Contacts of the helix formed by residues 132 - 147 (chain A) in PDB entry 3ORY
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 THR 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO* 3.5 5.2 - - - -
89A GLU* 3.4 14.1 - - + +
130A LYS* 4.0 12.8 - - + +
131A LEU* 1.3 76.5 - - - +
133A GLU* 1.3 64.1 + - - +
134A GLU* 3.4 9.6 + - - +
135A MET* 3.1 37.9 + - - +
136A VAL* 3.1 22.9 + - - +
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Residues in contact with GLU 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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33A TYR* 4.2 4.7 + - - -
87A PRO* 3.5 26.1 - - + +
88A PRO* 3.6 10.1 - - - +
89A GLU* 2.8 25.2 + - - +
132A THR* 1.3 71.2 - - - +
134A GLU* 1.3 57.3 + - - +
136A VAL* 3.2 11.7 + - - +
137A ARG* 2.9 58.9 + - - +
140A LYS* 5.1 5.9 + - - -
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Residues in contact with GLU 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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57A ARG* 4.7 19.0 + - - -
132A THR* 3.3 8.1 + - - +
133A GLU* 1.3 76.9 - - - +
135A MET* 1.3 58.9 + - + +
137A ARG* 3.3 19.4 + - + +
138A ASP* 2.9 43.9 + - - +
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Residues in contact with MET 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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40A LEU* 3.6 35.9 - - + -
58A ILE* 5.0 10.5 - - + +
61A HIS* 3.5 39.3 - - + +
129A ALA* 5.7 0.4 - - + -
130A LYS 3.4 26.2 - - - +
131A LEU* 3.9 12.1 - - + -
132A THR* 3.1 30.0 + - - +
134A GLU* 1.3 78.7 - - + +
136A VAL* 1.3 58.0 + - - +
138A ASP* 3.4 5.9 + - - +
139A ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 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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33A TYR* 3.6 38.1 - - + +
36A LEU* 4.3 4.3 - - + -
83A PHE* 4.1 6.3 - - + -
88A PRO* 3.9 14.8 - - + -
131A LEU* 4.0 14.8 - - + -
132A THR 3.1 14.1 + - - +
133A GLU* 3.5 15.7 - - - +
135A MET* 1.3 73.1 - - - +
137A ARG* 1.3 66.1 + - - +
139A ALA* 3.2 7.8 + - - +
140A LYS* 2.9 50.1 + - - +
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Residues in contact with ARG 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 GLU* 2.9 40.7 + - - +
134A GLU* 3.4 28.3 - - - +
136A VAL* 1.3 76.5 - - - +
138A ASP* 1.3 63.1 + - - +
140A LYS* 3.3 12.6 + - - +
141A SER* 3.0 36.4 + - - +
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Residues in contact with ASP 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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61A HIS* 4.9 1.7 + - - +
62A LEU* 4.0 20.2 - - + +
134A GLU* 2.9 36.5 + - - +
135A MET* 3.8 8.3 - - - +
136A VAL 3.3 0.2 - - - -
137A ARG* 1.3 81.8 - - - +
139A ALA* 1.3 56.8 - - - +
141A SER* 3.2 8.9 + - - -
142A LEU* 2.8 29.8 + - - +
311A ILE* 5.0 6.0 - - + +
315A GLU* 5.7 1.7 - - - +
316A HIS* 4.0 22.9 + - - +
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Residues in contact with ALA 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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36A LEU* 3.8 25.8 - - + -
61A HIS* 5.2 0.4 - - + -
62A LEU* 4.0 8.2 - - + +
65A LEU* 3.6 25.6 - - + +
83A PHE* 4.4 6.5 - - + -
135A MET 2.9 15.1 + - - +
136A VAL 3.2 8.3 + - - +
138A ASP* 1.3 76.8 - - - +
140A LYS* 1.3 61.9 + - - +
142A LEU 3.3 0.7 + - - -
143A LEU* 3.0 30.8 + - - +
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Residues in contact with LYS 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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33A TYR* 5.7 0.6 + - - -
83A PHE* 3.6 43.9 - - + +
84A ASP 5.2 2.2 + - - -
133A GLU* 5.1 6.3 + - - -
136A VAL* 2.9 33.0 + - + +
137A ARG* 3.3 10.5 + - - +
139A ALA* 1.3 75.9 - - - +
141A SER* 1.3 62.2 + - - +
143A LEU* 3.3 3.0 + - - +
144A ASP* 3.0 30.3 + - - +
150A TRP* 3.6 42.1 + - + +
152A GLN* 3.2 21.6 + - - +
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Residues in contact with SER 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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137A ARG* 3.0 20.7 + - - +
138A ASP* 3.5 12.3 + - - -
140A LYS* 1.3 75.8 - - - +
142A LEU* 1.3 62.6 + - - +
144A ASP* 3.4 12.2 + - - +
145A ALA* 3.0 22.7 + - - +
311A ILE* 3.7 17.3 - - - +
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Residues in contact with LEU 142 (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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62A LEU* 3.7 35.9 - - + +
65A LEU* 4.1 15.3 - - + -
66A PHE* 4.0 17.5 - - + +
138A ASP 2.8 16.0 + - - +
139A ALA* 3.6 5.8 - - - +
140A LYS 3.3 0.2 - - - -
141A SER* 1.3 77.6 - - - +
143A LEU* 1.3 57.3 + - - +
145A ALA* 3.1 4.5 + - - +
146A MET* 2.9 44.1 + - + +
308A VAL* 4.1 24.9 - - + -
311A ILE* 3.9 17.2 - - + +
312A LEU* 4.1 22.9 - - + -
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Residues in contact with LEU 143 (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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65A LEU* 3.9 22.7 - - + -
69A THR* 4.4 5.2 - - - +
81A TYR* 3.8 40.8 - - + -
83A PHE* 3.8 32.3 - - + -
139A ALA 3.0 21.6 + - - +
140A LYS 3.3 3.3 + - - +
142A LEU* 1.3 74.6 - - - +
144A ASP* 1.3 62.8 - - - +
146A MET* 3.0 12.2 + - - -
147A GLY 3.0 18.7 + - - -
148A ILE* 3.0 34.8 + - + +
150A TRP* 4.1 9.2 - - + -
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Residues in contact with ASP 144 (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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140A LYS* 3.0 19.2 + - - +
141A SER* 3.4 11.9 - - - +
143A LEU* 1.3 74.2 - - - +
145A ALA* 1.3 61.7 + - - +
147A GLY* 3.1 14.1 + - - -
148A ILE 4.7 3.1 - - - +
150A TRP* 2.9 33.5 + - - -
301A HIS* 6.0 0.2 - - - +
302A THR 5.5 0.9 - - - +
304A ASP* 5.5 0.9 - - - +
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Residues in contact with ALA 145 (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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141A SER 3.0 13.8 + - - +
142A LEU* 3.1 8.7 + - - +
144A ASP* 1.3 76.8 - - - +
146A MET* 1.3 56.0 + - - +
147A GLY 3.5 0.3 + - - -
302A THR 4.8 0.2 - - - +
304A ASP* 2.7 38.3 + - - +
307A ALA* 3.7 28.0 - - + -
308A VAL* 3.6 21.6 - - + +
311A ILE* 4.1 9.0 - - + -
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Residues in contact with MET 146 (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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65A LEU 4.5 2.9 - - - +
66A PHE* 3.7 44.9 - - + +
69A THR* 3.9 19.7 - - + -
70A ILE* 3.9 15.7 - - + -
142A LEU* 2.9 33.2 + - + +
143A LEU* 3.0 17.9 + - - +
145A ALA* 1.3 74.8 - - - +
147A GLY* 1.3 58.4 + - - +
148A ILE* 3.9 4.9 - - + -
303A PRO* 3.5 11.2 - - - +
308A VAL* 4.0 16.4 - - + -
330A TYR* 2.5 49.5 + - + +
334A PHE* 4.1 0.5 - - - -
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Residues in contact with GLY 147 (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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143A LEU 3.0 2.6 + - - -
144A ASP* 3.1 13.0 + - - -
145A ALA 3.3 1.2 + - - -
146A MET* 1.3 78.2 - - - +
148A ILE* 1.3 60.9 + - - +
149A PRO* 3.7 0.3 - - - +
299A GLU 4.5 0.4 - - - +
300A TRP* 3.5 12.0 - - - +
301A HIS* 3.0 52.9 + - - +
302A THR 4.4 2.9 - - - -
334A PHE* 4.1 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