Contacts of the helix formed by residues 129 - 141 (chain A) in PDB entry 2PGY
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 PHE 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LYS* 4.7 4.5 - - + -
126A TYR* 3.1 52.7 + + - +
128A ALA* 1.3 84.3 - - + +
130A LEU* 1.3 62.0 + - - +
131A LYS 3.4 2.0 + - - -
132A LEU* 3.7 7.8 + - + +
133A PHE* 3.1 22.2 + - - +
212A VAL* 3.5 19.8 - - - +
213A ASP* 3.8 24.0 - - + -
214A MET 5.0 0.5 - - - +
344A VAL* 4.3 31.2 - - + -
345A PRO 5.7 1.6 - - - -
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Residues in contact with LEU 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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120A VAL* 4.3 10.8 - - + -
122A ALA* 3.8 24.9 - - + -
127A VAL* 3.4 23.7 + - + +
128A ALA 3.4 0.2 - - - -
129A PHE* 1.3 75.4 - - - +
131A LYS* 1.3 68.2 + - - +
133A PHE* 4.1 4.0 - - + -
134A LEU* 2.9 38.6 + - + +
151A VAL* 3.9 32.5 - - + -
159A VAL* 4.2 14.1 - - + -
160A PRO* 3.8 24.0 - - + -
212A VAL* 3.6 19.1 - - + -
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Residues in contact with LYS 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 VAL 4.9 0.6 + - - -
128A ALA 4.6 5.8 + - - +
129A PHE 3.4 1.0 - - - -
130A LEU* 1.3 79.0 - - - +
132A LEU* 1.3 58.0 + - - +
134A LEU* 4.1 0.7 - - - +
135A GLU* 2.8 77.4 + - + +
160A PRO* 3.7 29.1 - - + +
161A ARG 6.1 1.1 - - - -
162A VAL* 4.5 5.6 - - + +
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Residues in contact with LEU 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 ALA 5.4 0.4 + - - -
129A PHE* 3.7 8.3 + - + +
131A LYS* 1.3 77.0 - - - +
133A PHE* 1.3 64.6 + - - +
135A GLU* 4.6 7.2 - - + +
136A THR* 2.8 51.0 + - + +
214A MET 4.9 0.2 - - - +
215A GLU* 3.9 36.1 - - + +
344A VAL* 4.2 24.5 - - + -
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Residues in contact with PHE 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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118A LEU* 4.0 23.3 - - + -
120A VAL* 4.0 20.0 - - + -
129A PHE 3.1 20.4 + - - +
130A LEU* 3.6 7.0 - - + +
131A LYS 3.3 0.2 - - - -
132A LEU* 1.3 76.2 - - - +
134A LEU* 1.3 76.5 + - + +
136A THR* 3.1 6.0 + - - -
137A ALA* 2.9 30.7 + - + +
149A TYR* 5.0 0.9 - + - -
210A VAL* 3.4 25.6 - - + -
211A ASP 3.6 18.2 - - - -
212A VAL* 3.6 30.3 - - + +
214A MET 3.8 16.9 + - - -
216A PHE* 4.0 13.1 - + - -
341A PHE* 4.0 11.2 - + - -
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Residues in contact with LEU 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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120A VAL* 5.7 0.2 - - + -
130A LEU* 2.9 37.8 + - + +
131A LYS 4.2 1.3 - - - +
133A PHE* 1.3 85.7 - - + +
135A GLU* 1.3 59.8 + - - +
137A ALA* 3.4 5.2 + - - +
138A GLU* 2.9 32.2 + - - +
149A TYR* 3.9 34.5 + - + -
151A VAL* 4.7 7.0 - - + -
159A VAL* 5.0 5.6 - - + -
160A PRO* 4.7 9.6 - - + +
162A VAL* 4.3 29.8 - - + -
164A LEU* 5.6 2.2 - - + -
170A LEU* 3.9 28.0 - - + -
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Residues in contact with GLU 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 LYS* 2.8 58.8 + - - +
132A LEU* 4.1 6.4 - - + +
134A LEU* 1.3 73.6 - - - +
136A THR* 1.3 67.1 + - + +
138A GLU* 3.5 6.4 + - - +
139A LYS* 3.4 24.1 + - - +
161A ARG 5.5 0.7 - - - +
162A VAL* 3.7 27.2 - - + +
163A THR 5.7 0.3 + - - -
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Residues in contact with THR 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 LEU* 2.8 41.5 + - + +
133A PHE 3.1 6.9 + - - -
135A GLU* 1.3 75.3 - - + +
137A ALA* 1.3 63.8 - - - +
139A LYS* 3.1 10.7 + - + +
140A HIS* 3.1 27.7 + - + +
215A GLU* 3.7 14.6 - - + +
216A PHE* 3.1 40.7 + - - +
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Residues in contact with ALA 137 (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 LEU* 4.9 0.2 - - + -
133A PHE* 2.9 22.0 + - + +
134A LEU* 3.5 7.6 - - - +
135A GLU 3.3 0.2 - - - -
136A THR* 1.3 76.4 + - - +
138A GLU* 1.3 57.8 + - - +
141A PHE* 2.9 35.2 + - + +
149A TYR* 3.6 27.1 - - + +
168A ARG* 3.4 5.7 + - - -
216A PHE* 3.6 24.8 - - + -
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Residues in contact with GLU 138 (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 LEU 2.9 19.2 + - - +
135A GLU* 3.7 8.1 - - - +
136A THR 3.3 0.2 - - - -
137A ALA* 1.3 76.9 - - - +
139A LYS* 1.3 60.8 + - + +
143A VAL* 3.5 15.4 - - - +
149A TYR* 2.5 33.1 + - - -
162A VAL* 4.7 3.6 - - + -
163A THR 3.9 11.9 - - - +
164A LEU* 3.4 21.9 - - + +
165A GLY* 2.7 28.7 + - - -
168A ARG* 2.7 25.1 + - - +
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Residues in contact with LYS 139 (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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135A GLU 3.4 13.0 + - - +
136A THR* 3.1 13.1 + - + +
138A GLU* 1.3 81.4 - - + +
140A HIS* 1.3 90.6 + - + +
143A VAL* 3.6 11.0 - - - +
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Residues in contact with HIS 140 (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* 3.1 19.5 + - + +
137A ALA 3.3 0.2 + - - -
139A LYS* 1.3 113.1 + - + +
141A PHE* 1.3 60.7 + - - +
142A MET 3.7 1.1 + - - -
143A VAL* 4.0 6.2 + - - +
216A PHE* 3.4 33.3 + - + -
217A ARG* 3.6 20.5 + - - -
218A ASP* 3.3 31.0 + - - +
219A HIS* 3.9 8.3 + - - +
220A VAL 3.1 24.5 + - - +
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Residues in contact with PHE 141 (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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116A ILE* 4.0 13.7 - - + -
118A LEU* 3.7 39.3 - - + -
137A ALA* 2.9 24.3 + - - +
140A HIS* 1.3 74.7 - - - +
142A MET* 1.3 99.8 + - + +
143A VAL* 3.1 2.8 + - - +
147A VAL* 4.1 14.4 - - + -
149A TYR* 4.8 1.8 - + - -
168A ARG* 2.8 37.7 + - - -
208A VAL* 4.6 15.0 - - + -
216A PHE* 3.8 29.2 - + + -
220A VAL* 3.4 19.1 - - + -
224A ILE* 4.7 1.8 - - + -
269A PHE* 5.5 1.6 - + - -
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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