Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 1PJR
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 PRO 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.8 20.2 - - + -
125A MET* 3.9 21.5 - - + +
126A LYS* 4.0 24.7 - - + -
129A LEU* 4.2 7.0 - - + -
135A ASP* 3.2 23.8 - - - +
139A PHE 3.3 3.6 - - - +
140A GLU* 1.3 98.1 - - + +
142A ARG* 1.3 60.6 + - - +
144A ILE* 3.0 13.9 + - + +
145A LEU* 3.1 16.9 + - - +
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Residues in contact with ARG 142 (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 PRO* 3.4 42.4 + - - +
119A THR* 4.7 7.3 - - - +
121A GLN* 6.3 0.4 - - - -
122A LEU* 4.0 28.3 - - + +
140A GLU* 2.7 20.5 + - - +
141A PRO* 1.3 74.2 - - - +
143A THR* 1.3 59.5 + - - +
145A LEU* 3.6 26.7 - - - +
146A GLY* 3.3 18.5 + - - -
500A GLU* 4.2 25.1 - - + +
502A THR* 5.0 4.1 - - - +
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Residues in contact with THR 143 (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 GLU* 2.9 22.6 + - - +
142A ARG* 1.3 75.8 - - - +
144A ILE* 1.3 61.8 + - - +
146A GLY* 3.3 3.8 + - - -
147A THR* 3.2 23.9 + - - +
169A TYR* 3.9 6.7 - - - +
499A ALA 3.6 6.2 + - - -
500A GLU 2.6 32.4 + - - +
501A ARG* 3.6 42.8 - - + +
502A THR* 4.7 6.1 - - + -
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Residues in contact with ILE 144 (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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125A MET* 4.2 9.0 - - + -
129A LEU* 4.4 11.0 - - + -
138A LYS 4.8 0.2 - - - +
139A PHE* 3.8 45.1 - - + +
140A GLU 3.1 9.9 + - - +
141A PRO* 3.0 9.2 + - + +
143A THR* 1.3 70.9 - - - +
145A LEU* 1.3 58.8 + - - +
146A GLY 3.0 4.3 - - - -
147A THR* 2.9 21.4 + - - -
148A ILE* 3.0 21.1 + - + +
169A TYR* 4.1 18.4 - - + +
172A VAL* 6.0 0.4 - - + -
173A VAL* 4.5 14.1 - - + -
176A VAL* 3.7 34.1 - - + -
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Residues in contact with LEU 145 (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 PRO 5.3 0.4 - - - +
121A GLN* 3.6 58.9 + - + +
122A LEU* 4.0 9.4 - - + +
125A MET* 3.8 24.2 - - + +
141A PRO 3.1 10.9 + - - +
142A ARG* 3.6 44.4 - - - +
144A ILE* 1.3 76.3 - - - +
146A GLY* 1.3 56.2 + - - +
148A ILE* 3.5 15.5 - - + +
149A SER* 2.9 29.6 + - - -
180A TYR* 5.4 1.3 - - + -
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Residues in contact with GLY 146 (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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142A ARG 3.3 11.7 + - - -
143A THR* 3.3 7.4 + - - -
144A ILE 3.0 1.2 - - - -
145A LEU* 1.3 78.4 - - - +
147A THR* 1.3 60.7 + - - +
149A SER* 3.2 8.1 + - - -
150A ALA* 3.1 21.5 + - - +
502A THR* 6.3 2.0 - - - -
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Residues in contact with THR 147 (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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143A THR* 3.2 13.6 + - - +
144A ILE* 2.9 11.0 + - - -
146A GLY* 1.3 73.6 - - - +
148A ILE* 1.3 62.9 + - - +
150A ALA* 3.4 8.1 + - + +
151A ALA* 3.1 21.7 + - - +
161A PHE* 4.1 25.0 - - + -
169A TYR* 3.8 20.1 + - + -
170A GLU* 5.3 5.2 - - + +
173A VAL* 4.3 13.7 - - + -
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 5.6 1.8 - - - +
125A MET* 3.8 29.4 - - + -
144A ILE* 3.0 19.6 + - + +
145A LEU* 3.5 11.7 - - + +
147A THR* 1.3 74.4 - - - +
149A SER* 1.3 62.4 + - - +
151A ALA* 2.9 19.3 + - - +
152A LYS* 3.0 29.2 + - + +
161A PHE* 6.0 1.1 - - + -
173A VAL* 5.1 6.1 - - + -
176A VAL 4.8 0.2 - - - -
177A TYR* 3.9 54.7 - - + +
180A TYR* 4.1 17.5 - - + -
191A ASP* 5.2 1.3 - - - +
193A ASP* 5.8 0.2 - - - +
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Residues in contact with SER 149 (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 GLN* 5.7 2.2 - - - -
145A LEU 2.9 18.4 + - - -
146A GLY* 3.2 9.4 + - - -
148A ILE* 1.3 76.4 - - - +
150A ALA* 1.3 57.7 + - - +
152A LYS* 3.1 5.4 + - - +
153A ASN* 2.8 38.3 + - - +
193A ASP* 2.9 34.6 + - - -
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Residues in contact with ALA 150 (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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146A GLY 3.1 9.5 + - - +
147A THR* 3.6 10.8 - - + +
149A SER* 1.3 79.5 - - - +
151A ALA* 1.3 61.1 + - - +
153A ASN* 3.7 10.1 + - - +
154A GLU* 3.2 28.9 + - + +
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Residues in contact with ALA 151 (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 THR 3.1 12.4 + - - +
148A ILE* 2.9 11.5 + - - +
150A ALA* 1.3 76.0 - - - +
152A LYS* 1.3 56.2 + - - +
154A GLU* 3.0 15.5 + - - -
155A LEU 3.1 0.2 + - - -
156A LEU* 2.9 40.0 + - + +
161A PHE* 3.7 32.3 - - + -
177A TYR* 4.1 8.5 - - + -
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Residues in contact with LYS 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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148A ILE* 3.0 29.7 + - + +
149A SER 3.7 5.2 - - - +
151A ALA* 1.3 74.7 - - - +
153A ASN* 1.3 58.2 + - - +
155A LEU* 2.9 29.1 + - - +
156A LEU 4.4 0.9 - - - -
177A TYR* 3.5 20.0 - - + +
180A TYR* 4.1 0.6 - - - -
181A GLN* 3.2 23.1 + - - -
191A ASP* 2.6 31.9 + - - +
193A ASP* 3.6 30.8 - - + +
194A ASP* 2.7 30.5 + - - +
197A MET* 4.3 20.8 - - + +
231A ALA* 4.3 2.4 - - - +
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Residues in contact with ASN 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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149A SER* 2.8 24.0 + - - +
150A ALA* 3.9 9.1 - - - +
151A ALA 3.3 0.2 - - - -
152A LYS* 1.3 76.4 - - - +
154A GLU* 1.3 64.3 + - + +
155A LEU 3.3 0.7 - - - -
193A ASP* 3.8 20.7 + - - +
196A ILE* 5.8 2.6 - - - +
229A ASN* 3.3 30.0 + - + +
230A ARG* 4.0 1.6 + - - +
231A ALA* 3.2 32.7 + - - +
260A ARG 4.2 13.7 + - - +
261A GLY* 5.5 3.5 - - - -
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Residues in contact with GLU 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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150A ALA* 3.2 17.1 + - + +
151A ALA* 3.0 8.4 + - - +
153A ASN* 1.3 78.8 - - + +
155A LEU* 1.3 69.9 + - - +
156A LEU* 3.3 17.6 + - + +
229A ASN* 5.0 0.7 - - - +
230A ARG* 3.7 37.8 + - - +
261A GLY* 4.5 13.0 - - - +
263A ASP* 6.0 1.2 - - - +
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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