Contacts of the helix formed by residues 141 - 153 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C LEU* 5.4 0.2 - - - -
136C THR* 3.8 17.8 + - - +
137C VAL 4.5 3.0 + - - -
139C THR 3.3 1.0 - - - -
140C LYS* 1.3 76.7 - - - +
142C ILE* 1.3 63.8 + - - +
143C PRO* 3.4 0.9 - - - -
144C LEU* 3.2 12.6 + - - +
145C ALA* 3.1 21.3 + - - +
202C ILE* 5.0 0.9 - - - +
203C ASP* 5.4 0.9 - - - -
204C ASP* 3.9 25.9 + - - -
606C PCP 4.2 2.2 + - - -
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C THR* 3.9 13.2 - - + -
138C ALA* 3.8 2.7 - - - -
139C THR* 3.1 26.2 + - - +
141C GLY* 1.3 76.3 - - - +
143C PRO* 1.3 65.2 - - + +
145C ALA* 3.0 4.3 + - - +
146C TYR* 2.9 27.3 + - + +
156C VAL* 5.0 2.0 - - + +
158C ILE* 3.8 29.2 - - + -
139D THR* 3.7 30.3 - - + +
142D ILE* 3.7 30.1 - - + -
143D PRO* 3.8 24.7 - - + -
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Residues in contact with PRO 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 3.6 11.4 - - + +
115C LEU* 3.9 7.2 - - + +
139C THR 4.0 2.7 - - - +
140C LYS 3.3 14.6 - - - +
141C GLY 3.5 0.9 - - - -
142C ILE* 1.3 95.4 - - + +
144C LEU* 1.3 55.5 + - - +
146C TYR* 3.4 7.6 + - + +
147C ALA* 2.9 30.8 + - - +
142D ILE* 4.0 6.5 - - + -
143D PRO* 6.3 0.2 - - + -
146D TYR* 2.8 61.6 - - + +
158D ILE* 4.2 6.5 - - + -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 4.0 20.6 - - + +
115C LEU* 3.9 13.1 - - + +
118C VAL* 3.1 39.3 - - + -
119C GLY* 4.9 1.5 - - - +
122C PHE* 4.2 8.1 - - + -
140C LYS 5.1 0.2 + - - -
141C GLY* 3.2 13.5 + - - +
143C PRO* 1.3 80.0 - - - +
145C ALA* 1.3 61.2 + - - +
147C ALA* 3.3 3.6 + - - +
148C ALA* 3.1 23.0 + - - +
202C ILE* 4.0 11.7 - - + +
203C ASP 3.9 9.2 - - - +
204C ASP* 3.8 31.6 - - + +
232C LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.7 26.3 - - + +
136C THR* 3.6 31.6 - - + +
141C GLY 3.1 1.5 + - - +
142C ILE 3.0 8.5 + - - +
144C LEU* 1.3 79.0 - - - +
146C TYR* 1.3 58.6 + - - +
148C ALA* 3.3 1.4 + - - +
149C ALA* 2.8 30.1 + - - +
156C VAL* 3.6 13.2 - - + +
202C ILE* 4.3 7.9 - - + -
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Residues in contact with TYR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ILE 2.9 15.2 + - - +
143C PRO* 3.8 6.3 - - + +
145C ALA* 1.3 78.6 - - - +
147C ALA* 1.3 67.0 + - + +
149C ALA* 3.3 0.3 + - - +
150C SER* 2.9 35.4 + - - -
156C VAL* 3.4 19.6 - - + +
112D PRO* 4.4 18.0 + - + +
115D LEU* 3.4 37.3 - - + +
116D SER* 4.2 9.0 + - - -
143D PRO* 4.1 19.3 - - + -
146D TYR* 4.2 17.5 - - + -
147D ALA* 3.5 39.6 - - + +
150D SER* 5.5 1.8 - - - -
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU* 3.5 35.7 - - + +
116C SER* 4.8 3.4 - - - +
119C GLY* 4.0 5.4 - - - -
143C PRO 2.9 17.6 + - - +
144C LEU* 3.6 6.7 - - + +
146C TYR* 1.3 82.5 - - + +
148C ALA* 1.3 61.7 + - - +
150C SER* 2.7 24.0 + - - -
151C TYR* 3.2 13.8 - - + -
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY* 3.7 21.9 - - - +
122C PHE* 4.1 21.5 - - + -
123C ALA* 4.1 0.3 - - - +
134C VAL* 4.7 2.9 - - + -
144C LEU 3.1 15.8 + - - +
145C ALA 3.8 4.0 - - - +
147C ALA* 1.3 75.8 - - - +
149C ALA* 1.3 62.9 + - - +
151C TYR* 3.2 13.9 + - - +
152C LEU* 3.2 27.3 + - + +
200C LEU* 4.9 0.7 - - + -
202C ILE* 4.7 11.4 - - + -
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.8 18.3 - - + +
145C ALA 2.8 7.2 + - - +
146C TYR 3.3 2.4 + - - +
148C ALA* 1.3 77.3 - - - +
150C SER* 1.3 57.9 + - - +
152C LEU* 4.4 0.2 - - - -
153C ASN* 2.7 25.5 + - - -
154C VAL* 3.1 29.0 + - - +
155C PRO 4.3 0.2 - - - +
156C VAL* 3.1 36.8 - - + -
112D PRO* 3.8 3.9 - - + +
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Residues in contact with SER 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 3.6 15.6 - - - +
146C TYR* 2.9 33.8 + - - -
147C ALA* 2.7 23.6 + - - -
149C ALA* 1.3 77.3 - - - +
151C TYR* 1.3 67.6 + - - +
153C ASN* 3.7 4.9 + - - +
112D PRO* 4.1 14.8 - - - +
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Residues in contact with TYR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 3.5 15.9 - - + +
21C HIS* 3.1 19.1 - - - -
71C TYR* 5.6 2.2 - + - -
73C PRO* 3.7 27.1 - - + +
116C SER* 2.7 50.2 + - - -
119C GLY* 3.8 0.9 - - - -
120C LYS* 3.6 36.3 - - + +
123C ALA* 3.3 22.2 - - + -
147C ALA* 3.2 22.2 - - + -
148C ALA 3.2 2.9 + - - +
150C SER* 1.3 85.9 + - - +
152C LEU* 1.3 60.8 + - - +
153C ASN 3.2 2.7 - - - -
18D THR* 6.0 1.4 - - - +
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C HIS* 3.5 34.6 - - + +
123C ALA* 3.6 39.9 - - + +
126C PHE 4.8 0.4 - - - +
127C ALA* 4.5 5.4 - - - +
131C ILE* 3.9 21.3 - - + -
134C VAL* 4.3 6.7 - - + -
148C ALA* 3.2 23.5 + - + +
149C ALA 3.9 3.8 - - - +
151C TYR* 1.3 77.1 - - - +
153C ASN* 1.3 71.1 + - - +
154C VAL* 3.8 19.1 - - + +
200C LEU* 3.8 29.6 - - + -
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Residues in contact with ASN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C HIS* 5.9 0.9 - - - -
20C PRO* 3.4 31.5 + - + +
21C HIS* 4.3 8.9 + - + -
22C GLU* 4.5 14.9 + - - +
149C ALA 2.7 10.0 + - - -
150C SER 3.7 5.0 + - - +
151C TYR 3.2 2.6 - - - -
152C LEU* 1.3 84.2 - - - +
154C VAL* 1.3 60.2 + - - +
155C PRO* 4.8 0.3 - - - +
112D PRO* 4.4 15.8 - - - +
113D SER* 4.6 13.2 + - - -
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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