Contacts of the helix formed by residues 148 - 158 (chain H) in PDB entry 5A31
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 LEU 148 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F ALA* 5.6 3.8 - - + +
15F ALA* 4.9 4.9 - - + -
23F ASP* 3.6 27.4 - - + +
27F LEU* 5.0 5.2 - - + -
115H CYS* 4.0 21.1 - - + +
116H PHE* 3.8 40.2 - - + +
119H SER* 5.4 2.5 - - - -
141H SER* 5.5 3.8 - - - +
142H LEU* 4.1 6.6 - - + +
145H ASN* 5.1 4.7 - - + +
146H PRO* 2.7 25.5 + - + +
147H PHE* 1.3 78.4 - - + +
149H TRP* 1.3 65.4 + - - +
151H PRO* 3.3 32.2 - - + +
152H PHE* 3.9 5.9 + - - +
167H THR* 5.5 2.8 - - - +
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Residues in contact with TRP 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ARG 5.8 0.4 - - - -
23F ASP* 3.2 6.2 + - - +
26F PHE* 3.2 68.9 - + + -
147H PHE 3.7 3.6 + - - +
148H LEU* 1.3 73.5 - - - +
150H SER* 1.3 54.7 + - - +
152H PHE* 3.2 25.9 + + + +
153H GLU* 2.8 73.7 + - + +
167H THR* 4.6 13.7 - - + -
466H LEU* 4.4 14.1 - - + -
469H MET* 4.6 3.4 - - + -
470H GLY* 3.8 31.4 - - - -
473H TYR* 4.0 17.3 - + + -
500H TRP* 3.8 23.9 - + - -
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Residues in contact with SER 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ALA* 5.6 0.5 - - - +
22F ARG* 3.8 35.9 + - - +
23F ASP* 2.5 43.9 + - - +
119H SER* 4.4 6.3 + - - -
138H TYR* 5.6 0.2 - - - -
149H TRP* 1.3 71.3 - - - +
151H PRO* 1.4 55.5 - - - +
153H GLU* 3.8 9.2 - - - +
154H SER* 2.3 35.2 + - - -
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Residues in contact with PRO 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ASP* 3.3 8.5 - - - +
119H SER* 4.2 11.4 - - - +
138H TYR* 3.8 24.7 - - + +
141H SER* 4.2 16.6 - - - -
142H LEU* 3.4 19.1 - - + -
148H LEU* 3.3 31.6 - - + +
150H SER* 1.4 97.9 - - - +
152H PHE* 1.3 55.1 - - - +
154H SER* 2.9 6.7 + - - +
155H LEU* 2.9 30.4 + - - +
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Residues in contact with PHE 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H LEU* 3.6 29.5 - - + +
148H LEU 4.2 6.1 - - - +
149H TRP* 3.2 35.8 + + + +
151H PRO* 1.3 79.6 - - - +
153H GLU* 1.3 71.8 + - - +
155H LEU* 3.1 7.4 + - - +
156H CYS* 2.9 37.4 + - + +
162H PRO* 4.0 22.6 - - + +
163H ASP 4.1 16.4 - - - -
164H PRO* 4.7 5.8 - - + -
167H THR* 3.9 18.4 - - + -
470H GLY* 4.1 23.6 - - - -
473H TYR* 4.8 4.9 - + - -
474H LEU* 4.4 11.0 - - + -
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Residues in contact with GLU 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ARG* 3.0 43.0 + - - +
149H TRP* 2.8 53.8 + - + +
150H SER* 3.8 7.5 - - - +
152H PHE* 1.3 74.9 - - - +
154H SER* 1.3 62.1 + - - +
156H CYS* 2.9 24.7 - - - -
157H GLU* 3.0 17.7 + - - +
473H TYR* 3.7 32.8 + - + +
500H TRP* 3.9 11.3 + - - -
504H GLN* 4.9 0.7 + - - -
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Residues in contact with SER 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ARG* 5.2 3.3 - - - +
138H TYR* 3.6 28.0 - - - -
150H SER 2.3 31.7 + - - -
151H PRO* 2.9 12.8 + - - +
153H GLU* 1.3 75.1 - - - +
155H LEU* 1.3 61.5 + - - +
157H GLU* 3.2 20.5 + - - +
158H ILE* 3.2 20.9 + - - +
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H SER* 3.8 26.2 - - - +
138H TYR* 4.3 8.2 - - + -
139H GLN* 3.8 36.3 - - + +
142H LEU* 4.7 7.6 - - + -
151H PRO 2.9 18.3 + - - +
152H PHE 3.3 5.8 - - - +
154H SER* 1.3 77.5 - - - +
156H CYS* 1.3 59.6 + - - +
158H ILE* 3.5 17.5 + - + +
160H GLU* 2.9 35.7 - - + +
162H PRO* 3.7 30.7 - - + -
166H GLN* 4.4 4.7 - - - +
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Residues in contact with CYS 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H PHE* 2.9 27.1 + - + +
153H GLU* 2.9 26.2 - - - -
155H LEU* 1.3 78.6 - - - +
157H GLU* 1.3 56.7 + - - +
158H ILE 2.8 14.2 - - - +
160H GLU 3.5 9.4 - - - +
161H LYS* 5.5 1.7 - - - +
162H PRO* 4.1 15.7 - - + -
473H TYR* 3.4 35.9 - - - -
474H LEU* 4.7 10.8 - - + +
477H CYS* 3.6 16.1 - - + +
633H ARG* 3.8 5.5 + - - -
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Residues in contact with GLU 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ARG* 4.5 15.2 + - - -
153H GLU* 3.0 31.7 + - - +
154H SER* 3.2 14.8 + - - +
156H CYS* 1.3 71.7 - - - +
158H ILE* 1.3 66.8 + - - +
473H TYR* 2.6 25.5 + - - +
477H CYS* 3.5 22.1 - - - -
507H ARG* 5.4 1.0 + - - -
631H ASN* 4.9 11.9 + - - +
633H ARG* 4.0 21.5 + - - +
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Residues in contact with ILE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H CYS* 3.8 30.1 - - + -
131H LEU* 4.5 34.8 - - + +
135H SER* 4.4 16.4 - - - +
138H TYR* 4.3 14.6 - - + -
154H SER* 3.2 17.6 + - - +
155H LEU* 3.6 11.2 - - - +
156H CYS 2.8 18.8 - - - +
157H GLU* 1.3 78.0 - - - +
159H GLY* 1.3 72.9 + - - +
160H GLU* 3.0 12.7 + - + +
632H PRO* 6.1 4.7 - - + -
633H ARG* 3.6 4.7 + - - -
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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