Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 1P4A
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 5.1 0.7 - - - -
136A THR* 4.1 11.6 + - - -
137A VAL 5.0 3.5 + - - -
139A THR 3.3 1.0 - - - +
140A LYS* 1.3 78.4 - - - +
142A ILE* 1.3 63.6 + - - +
143A PRO* 3.4 2.5 - - - -
144A LEU* 3.3 12.3 + - - +
145A ALA* 3.1 20.8 + - - +
202A ILE* 4.9 1.9 - - - +
203A ASP* 5.6 0.7 - - - -
204A ASP* 3.2 28.4 + - - -
604A PCP 5.0 0.8 + - - -
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Residues in contact with ILE 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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136A THR* 4.1 20.4 - - + -
137A VAL 4.6 0.4 + - - +
138A ALA* 3.7 25.1 - - - -
139A THR* 3.2 16.1 + - - +
141A GLY* 1.3 76.8 - - - +
143A PRO* 1.3 72.2 - - + +
145A ALA* 3.1 4.7 + - - +
146A TYR* 3.0 44.3 + - + -
158A ILE* 4.0 17.7 - - + -
139B THR* 3.9 18.8 - - + -
142B ILE* 3.6 36.3 - - + -
143B PRO* 4.6 0.7 - - + -
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Residues in contact with PRO 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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109A LEU 4.1 8.1 - - - +
115A LEU* 3.8 26.0 - - + -
139A THR 4.1 2.7 - - - +
140A LYS 3.5 13.0 - - - +
141A GLY 3.6 0.4 - - - -
142A ILE* 1.3 96.1 - - + +
144A LEU* 1.3 54.2 + - - +
146A TYR* 3.1 6.8 + - + +
147A ALA* 2.8 28.8 + - - +
142B ILE* 3.9 18.4 - - + -
146B TYR* 3.9 22.9 - - + -
156B VAL* 4.3 12.6 - - + -
158B ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 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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109A LEU* 4.7 3.8 - - + -
115A LEU* 3.7 27.7 - - + +
118A VAL* 3.5 32.1 - - + -
119A GLY* 4.6 2.4 - - - +
122A PHE* 4.1 13.2 - - + -
140A LYS 5.3 0.2 + - - -
141A GLY* 3.3 14.1 + - - +
142A ILE 3.3 0.2 - - - -
143A PRO* 1.3 74.7 - - - +
145A ALA* 1.3 65.9 + - - +
147A ALA* 3.2 3.8 + - - +
148A ALA* 3.1 23.9 + - - +
202A ILE* 4.0 19.5 - - + -
203A ASP 4.2 13.5 - - - +
204A ASP* 4.4 10.5 - - + -
232A LEU* 4.2 23.8 - - + -
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Residues in contact with ALA 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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134A VAL* 3.7 23.0 - - + +
136A THR* 3.5 35.2 - - + -
141A GLY 3.1 4.6 + - - +
142A ILE 3.3 9.0 - - - +
144A LEU* 1.3 78.1 - - - +
146A TYR* 1.3 58.6 + - - +
148A ALA* 3.4 1.2 + - - +
149A ALA* 2.9 29.1 + - - +
156A VAL* 4.1 10.3 - - + -
202A ILE* 4.0 10.2 - - + +
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Residues in contact with TYR 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 ILE* 3.0 36.9 + - + +
143A PRO* 3.6 8.5 - - + +
145A ALA* 1.3 75.0 - - - +
147A ALA* 1.3 65.5 + - - +
149A ALA* 3.8 1.6 - - + +
150A SER* 3.0 26.0 + - - -
156A VAL* 3.6 37.8 + - + +
158A ILE* 3.9 10.5 - - + +
109B LEU* 2.7 20.5 + - - +
110B GLY* 3.4 14.5 - - - -
112B PRO* 5.9 2.9 - - + -
115B LEU* 2.9 34.3 - - + -
143B PRO* 3.4 28.9 - - + +
146B TYR* 3.8 22.9 + + + -
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Residues in contact with ALA 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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115A LEU* 3.3 31.6 - - + +
116A SER* 4.7 2.5 - - - +
119A GLY* 4.1 5.6 - - - -
143A PRO 2.8 12.1 + - - +
144A LEU* 3.2 10.9 + - - +
146A TYR* 1.3 76.8 - - - +
148A ALA* 1.3 60.5 + - - +
150A SER* 2.7 21.0 + - - -
151A TYR* 3.2 14.7 - - + -
146B TYR* 3.2 24.2 + - + +
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Residues in contact with ALA 148 (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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119A GLY* 3.7 23.1 - - - +
122A PHE* 4.2 23.1 - - + -
134A VAL* 4.9 2.7 - - + -
144A LEU 3.1 12.1 + - - +
145A ALA 3.7 6.7 - - - +
147A ALA* 1.3 77.2 - - - +
149A ALA* 1.3 61.5 + - - +
150A SER 3.3 0.3 + - - -
151A TYR* 3.3 5.2 + - - +
152A LEU* 3.2 33.6 + - + +
200A LEU* 5.0 0.7 - - + -
202A ILE* 4.5 12.8 - - + -
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Residues in contact with ALA 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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134A VAL* 3.9 18.6 - - + +
145A ALA 2.9 8.7 + - - +
146A TYR* 3.8 4.3 - - + +
147A ALA 3.3 0.2 - - - -
148A ALA* 1.3 75.8 - - - +
150A SER* 1.3 58.1 + - - +
152A LEU* 3.3 0.6 + - - -
153A ASN* 2.8 24.6 + - - -
154A VAL* 3.0 29.9 + - - +
156A VAL* 3.3 34.5 - - + -
112B PRO* 4.6 1.5 - - + +
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Residues in contact with SER 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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20A PRO* 3.5 15.9 - - - +
146A TYR 3.0 12.9 + - - -
147A ALA* 2.7 23.2 + - - -
149A ALA* 1.3 78.1 - - - +
151A TYR* 1.3 64.9 + - - +
153A ASN* 3.6 8.5 + - - +
112B PRO* 4.4 17.5 - - - +
146B TYR* 4.6 6.1 + - - -
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Residues in contact with TYR 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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20A PRO* 3.4 18.9 - - + +
21A HIS* 3.1 19.4 - - - -
71A TYR* 5.7 1.8 - + - -
73A PRO* 3.7 25.2 - - + +
116A SER* 2.7 50.2 + - - -
119A GLY* 3.7 2.2 - - - -
120A LYS* 3.5 40.6 - - + +
123A ALA* 3.4 20.2 - - + -
147A ALA* 3.2 23.5 + - + -
148A ALA 3.3 2.9 + - - +
150A SER* 1.3 86.5 + - - +
152A LEU* 1.3 57.7 + - - +
153A ASN 3.2 0.2 - - - -
18B THR* 5.9 2.6 - - - +
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Residues in contact with LEU 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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21A HIS* 3.6 38.6 - - + +
122A PHE 4.9 0.4 - - - +
123A ALA* 3.7 35.4 - - + +
126A PHE* 4.5 0.9 - - + +
127A ALA* 4.3 7.4 - - - +
131A ILE* 4.3 20.9 - - + -
134A VAL* 4.9 2.2 - - + -
148A ALA* 3.2 28.6 + - + +
149A ALA* 3.9 4.0 - - - +
151A TYR* 1.3 75.8 - - - +
153A ASN* 1.3 71.1 + - - +
154A VAL* 3.6 20.5 + - + +
200A LEU* 4.1 24.2 - - + -
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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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18A THR 5.8 0.6 + - - -
20A PRO* 3.4 25.8 - - + +
21A HIS* 4.3 5.0 - - + +
22A GLU* 3.4 30.6 + - - +
149A ALA 2.8 9.3 + - - -
150A SER 3.6 8.2 + - - +
151A TYR 3.2 3.4 - - - -
152A LEU* 1.3 81.9 - - - +
154A VAL* 1.3 59.8 + - - +
155A PRO* 4.8 0.2 - - - +
112B PRO* 3.7 23.4 - - - +
113B SER* 5.1 6.3 - - - +
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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