues in contact with ARG 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* 3.1 32.5 + - + +
162A HIS* 3.9 8.3 - - - +
164A TYR* 1.3 75.9 - - + +
166A GLN* 1.3 54.6 + - - +
168A GLY* 2.8 25.5 + - - -
169A GLY 4.4 13.7 + - - +
170A THR* 6.1 0.8 - - - +
171A VAL* 6.1 3.4 - - + -
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Residues in contact with GLN 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 HIS 3.1 17.7 + - - +
163A LEU* 3.6 7.4 - - - +
164A TYR 3.3 0.2 - - - -
165A ARG* 1.3 74.2 - - - +
167A HIS* 1.3 68.4 + - + +
168A GLY 3.4 1.5 + - - -
369A VAL* 3.8 27.5 + - + +
370A HIS* 3.3 35.5 + - - +
374A ASP* 4.6 12.5 + - - +
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Residues in contact with HIS 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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129A ALA 4.7 4.7 - - - -
132A ALA* 4.2 7.8 - - + +
133A ALA* 4.0 32.4 + - + +
136A ILE* 3.2 38.8 - - + +
137A ARG* 4.2 21.6 + - - +
141A GLU* 5.4 0.2 - - - +
163A LEU* 3.5 18.8 + - + -
164A TYR 3.0 4.0 + - - +
166A GLN* 1.3 89.1 - - + +
168A GLY* 1.3 65.2 + - - +
169A GLY* 2.9 3.5 + - - -
374A ASP* 3.3 28.5 + - - +
375A TRP* 5.4 2.3 + + - -
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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