Contacts of the strand formed by residues 150 - 156 (chain B) in PDB entry 6CIM
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 LYS 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B VAL 3.7 0.5 - - - +
146B TYR* 3.1 10.3 - - - +
147B SER 2.9 33.1 + - - +
148B ARG* 3.2 13.0 - - - +
149B GLY* 1.3 80.7 - - - +
151B SER* 1.3 59.7 + - - +
152B MET* 5.9 1.6 - - + -
240B LEU* 3.6 32.3 - - + +
242B LEU* 2.6 52.7 + - - +
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Residues in contact with SER 151 (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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80B TYR* 3.0 31.4 + - - -
144B VAL* 4.4 2.2 - - - -
145B VAL 3.4 4.7 - - - -
146B TYR* 3.8 24.7 - - - -
150B LYS* 1.3 73.8 - - - +
152B MET* 1.3 71.2 + - - +
186B ASP* 4.3 9.5 + - - +
187B PHE* 6.4 0.7 - - - -
240B LEU* 4.5 0.7 - - - -
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Residues in contact with MET 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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144B VAL* 3.5 5.9 - - - +
145B VAL* 2.9 44.2 + - + +
150B LYS* 5.9 1.6 - - + -
151B SER* 1.3 79.6 - - - +
153B GLY* 1.3 68.7 + - - +
184B LEU* 3.9 24.2 - - + -
185B ILE 3.6 25.8 - - - +
186B ASP* 3.7 20.6 - - + -
187B PHE* 5.1 2.9 - - - -
240B LEU* 3.8 38.6 - - + -
245B PRO* 5.7 4.5 - - + -
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Residues in contact with GLY 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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142B ILE* 5.1 2.5 - - - -
143B ASP 3.4 9.2 - - - -
144B VAL* 4.5 0.4 - - - -
152B MET* 1.3 72.7 - - - +
154B VAL* 1.3 61.3 + - - -
183B PHE 3.1 0.7 - - - +
184B LEU* 3.1 10.0 - - - +
185B ILE* 2.8 46.9 + - - -
187B PHE* 4.2 21.0 - - - -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 3.9 0.7 - - - +
142B ILE* 3.1 5.4 - - - +
143B ASP* 2.9 35.5 + - - +
145B VAL* 4.0 29.2 - - + -
153B GLY* 1.3 75.4 - - - -
155B LEU* 1.3 64.4 + - - +
156B PHE* 5.3 3.6 - - + -
182B VAL* 3.7 22.7 - - + -
183B PHE 3.3 2.9 - - - -
184B LEU* 3.6 20.0 - - + -
216B VAL* 3.8 30.1 - - + -
236B ILE* 4.9 2.5 - - + -
238B VAL* 4.4 7.9 - - + -
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Residues in contact with LEU 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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94B HIS* 3.3 41.1 - - + +
134B PRO* 4.0 22.9 - - + -
137B ARG* 4.1 17.7 - - - +
140B HIS* 3.8 12.6 - - + -
141B SER 3.1 11.7 - - - +
142B ILE* 3.9 13.0 - - + -
154B VAL* 1.3 76.1 - - - +
156B PHE* 1.3 66.5 + - - +
181B HIS 3.8 1.0 - - - +
182B VAL* 3.7 2.4 - - - -
183B PHE* 2.9 38.9 + - + +
185B ILE* 3.9 25.8 - - + -
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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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137B ARG* 4.5 0.7 - - - -
140B HIS* 4.1 1.3 - - - -
141B SER* 2.9 45.1 + - - +
154B VAL* 5.3 3.8 - - + -
155B LEU* 1.3 79.8 - - - +
157B GLY* 1.3 70.0 + - - +
180B PRO* 3.5 39.3 - - + -
181B HIS 4.2 16.2 - - - -
182B VAL* 4.6 9.4 - - + -
200B LEU* 3.9 30.7 - - + -
202B ASP 4.8 1.8 - - - -
204B LEU* 4.1 29.4 - - + -
207B HIS* 3.4 18.0 + + - -
218B ILE* 4.2 30.1 - - + -
236B ILE* 5.4 3.1 - - + -
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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