Contacts of the helix formed by residues 151 - 158 (chain B) in PDB entry 5XFR
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 CYS 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B CYS* 3.5 5.9 - - - -
125B CYS* 4.1 1.8 - - - -
129B TYR* 3.5 39.5 - - + -
134B HIS* 3.5 9.4 - - - +
149B TRP* 3.6 12.4 - - + -
150B LEU* 1.3 74.0 - - - +
152B ARG* 1.3 56.0 + - - +
153B GLN* 3.9 7.0 - - - -
154B CYS* 3.2 13.9 + - - -
155B VAL* 2.8 36.6 + - - +
178B MET* 4.4 0.2 - - - -
401B ZN 2.5 33.6 - - - -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 3.0 21.5 + - + +
135B THR* 3.0 35.5 + - - +
136B PRO* 3.9 0.2 - - - +
151B CYS* 1.3 72.1 - - - +
153B GLN* 1.3 60.6 + - + +
155B VAL* 3.1 1.9 + - - +
156B PHE* 2.8 60.6 + - + -
178B MET* 2.8 43.2 + - - +
181B THR 2.9 23.1 + - - -
183B PRO* 3.5 20.0 - - - +
205B TYR* 3.0 28.7 + - - +
206B CYS* 5.6 1.4 + - - +
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Residues in contact with GLN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.7 14.0 - - - +
61B PHE* 3.6 31.6 - - + -
91B LYS 5.7 2.2 + - - -
94B GLN* 3.4 42.2 + - - +
129B TYR* 5.5 3.8 + - - +
151B CYS* 3.4 7.8 - - - -
152B ARG* 1.3 80.8 - - + +
154B CYS* 1.3 59.6 + - - +
156B PHE* 4.1 8.7 - - + +
157B ALA* 3.2 22.7 + - - +
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Residues in contact with CYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B CYS* 4.0 2.7 - - - -
124B LYS* 4.2 13.7 - - + -
125B CYS* 3.5 21.5 - - - -
150B LEU* 3.9 17.4 - - + +
151B CYS* 3.2 8.7 + - - +
152B ARG 3.1 0.6 - - - -
153B GLN* 1.3 80.8 - - - +
155B VAL* 1.3 60.7 + - - +
156B PHE 3.3 0.2 - - - -
157B ALA* 3.8 4.7 - - - +
158B THR* 3.0 33.8 + - - +
401B ZN 2.4 35.0 - - - -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 3.7 26.0 - - + +
151B CYS 2.8 20.4 + - - +
152B ARG 3.4 4.9 - - - +
154B CYS* 1.3 77.8 - - - +
156B PHE* 1.3 54.5 + - + +
158B THR* 3.4 5.1 + - - -
159B THR* 2.4 37.0 + - - +
171B ASN* 3.9 7.0 - - - +
174B ALA* 3.7 21.5 - - + +
175B LEU* 3.4 43.3 - - + +
178B MET* 3.9 12.3 - - + -
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 6.1 4.9 - - + -
152B ARG* 2.8 66.6 + - + +
153B GLN* 4.5 8.7 - - + +
155B VAL* 1.3 80.5 - - + +
157B ALA* 1.3 53.5 + - - +
159B THR* 3.5 4.7 - - - -
160B THR* 2.5 60.2 + - + +
175B LEU* 3.7 24.5 - - + -
178B MET* 4.9 5.8 - - + -
179B LYS* 4.2 4.5 - - + -
205B TYR* 4.0 18.6 - - + -
206B CYS* 3.9 30.7 - - + -
230B CYS* 4.5 8.1 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 5.7 10.5 - - + -
124B LYS* 6.3 0.9 - - - -
153B GLN 3.2 20.5 + - - +
154B CYS* 3.9 7.2 - - - +
155B VAL 3.3 0.6 - - - -
156B PHE* 1.3 80.2 - - - +
158B THR* 1.3 63.8 + - + +
159B THR 3.3 1.1 + - - -
160B THR* 4.2 10.6 + - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 3.2 39.0 - - + +
150B LEU* 5.5 3.1 - - + +
154B CYS 3.0 19.2 + - - +
155B VAL* 3.4 7.4 + - - -
157B ALA* 1.3 80.2 - - + +
159B THR* 1.3 57.8 + - - +
160B THR 5.2 0.2 - - - -
166B LEU* 3.3 19.1 - - - +
171B ASN* 3.5 31.7 + - - +
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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