Contacts of the helix formed by residues 141 - 153 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B THR* 3.5 13.5 + - - -
137B VAL 4.1 1.6 + - - -
139B THR 3.4 1.0 - - - -
140B LYS* 1.3 77.2 - - - +
142B ILE* 1.3 64.9 + - - +
143B PRO 3.4 0.4 - - - -
144B LEU* 3.1 7.9 + - - +
145B ALA* 2.9 22.2 + - - +
202B ILE* 4.7 0.9 - - - +
203B ASP* 3.5 21.5 + - - -
204B ASP* 3.8 11.0 + - - -
605B PCP 3.3 7.5 + - - -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A THR* 3.8 24.7 - - + +
142A ILE* 3.6 39.9 - - + -
143A PRO* 3.9 22.7 - - + -
136B THR* 3.8 19.1 - - + -
138B ALA* 3.8 16.2 - - - -
139B THR* 3.1 18.4 - - - +
140B LYS 3.1 0.2 - - - -
141B GLY* 1.3 76.7 - - - +
143B PRO* 1.3 65.7 - - + +
145B ALA* 3.1 1.7 + - - +
146B TYR* 2.9 29.1 + - - +
156B VAL* 5.7 1.3 - - + -
158B ILE* 3.9 14.6 - - + -
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Residues in contact with PRO 143 (chain B).
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* 4.6 1.3 - - + -
146A TYR* 3.4 50.3 - - + +
158A ILE* 4.3 8.7 - - + -
109B LEU* 3.7 16.2 - - + +
115B LEU* 3.8 14.4 - - + +
139B THR 3.8 5.6 - - - +
140B LYS* 3.2 16.6 - - - +
141B GLY 3.5 0.2 - - - -
142B ILE* 1.3 97.1 - - + +
144B LEU* 1.3 55.8 + - + +
146B TYR* 3.5 7.1 + - + +
147B ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.7 18.8 - - + -
114B VAL* 6.6 0.2 - - + -
115B LEU* 3.3 26.2 - - + -
118B VAL* 4.0 31.6 - - + -
119B GLY* 4.8 1.7 - - - -
122B PHE* 4.4 6.3 - - + -
140B LYS 4.7 1.1 + - - +
141B GLY 3.1 8.8 + - - +
143B PRO* 1.3 76.5 - - - +
145B ALA* 1.3 67.2 + - - +
147B ALA* 3.4 3.6 + - + +
148B ALA* 3.0 25.6 + - - +
202B ILE* 3.8 12.7 - - + +
203B ASP 4.0 3.4 - - - +
204B ASP* 3.5 41.7 - - + +
232B LEU* 4.0 14.8 - - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 3.5 26.2 - - + +
136B THR* 3.7 27.6 - - + +
141B GLY 2.9 15.7 + - - +
142B ILE 3.1 3.8 + - - +
144B LEU* 1.3 76.7 - - - +
146B TYR* 1.3 58.0 + - - +
148B ALA* 3.4 0.3 + - - +
149B ALA* 2.9 30.1 + - - +
156B VAL* 3.8 10.8 - - + -
202B ILE* 4.1 9.2 - - + -
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 5.6 4.3 - - + -
115A LEU* 3.7 37.5 - - + +
116A SER* 5.4 1.9 + - - -
143A PRO* 3.9 31.6 - - + -
146A TYR* 3.8 30.2 + + + -
147A ALA* 3.2 24.3 - - - +
150A SER* 4.6 6.2 + - - -
115B LEU* 6.2 0.2 - - + -
142B ILE 2.9 16.5 + - - +
143B PRO* 3.9 6.3 - - + +
145B ALA* 1.3 73.6 - - - +
147B ALA* 1.3 67.4 + - + +
149B ALA* 3.3 6.5 + - + +
150B SER* 2.8 42.7 + - - -
156B VAL* 4.1 9.5 - - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.5 35.7 - - + +
116B SER* 4.8 3.1 - - - +
119B GLY* 3.8 7.9 - - - +
143B PRO 3.0 18.5 + - - +
144B LEU* 3.7 6.7 - - - +
145B ALA 3.4 0.2 - - - -
146B TYR* 1.3 82.7 - - + +
148B ALA* 1.3 62.2 + - - +
150B SER* 2.6 25.0 + - - -
151B TYR* 3.3 13.0 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY* 3.7 14.0 - - - +
122B PHE* 4.1 24.5 - - + -
123B ALA* 4.2 0.2 - - - +
134B VAL* 4.7 3.1 - - + -
144B LEU 3.0 17.4 + - - +
145B ALA 3.7 4.0 - - - +
147B ALA* 1.3 76.0 - - - +
149B ALA* 1.3 58.8 + - - +
151B TYR* 3.3 5.0 + - - +
152B LEU* 3.0 40.7 + - + +
200B LEU* 5.0 0.9 - - + -
202B ILE* 4.4 15.0 - - + -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.0 3.4 - - + +
134B VAL* 3.9 21.9 - - + +
145B ALA 2.9 19.0 + - - +
146B TYR* 3.3 5.6 + - + +
148B ALA* 1.3 76.7 - - - +
150B SER* 1.3 59.6 + - - +
152B LEU* 4.4 0.4 - - - +
153B ASN* 2.8 26.0 + - - -
154B VAL* 3.2 31.2 + - - +
156B VAL* 4.2 14.4 - - + -
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.4 14.8 - - - +
20B PRO* 3.7 13.9 - - - +
146B TYR* 2.8 33.3 + - - -
147B ALA* 2.6 24.8 + - - -
149B ALA* 1.3 79.1 - - - +
151B TYR* 1.3 68.4 + - - +
153B ASN* 3.7 6.8 + - - -
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Residues in contact with TYR 151 (chain B).
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* 6.1 1.6 - - - +
20B PRO* 3.5 17.1 - - + +
21B HIS* 3.3 17.3 - - - -
71B TYR* 5.5 4.0 - + - -
73B PRO* 3.8 27.2 - - + +
116B SER* 3.3 46.3 + - - -
119B GLY* 3.7 1.6 - - - -
120B LYS* 3.6 36.7 - - + +
123B ALA* 3.4 21.1 - - + -
147B ALA* 3.3 21.7 + - - -
148B ALA 3.3 2.5 + - - +
149B ALA 3.2 0.2 - - - -
150B SER* 1.3 84.7 + - - +
152B LEU* 1.3 59.8 + - - +
153B ASN 3.2 4.6 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 3.6 38.9 - - + +
122B PHE 4.9 0.2 - - - +
123B ALA* 3.7 38.4 - - + +
126B PHE* 4.4 4.9 - - + +
127B ALA* 4.4 6.1 - - - -
131B ILE* 4.5 14.8 - - + -
134B VAL* 4.6 4.7 - - + -
148B ALA* 3.0 28.0 + - + +
149B ALA 3.3 0.2 + - - -
151B TYR* 1.3 76.5 - - - +
153B ASN* 1.3 70.3 + - - +
154B VAL* 3.5 23.9 + - + +
200B LEU* 3.9 26.5 - - + -
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Residues in contact with ASN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.2 20.3 - - - +
113A SER* 4.7 12.3 - - - +
18B THR 5.9 0.8 + - - -
19B HIS* 5.8 2.3 - - - +
20B PRO* 3.3 35.1 - - + +
21B HIS* 4.4 6.6 - - + +
22B GLU* 4.7 11.8 - - - +
149B ALA 2.8 10.8 + - - -
150B SER 3.7 4.5 + - - -
151B TYR 3.2 3.0 - - - -
152B LEU* 1.3 82.1 - - - +
154B VAL* 1.3 59.1 + - - +
155B PRO* 4.8 0.2 - - - +
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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