Contacts of the helix formed by residues 139 - 152 (chain C) in PDB entry 4OE5
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 ARG 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C MET* 2.8 41.0 + - + +
135C LEU* 3.9 3.6 - - - -
138C PRO* 1.3 87.6 - - + +
140C ARG* 1.3 64.5 + - - +
141C ALA 3.4 2.7 - - - -
142C GLU* 2.8 38.5 + - - +
143C ILE* 3.1 23.6 + - - +
244C ALA 5.0 0.4 + - - -
247C ARG* 4.9 4.6 - - - +
248C ILE* 3.6 39.2 - - + +
251C GLU* 2.9 38.8 + - - -
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 2.9 31.5 + - - +
36C PRO 3.0 20.6 + - - -
38C LEU* 3.3 26.8 - - - +
40C PHE* 5.1 0.9 - - - -
46C GLU* 6.0 0.4 - - - -
135C LEU 3.1 19.6 + - - +
136C SER* 2.9 22.7 + - - +
137C GLY 3.3 14.5 + - - +
139C ARG* 1.3 73.8 - - - +
141C ALA* 1.3 67.8 + - - +
143C ILE* 3.2 7.4 + - + +
144C LEU* 3.0 41.4 + - + +
159C GLU* 2.5 40.2 + - - -
162C ALA* 5.6 2.7 - - + -
163C ALA* 4.2 6.6 - - - +
167C ILE* 4.3 6.3 - - + +
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ALA* 3.6 40.2 - - + +
50C LEU* 4.0 7.4 - - - +
53C ALA* 3.5 9.3 - - + +
137C GLY 4.8 0.8 + - - -
138C PRO 5.1 2.6 + - - +
139C ARG 3.4 0.4 - - - -
140C ARG* 1.3 78.9 - - - +
142C GLU* 1.3 58.4 + - - +
144C LEU* 3.8 8.2 - - - +
145C ALA* 2.9 32.1 + - - +
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ALA* 4.1 9.3 - - + +
138C PRO 5.5 0.8 + - - +
139C ARG* 2.8 51.5 + - - +
140C ARG 3.2 0.6 - - - -
141C ALA* 1.3 79.6 - - - +
143C ILE* 1.3 57.5 + - - +
145C ALA* 3.9 1.5 - - - +
146C LYS* 2.7 68.0 + - + +
244C ALA* 3.5 16.0 - - - +
248C ILE* 5.2 2.7 - - - -
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 4.0 21.1 - - + +
139C ARG 3.1 15.9 + - - +
140C ARG* 3.2 16.6 - - + +
142C GLU* 1.3 77.8 - - - +
144C LEU* 1.3 66.3 + - + +
146C LYS* 3.3 2.2 + - - -
147C THR* 3.1 35.5 + - + +
162C ALA* 4.4 21.1 - - + -
166C LEU* 4.0 17.7 - - + -
167C ILE* 6.1 0.4 - - + -
215C ILE* 4.1 3.4 - - + -
241C ALA* 3.7 25.6 - - + +
244C ALA* 4.2 10.3 - - + -
245C VAL* 3.6 28.0 - - + -
248C ILE* 5.8 0.9 - - + -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.4 36.1 - - + -
50C LEU* 3.8 15.7 - - + -
140C ARG* 3.0 31.9 + - + +
141C ALA* 3.8 5.6 - - - +
143C ILE* 1.3 76.9 - - - +
145C ALA* 1.3 57.6 + - - +
147C THR* 3.1 6.7 + - - +
148C MET* 2.9 35.7 + - - +
155C VAL 5.5 1.1 - - - +
158C ALA* 3.4 38.6 - - + +
159C GLU* 3.5 16.6 - - + +
162C ALA* 3.8 15.5 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.9 2.7 - - + +
53C ALA* 3.8 28.3 - - + +
54C LEU* 3.7 27.6 - - + +
57C LEU* 3.5 8.1 - - + -
141C ALA 2.9 18.8 + - - +
142C GLU* 3.9 2.5 - - - +
144C LEU* 1.3 77.4 - - - +
146C LYS* 1.3 57.4 + - - +
148C MET* 3.9 0.2 - - - +
149C VAL* 2.9 35.0 + - - +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 3.8 23.6 - - + -
62C GLU* 4.2 13.5 + - - -
81C GLN* 5.3 0.2 + - - -
142C GLU* 2.7 51.3 + - + +
143C ILE* 3.9 4.3 - - - +
144C LEU 3.2 0.2 - - - -
145C ALA* 1.3 78.1 - - - +
147C THR* 1.3 57.2 + - - +
150C GLY* 2.9 27.0 + - - -
151C GLN* 4.4 0.9 - - - +
240C LEU* 3.7 36.8 + - + +
241C ALA* 4.0 17.3 + - + +
244C ALA* 3.8 25.7 - - + +
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ILE* 3.1 18.1 + - + +
144C LEU* 3.1 12.6 + - - +
146C LYS* 1.3 74.0 - - - +
148C MET* 1.3 61.2 + - - +
151C GLN* 2.8 47.2 + - - +
152C GLY 3.3 1.7 + - - -
153C LYS* 3.5 24.4 + - - +
158C ALA* 3.2 20.4 + - - +
215C ILE* 4.2 13.5 - - + -
241C ALA* 3.6 19.7 - - + -
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Residues in contact with MET 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.9 25.6 - - + -
54C LEU* 4.1 25.6 - - + -
85C PHE* 3.3 9.5 - - + -
144C LEU* 2.9 22.4 + - - +
145C ALA 3.9 2.9 - - - +
147C THR* 1.3 76.5 + - - +
149C VAL* 1.3 57.9 + - + +
152C GLY* 2.9 28.9 + - - -
153C LYS 3.2 22.1 + - - +
154C THR* 3.9 2.0 - - - +
155C VAL* 3.7 34.1 - - + +
158C ALA* 3.7 14.6 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.7 23.3 - - + +
57C LEU* 4.1 23.6 - - + -
83C SER* 2.8 33.7 + - - +
84C PRO* 3.5 3.3 - - - +
85C PHE* 3.9 14.8 - - + -
89C HIS* 3.8 29.8 - - + +
91C VAL* 3.9 9.9 - - + -
145C ALA 2.9 20.5 + - - +
148C MET* 1.3 76.0 - - - +
150C GLY* 1.3 62.5 + - - +
240C LEU* 5.3 1.1 - - + -
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLN* 3.1 29.8 + - - +
82C VAL 3.8 4.7 - - - +
84C PRO* 3.3 14.3 - - - +
91C VAL* 4.4 12.6 - - - -
146C LYS* 2.9 19.8 + - - +
149C VAL* 1.3 79.7 - - - +
151C GLN* 1.3 57.2 + - - +
152C GLY 3.7 0.2 - - - -
237C THR* 3.5 4.9 - - - +
240C LEU* 4.7 1.9 - - - +
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLN* 5.2 0.5 + - - -
84C PRO* 3.6 12.2 - - - +
146C LYS 4.4 1.0 - - - +
147C THR* 2.8 24.8 + - - +
150C GLY* 1.3 73.6 - - - -
152C GLY* 1.3 62.3 + - - +
153C LYS* 3.3 20.7 - - + +
213C THR* 2.9 29.8 + - - +
214C ALA* 4.2 4.4 - - - +
215C ILE* 4.3 4.6 - - - +
237C THR 3.3 22.4 - - - +
238C ALA* 3.5 22.2 - - + +
241C ALA* 3.6 25.1 - - - +
343C TYR* 2.9 32.8 + - - +
346C GLN* 5.0 2.6 + - - -
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Residues in contact with GLY 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PRO* 3.7 14.8 - - - +
85C PHE* 4.1 15.2 - - - -
148C MET 2.9 14.7 + - - -
150C GLY 3.7 1.2 - - - -
151C GLN* 1.3 78.4 - - - +
153C LYS* 1.3 66.5 + - - +
154C THR* 3.6 3.3 + - - +
343C TYR* 4.2 7.8 - - - -
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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