Contacts of the helix formed by residues 124 - 136 (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 PRO 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A TYR 3.7 7.8 - - - +
109A GLU* 3.1 34.1 - - - +
110A GLY* 3.8 4.5 - - - +
123A ALA* 1.4 88.8 - - + +
125A ASN* 1.3 57.0 + - - +
126A GLN 3.1 0.4 - - - -
127A ASN* 3.5 7.9 - - - +
128A SER* 2.8 34.7 + - - +
129A ALA* 2.9 10.8 + - - -
156A SER* 6.0 2.9 - - - -
159A VAL* 3.9 25.6 - - + -
163A LEU* 5.8 0.7 - - - -
367A VAL* 3.5 22.0 - - + -
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Residues in contact with ASN 125 (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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123A ALA* 3.2 4.9 + - - +
124A PRO* 1.3 77.8 - - - +
126A GLN* 1.3 61.3 + - - +
127A ASN 3.6 0.4 - - - -
129A ALA* 3.8 13.9 - - - +
130A PRO* 3.7 11.1 - - - +
361A ILE* 3.4 19.2 - - - +
362A ARG 3.3 20.4 + - - -
363A PRO* 3.7 3.8 - - - +
364A ASP* 2.7 46.1 + - - +
367A VAL* 4.0 4.6 - - + +
372A LEU* 3.9 27.3 - - + +
373A ASP* 5.9 0.4 + - - -
375A TRP* 4.6 2.9 + - - -
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Residues in contact with GLN 126 (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 GLY 4.5 0.7 - - - +
122A PRO* 3.2 18.4 - - + +
123A ALA 2.9 27.8 + - - +
125A ASN* 1.3 86.7 - - - +
127A ASN* 1.3 60.9 + - - +
130A PRO* 4.0 4.2 - - - +
336A SER 2.9 23.6 + - - +
338A LEU* 3.7 15.7 - - + +
339A SER 4.9 1.6 - - - +
340A SER* 3.2 28.1 + - - -
361A ILE* 2.8 48.8 + - + +
363A PRO* 3.6 17.5 - - - +
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Residues in contact with ASN 127 (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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107A PRO* 3.8 16.4 - - - +
108A TYR 5.2 1.9 + - - +
122A PRO* 3.4 33.5 + - + +
123A ALA 3.1 13.5 - - - +
124A PRO* 3.5 7.3 - - - +
126A GLN* 1.3 81.1 - - - +
128A SER* 1.3 75.6 + - - +
129A ALA 3.4 1.3 - - - -
130A PRO* 3.3 2.3 - - - +
131A LEU* 3.1 24.3 + - - +
232A LEU* 3.9 24.5 + - - +
253A VAL* 3.6 36.8 + - + +
254A ALA* 5.8 0.2 - - - -
255A PRO* 6.2 0.2 - - + -
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 2.8 27.2 + - - +
127A ASN* 1.3 78.4 + - - +
129A ALA* 1.3 61.4 + - - -
131A LEU* 3.6 2.9 - - - +
132A ALA* 3.0 21.5 + - - +
156A SER* 5.2 5.4 + - - -
159A VAL* 5.1 2.2 - - - +
160A MET* 4.0 12.4 - - - +
163A LEU* 3.6 23.1 - - - +
202A PHE* 4.8 1.4 - - - -
232A LEU* 3.6 30.0 - - - +
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Residues in contact with ALA 129 (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 2.9 9.6 + - - +
125A ASN* 3.8 13.0 - - - +
128A SER* 1.3 77.9 - - - +
130A PRO* 1.3 71.5 - - + +
132A ALA* 3.7 2.8 + - - +
133A ALA* 3.6 14.0 + - - +
163A LEU* 3.8 12.5 - - + +
167A HIS* 4.7 4.3 - - - -
372A LEU* 3.8 29.4 - - + -
373A ASP 5.3 0.4 - - - +
375A TRP* 3.6 19.9 - - + +
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Residues in contact with PRO 130 (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 ASN 3.7 9.0 - - - +
126A GLN 4.0 5.4 - - - +
127A ASN 3.3 14.4 - - - +
129A ALA* 1.3 95.2 - - + +
131A LEU* 1.3 61.2 + - - +
133A ALA* 3.3 6.9 + - - +
134A TYR* 3.1 20.8 + - - +
340A SER* 4.2 2.9 - - - +
342A ILE* 4.0 4.4 - - + +
355A TRP* 3.5 31.1 - - + -
361A ILE* 3.9 18.8 - - + -
375A TRP* 3.6 30.5 - - + +
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Residues in contact with LEU 131 (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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127A ASN 3.1 15.4 + - - +
128A SER 3.6 2.5 - - - +
130A PRO* 1.3 77.0 - - - +
132A ALA* 1.3 56.4 + - - +
134A TYR* 3.1 1.9 + - + +
135A LEU* 2.7 64.1 + - + +
160A MET* 4.1 6.1 - - + -
202A PHE* 4.0 17.5 - - + -
230A ALA* 4.4 8.5 - - + -
231A SER 4.3 6.1 - - - +
232A LEU* 3.6 28.0 - - + -
251A VAL* 4.1 18.2 - - + -
252A VAL 5.2 0.2 - - - -
253A VAL* 3.7 20.0 - - + +
342A ILE* 3.9 17.2 - - + +
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Residues in contact with ALA 132 (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 3.0 16.9 + - - +
129A ALA 4.1 1.8 - - - +
130A PRO 3.5 0.2 - - - -
131A LEU* 1.3 72.9 - - - +
133A ALA* 1.3 57.8 + - - +
135A LEU* 3.2 2.3 + - - +
136A ILE* 3.0 36.7 + - + +
160A MET* 3.9 24.1 - - - +
163A LEU* 4.1 20.0 - - + +
164A TYR* 4.3 15.7 - - + -
167A HIS* 4.2 10.8 - - + +
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Residues in contact with ALA 133 (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 3.6 5.6 + - - +
130A PRO 3.3 9.3 + - - +
131A LEU 3.2 0.6 - - - -
132A ALA* 1.3 77.1 - - - +
134A TYR* 1.3 56.8 + - - +
136A ILE* 4.9 0.2 - - - -
137A ARG* 3.0 46.4 + - - +
167A HIS* 4.0 19.8 - - + -
375A TRP* 3.8 34.1 - - + +
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Residues in contact with TYR 134 (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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130A PRO 3.1 6.5 + - - +
131A LEU* 3.1 4.6 + - + +
133A ALA* 1.3 75.4 - - - +
135A LEU* 1.3 72.3 + - + +
137A ARG* 4.9 2.2 - - - -
138A HIS* 2.7 65.2 + + - +
139A TYR* 3.8 23.9 + + - -
251A VAL* 4.5 5.3 - - + +
342A ILE* 3.4 52.4 - - + +
344A GLU* 3.5 11.1 + - - -
354A ARG* 3.3 37.9 - - + +
355A TRP* 4.1 16.8 - + + -
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Residues in contact with LEU 135 (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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131A LEU* 2.7 46.3 + - + +
132A ALA* 3.7 4.9 - - - +
134A TYR* 1.3 75.5 - - + +
136A ILE* 1.3 54.3 + - - +
139A TYR* 2.7 57.1 + - + +
140A GLY 3.2 3.5 + - - +
160A MET* 4.8 4.9 - - + -
164A TYR* 3.6 26.7 - - + +
200A VAL* 3.9 20.8 - - + +
202A PHE* 5.2 4.9 - - + -
228A PRO* 5.5 0.2 - - + -
230A ALA* 3.8 32.8 - - + -
251A VAL* 4.3 9.6 - - + -
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Residues in contact with ILE 136 (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 3.0 13.7 + - - +
135A LEU* 1.3 77.1 - - - +
137A ARG* 1.3 72.5 + - + +
138A HIS 2.8 7.3 + - - -
139A TYR 3.5 0.2 + - - -
140A GLY* 3.1 30.3 + - - +
141A GLU* 4.5 11.0 - - + -
164A TYR* 4.1 33.4 - - + +
167A HIS* 3.2 53.6 - - + +
169A GLY* 4.5 2.5 - - - -
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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