Contacts of the helix formed by residues 127 - 140 (chain A) in PDB entry 2Z1Z
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A SER* 3.1 17.7 + - - -
126A ASP* 1.3 79.5 - - - +
128A ALA* 1.3 59.6 + - - -
129A LYS 3.4 2.7 - - - -
130A CYS* 3.0 20.5 + - - +
131A ASP* 3.1 8.9 + - - -
278A ARG* 3.5 7.4 - - - -
279A LEU 4.1 2.0 - - - -
280A GLY 3.9 8.5 - - - -
500A PLP 3.4 13.2 - - - -
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Residues in contact with ALA 128 (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 GLY* 1.3 67.0 - - - -
129A LYS* 1.3 59.5 + - - +
130A CYS 3.1 1.8 - - - -
131A ASP* 3.1 10.9 + - - +
132A ILE* 2.9 38.5 + - + +
237A ASP* 5.0 3.6 - - - +
265A THR* 4.1 12.3 - - + -
266A ALA* 3.9 21.9 + - - +
267A SER* 4.1 5.3 + - - -
500A PLP 3.0 37.2 + - + +
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Residues in contact with LYS 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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37A TYR* 3.7 14.2 - - + +
128A ALA* 1.3 75.4 - - - +
130A CYS* 1.3 62.7 + - - +
132A ILE* 3.7 10.9 - - - +
133A SER* 3.5 17.8 + - - -
152A TYR* 4.2 18.4 - - - +
154A ALA* 4.7 6.7 - - + -
433A MLT 4.1 5.6 + - - +
500A PLP 3.1 18.8 + - - +
97B GLU* 3.1 22.2 + - - -
305B CYS 2.6 28.0 + - - -
306B THR* 3.4 25.3 - - - +
307B CYS 3.8 6.8 - - - +
308B PHE 2.8 20.2 - - - +
309B ASN* 3.4 27.0 + - + +
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Residues in contact with CYS 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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126A ASP* 3.2 40.4 - - - +
127A GLY 3.0 7.6 + - - +
129A LYS* 1.3 80.3 - - - +
131A ASP* 1.3 57.9 + - - +
132A ILE 3.3 0.2 - - - -
133A SER* 4.1 1.2 - - - -
134A ARG* 3.1 45.7 + - - +
278A ARG* 4.3 12.3 - - - -
134B ARG* 4.8 2.2 - - - +
307B CYS 3.8 10.9 - - - +
308B PHE* 3.9 9.2 - - - -
309B ASN 3.9 24.2 - - - -
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Residues in contact with ASP 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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123A PHE* 4.6 1.0 - - - +
125A SER* 2.8 35.3 + - - -
127A GLY 3.1 7.7 + - - +
128A ALA* 3.1 12.1 + - - +
130A CYS* 1.3 73.5 - - - +
132A ILE* 1.3 56.4 + - - +
134A ARG* 3.2 8.5 - - - +
135A LEU* 2.7 41.1 + - - +
265A THR* 3.4 21.9 - - + +
281A TRP 3.5 10.6 + - - +
282A THR* 2.9 29.9 + - + +
300A PHE* 4.1 9.1 - - - -
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Residues in contact with ILE 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* 2.9 24.7 + - + +
129A LYS* 3.7 9.2 - - - +
130A CYS 3.3 0.2 - - - -
131A ASP* 1.3 78.6 - - + +
133A SER* 1.3 58.5 + - - +
135A LEU* 3.4 9.0 + - + +
136A GLN* 3.1 26.7 + - - +
152A TYR* 4.5 14.4 - - + -
154A ALA* 4.0 14.8 - - + +
155A TYR* 3.1 40.2 - - + -
158A SER* 3.9 20.6 - - - +
203A PHE* 4.9 10.2 - - + -
235A VAL* 6.1 1.6 - - + -
237A ASP* 4.3 9.4 - - - +
265A THR* 5.0 9.6 - - + +
500A PLP 4.9 2.0 - - + +
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Residues in contact with SER 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 LYS 3.5 7.4 + - - -
130A CYS 4.2 1.1 - - - -
131A ASP 3.2 0.4 - - - -
132A ILE* 1.3 76.5 - - - +
134A ARG* 1.3 60.5 + - - +
136A GLN* 3.2 8.3 + - - +
137A VAL* 3.0 35.6 + - - +
158A SER* 3.8 14.4 - - - -
162A MET* 5.3 0.2 - - - +
306B THR 4.4 1.7 + - - -
307B CYS* 3.3 51.2 - - - +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER* 3.8 17.3 - - - -
126A ASP* 2.8 24.5 + - - -
130A CYS* 3.1 32.2 + - - +
131A ASP* 3.2 11.0 - - - +
133A SER* 1.3 72.8 - - - +
135A LEU* 1.4 64.6 + - - +
137A VAL* 3.5 8.3 + - - +
138A MET* 3.2 22.7 + - - +
300A PHE* 3.8 16.1 - - + -
303A ILE* 4.0 17.8 - - + +
304A ILE* 3.0 35.2 - - + -
307A CYS* 5.0 5.6 + - + +
308A PHE* 3.2 40.0 - - + +
130B CYS* 4.7 0.6 - - - -
134B ARG* 3.5 24.9 - - - +
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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 ASP 2.7 27.6 + - - +
132A ILE* 3.6 9.0 - - + +
134A ARG* 1.4 70.8 - - - +
136A GLN* 1.3 58.9 + - + +
138A MET* 3.3 19.3 + - + +
139A PHE* 2.9 45.8 + - + -
203A PHE* 5.6 2.7 - - + -
235A VAL* 4.1 11.7 - - + -
263A MET* 3.4 34.1 - - + -
265A THR* 3.8 21.3 - - - +
282A THR* 4.4 10.1 - - + +
284A ILE* 4.4 2.9 - - + -
300A PHE* 3.7 25.8 - - + -
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Residues in contact with GLN 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 ILE* 3.1 15.2 + - + +
133A SER* 3.2 11.8 + - - +
135A LEU* 1.3 77.5 - - - +
137A VAL* 1.3 60.3 + - - +
139A PHE* 3.4 23.4 + - - +
140A GLY* 3.2 18.0 + - - -
145A ILE* 4.6 2.6 - - - +
155A TYR 4.1 0.2 - - - +
158A SER* 3.3 26.6 + - - +
159A SER* 3.7 10.1 - - - -
162A MET* 3.7 23.8 - - + +
164A GLN* 3.0 38.4 + - - +
203A PHE* 3.8 27.0 - - + -
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Residues in contact with VAL 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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133A SER* 3.0 24.7 + - - +
134A ARG* 3.9 7.2 - - - +
135A LEU 3.4 0.2 - - - -
136A GLN* 1.3 75.3 - - - +
138A MET* 1.3 62.3 + - - +
140A GLY* 3.6 4.3 + - - -
162A MET* 3.7 17.0 - - - +
303A ILE* 3.6 12.1 - - + +
307A CYS* 5.2 5.4 - - - -
27B ASN* 3.2 15.2 + - - -
137B VAL* 4.0 24.2 - - + -
161B ILE* 3.5 31.5 - - + +
162B MET* 4.3 14.6 - - + -
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Residues in contact with MET 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 ARG 3.2 10.8 + - - +
135A LEU* 3.4 23.6 - - + +
137A VAL* 1.3 79.7 - - - +
139A PHE* 1.3 93.5 + - + +
290A TYR* 3.7 13.3 + - - +
296A VAL* 3.7 20.2 - - + +
299A ASP* 3.9 15.9 - - + -
300A PHE* 3.3 40.6 - - + +
303A ILE* 4.0 19.0 - - + +
27B ASN* 2.9 27.2 + - - +
30B MET* 4.4 2.5 - - - +
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Residues in contact with PHE 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 LEU* 2.9 32.5 + - + +
136A GLN* 3.4 23.3 - - - +
137A VAL 3.4 0.2 - - - -
138A MET* 1.3 95.0 - - + +
140A GLY* 1.3 60.5 + - - +
142A ASN* 5.1 1.4 + - - +
143A VAL* 3.5 34.1 + - + +
201A ILE* 3.7 35.4 - - + -
203A PHE* 4.8 1.3 - + - -
233A ILE* 4.1 15.0 - - + -
235A VAL* 3.9 23.1 - - + -
263A MET* 3.9 24.2 - - + -
290A TYR* 4.0 14.0 - + - -
296A VAL* 4.8 0.7 - - + -
25B SER 5.1 0.7 - - - +
27B ASN* 3.7 16.2 + - - +
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Residues in contact with GLY 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 GLN 3.2 8.4 + - - -
137A VAL 3.8 5.6 - - - -
138A MET 3.4 0.8 - - - -
139A PHE* 1.3 80.9 - - - +
141A SER* 1.3 63.9 + - - -
142A ASN 3.5 2.4 + - - -
143A VAL* 3.9 3.5 - - - +
162A MET* 4.5 8.1 - - - -
164A GLN* 2.8 24.6 + - - +
27B ASN* 3.5 20.2 - - - -
29B ASN* 5.8 1.1 - - - -
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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