Contacts of the helix formed by residues 134 - 149 (chain A) in PDB entry 4ORA
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 4.2 14.6 - - + -
102A GLY 3.1 19.7 + - - +
103A GLN* 5.1 2.5 - - - -
104A PHE* 3.5 15.9 - + + -
105A PHE* 3.9 23.3 - + - -
132A GLY* 5.7 0.2 - - - -
133A TYR* 1.3 93.4 - - + +
135A SER* 1.3 63.8 + - - +
137A GLU* 3.1 26.6 - - + +
138A CYS* 3.1 23.9 + - - -
174A GLU* 3.6 0.2 - - - -
178A LYS* 4.2 3.8 - - - -
348A HIS* 3.6 29.2 - + + -
349A PRO* 3.6 29.4 - - + -
351A TRP* 3.9 23.6 - + - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY* 3.5 12.6 - - - -
128A TYR 4.2 1.6 - - - -
129A VAL* 3.4 11.2 - - - +
130A ASP* 3.1 21.8 + - - -
132A GLY 3.2 14.4 + - - -
134A PHE* 1.3 75.6 - - - +
136A ILE* 1.3 62.0 + - - +
138A CYS* 3.0 5.9 + - - +
139A VAL* 2.9 29.5 + - - +
171A PHE* 3.4 21.7 - - - +
174A GLU* 3.0 16.4 + - - -
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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
----------------------------------------------------------
70A ALA* 6.2 0.2 - - + -
74A ILE* 4.5 2.2 - - + -
135A SER* 1.3 77.3 - - - +
137A GLU* 1.3 70.8 + - + +
139A VAL* 3.4 6.2 + - + -
140A LEU* 2.9 41.2 + - + +
171A PHE* 3.8 16.5 - - + -
174A GLU* 2.9 23.7 + - + +
175A CYS* 4.5 6.1 - - - -
178A LYS* 3.7 18.8 - - + -
179A TYR* 4.0 30.1 - - + -
183A VAL* 4.2 22.2 - - + -
187A CYS* 4.3 16.2 - - - -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.7 34.6 - - + +
62A GLU* 5.6 5.1 - - - +
63A GLY 4.8 6.6 - - - +
104A PHE* 3.7 25.2 - - + -
134A PHE* 3.1 35.1 - - + +
135A SER 3.1 0.2 - - - -
136A ILE* 1.3 77.4 - - + +
138A CYS* 1.3 60.3 + - - +
140A LEU* 3.8 5.9 - - + +
141A TYR* 2.9 33.3 + - - +
178A LYS* 2.9 29.9 + - - +
179A TYR* 5.6 3.8 + - - +
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Residues in contact with CYS 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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100A ILE* 3.8 17.9 - - + -
102A GLY* 3.7 14.4 - - - -
104A PHE* 3.6 35.2 - - - -
107A LEU* 4.3 11.0 - - + -
128A TYR* 4.0 15.3 - - + +
134A PHE 3.1 18.2 + - - -
135A SER 3.0 8.0 + - - +
137A GLU* 1.3 73.4 - - - +
139A VAL* 1.3 61.0 + - - +
141A TYR* 3.9 0.3 - - - +
142A LEU* 2.8 38.2 + - + +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.4 12.6 - - + -
128A TYR* 4.6 8.3 - - + -
129A VAL* 3.6 31.2 - - + -
135A SER 2.9 12.1 + - - +
136A ILE* 3.8 11.9 - - + +
138A CYS* 1.3 77.1 - - - +
140A LEU* 1.3 63.2 + - - +
142A LEU* 4.7 0.9 - - - -
143A TRP* 2.8 58.3 + - + +
171A PHE* 4.6 5.2 - - + -
187A CYS* 4.3 20.0 - - - -
191A PHE* 4.1 14.4 - - + -
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Residues in contact with LEU 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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55A LEU* 4.4 7.9 - - + -
59A LEU* 4.8 11.9 - - + -
65A VAL* 4.6 15.0 - - + -
70A ALA* 4.0 27.4 - - + +
73A ILE* 3.8 29.2 - - + +
74A ILE* 4.2 11.2 - - + -
136A ILE* 2.9 32.3 + - + +
137A GLU* 3.8 6.7 - - - +
139A VAL* 1.3 75.6 - - - +
141A TYR* 1.3 63.2 + - - +
144A VAL* 3.1 28.2 + - - +
179A TYR* 3.9 29.2 - - + +
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Residues in contact with TYR 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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52A VAL* 3.5 32.1 - - + +
53A ASP* 5.1 2.9 + - - -
55A LEU* 4.2 16.3 - - + +
56A LYS* 3.7 38.9 - - + +
59A LEU* 4.3 4.5 - - + +
104A PHE* 3.8 12.8 - + + -
107A LEU* 4.2 4.5 - - + -
108A MET* 3.6 26.8 - - + +
111A PHE* 3.8 20.0 - + - +
117A PRO* 5.4 4.2 - - - +
137A GLU 2.9 18.1 + - - +
138A CYS* 4.0 2.5 - - - +
140A LEU* 1.3 76.3 - - - +
142A LEU* 1.3 63.5 + - - +
144A VAL* 3.3 4.2 + - - +
145A LEU* 3.1 46.6 + - + +
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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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100A ILE* 5.3 2.9 - - + -
107A LEU* 4.1 18.2 - - + -
111A PHE* 3.9 28.5 - - + -
124A PHE* 4.1 22.9 - - + -
128A TYR* 3.5 40.4 - - + -
138A CYS* 2.8 28.8 + - + +
139A VAL 4.0 2.0 - - - +
141A TYR* 1.3 73.6 - - - +
143A TRP* 1.3 66.9 + - + +
145A LEU* 3.3 9.6 + - + +
146A LYS* 3.0 26.5 + - - +
153A LEU* 3.9 6.3 - - + +
155A LEU* 4.2 10.9 - - + +
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Residues in contact with TRP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.8 15.9 - - + +
74A ILE* 3.5 28.5 + - - +
77A GLY* 3.4 25.5 - - - -
78A ALA 3.9 5.1 - - - +
81A LEU* 4.0 18.8 - - + +
128A TYR* 4.4 18.4 - + - -
139A VAL* 2.8 55.8 + - + +
140A LEU* 4.7 0.2 - - - -
142A LEU* 1.3 79.6 - - + +
144A VAL* 1.3 59.9 + - - +
146A LYS* 3.3 6.6 + - + +
147A ILE* 3.0 34.1 + - - +
155A LEU* 4.0 15.5 - - + -
190A ALA* 3.7 18.4 - - + +
191A PHE* 3.8 31.4 - + - -
194A LEU* 4.2 15.5 - - + -
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Residues in contact with VAL 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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43A VAL* 6.0 0.9 - - + -
50A PRO* 4.0 26.5 - - + -
52A VAL* 3.7 34.5 - - + -
55A LEU* 3.6 19.5 - - + -
73A ILE* 3.9 26.5 - - + -
140A LEU 3.1 21.3 + - - +
141A TYR 3.6 4.5 - - - +
142A LEU 3.3 0.2 - - - -
143A TRP* 1.3 76.6 - - - +
145A LEU* 1.3 63.5 + - - +
147A ILE* 3.1 9.4 + - - +
148A LEU* 2.9 25.1 + - + +
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Residues in contact with LEU 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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52A VAL* 3.6 26.5 - - + -
111A PHE* 3.5 33.4 - - + -
117A PRO* 3.9 26.2 - - + -
141A TYR* 3.1 31.9 + - + +
142A LEU* 3.3 11.4 + - + +
144A VAL* 1.3 76.5 - - - +
146A LYS* 1.3 52.0 + - - +
148A LEU* 3.1 1.9 + - + +
149A TYR* 2.7 53.1 + - + +
153A LEU* 4.0 17.9 - - + -
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Residues in contact with LYS 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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77A GLY* 5.1 4.7 - - - +
80A ILE* 4.0 25.4 - - + +
81A LEU* 4.1 16.4 - - + +
84A GLU* 2.9 37.8 + - - -
142A LEU 3.0 13.3 + - - +
143A TRP* 3.5 12.1 - - + +
144A VAL 3.2 0.2 - - - -
145A LEU* 1.3 75.7 - - - +
147A ILE* 1.3 58.2 + - + +
149A TYR 4.7 1.1 - - - -
150A PRO* 3.0 50.8 + - + +
153A LEU* 2.9 37.5 + - + +
154A PHE* 3.5 10.5 - - - +
155A LEU* 4.1 20.4 - - + +
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Residues in contact with ILE 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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44A PHE* 5.9 1.3 - - + -
49A ILE* 5.7 6.9 - - + +
50A PRO* 4.0 30.7 - - + -
73A ILE* 3.8 30.3 - - + +
76A GLU* 3.8 42.6 - - + +
77A GLY* 4.1 7.4 - - - +
80A ILE* 3.9 12.7 - - + +
143A TRP 3.0 18.8 + - - +
144A VAL* 3.1 12.1 + - - +
146A LYS* 1.3 75.0 - - - +
148A LEU* 1.3 60.3 + - + +
150A PRO* 3.7 8.3 - - - +
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Residues in contact with LEU 148 (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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49A ILE* 3.5 31.6 - - + -
50A PRO* 3.9 17.3 - - + +
52A VAL* 3.7 36.6 - - + -
144A VAL* 2.9 22.3 + - + +
145A LEU* 3.1 0.6 + - + -
147A ILE* 1.3 78.0 - - + +
149A TYR* 1.3 97.1 + - + +
150A PRO* 3.5 5.2 - - - +
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Residues in contact with TYR 149 (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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52A VAL* 5.2 5.2 - - + +
117A PRO* 3.8 33.7 - - + +
118A ALA* 3.4 36.0 + - + +
145A LEU* 2.7 36.4 + - + +
146A LYS 3.4 2.5 - - - -
148A LEU* 1.3 109.2 - - + +
150A PRO* 1.3 65.8 - - - +
151A SER 3.0 3.8 + - - -
152A THR* 3.0 18.6 + - - +
153A LEU* 2.9 27.5 + - + +
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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
------------------------------------------------------------
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