Contacts of the strand formed by residues 150 - 156 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D TYR* 3.2 7.5 - - - -
147D SER 2.9 33.3 + - - +
148D ARG 3.2 7.4 - - - +
149D GLY* 1.3 82.1 - - - +
151D SER* 1.3 61.4 + - - +
152D MET* 5.7 4.0 - - + -
240D LEU* 3.3 30.0 - - + +
241D PRO 3.8 16.4 + - - +
242D LEU* 4.1 16.1 + - - +
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D TYR* 2.6 33.2 + - - -
144D VAL* 4.4 1.6 - - - -
145D VAL 3.5 4.7 - - - -
146D TYR* 3.9 25.1 - - - -
150D LYS* 1.3 74.9 - - - +
152D MET* 1.3 72.8 + - - +
186D ASP* 4.3 8.8 - - - +
240D LEU* 4.2 0.4 - - - -
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Residues in contact with MET 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D VAL* 3.5 5.9 - - - +
145D VAL* 2.8 41.9 + - + +
150D LYS* 5.7 4.9 - - + -
151D SER* 1.3 81.5 - - - +
153D GLY* 1.3 63.5 + - - +
184D LEU* 3.9 30.5 - - + -
185D ILE 3.8 23.6 - - - +
186D ASP* 4.0 19.3 - - + +
187D PHE* 5.3 1.6 - - - -
191D CYS* 6.1 0.2 - - - -
240D LEU* 3.8 37.7 - - + -
245D PRO* 5.6 1.3 - - + -
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ILE* 5.1 1.6 - - - -
143D ASP 3.3 10.1 - - - -
144D VAL* 4.4 0.2 - - - -
152D MET* 1.3 73.6 - - - +
154D VAL* 1.3 61.1 + - - -
183D PHE 3.3 0.9 - - - +
184D LEU* 3.2 9.4 - - - +
185D ILE* 2.9 41.9 + - - -
187D PHE* 3.9 21.9 - - - -
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D SER 4.1 0.3 - - - +
142D ILE* 3.2 4.4 - - - +
143D ASP* 2.8 35.7 + - - +
145D VAL* 3.8 30.3 - - + -
152D MET 4.0 0.2 + - - -
153D GLY* 1.3 73.2 - - - -
155D LEU* 1.3 65.5 + - - +
156D PHE* 5.3 3.4 - - + -
182D VAL* 3.8 22.4 - - + -
183D PHE 3.4 2.7 - - - -
184D LEU* 3.6 22.2 - - + -
216D VAL* 4.0 30.5 - - + -
236D ILE* 5.0 5.4 - - + -
238D VAL* 5.0 4.9 - - + -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D HIS* 3.6 39.7 - - + +
134D PRO* 4.1 7.6 - - + -
137D ARG* 3.8 22.7 - - - +
140D HIS* 3.9 11.0 - - + -
141D SER 3.3 10.3 - - - +
142D ILE* 3.8 13.9 - - + -
154D VAL* 1.3 76.7 - - - +
156D PHE* 1.3 67.0 + - - +
181D HIS 3.8 0.5 - - - +
182D VAL* 3.7 2.6 - - - +
183D PHE* 2.9 54.2 + - + +
185D ILE* 3.9 22.7 - - + -
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ARG* 4.6 1.1 - - - -
140D HIS* 3.7 1.1 - - - +
141D SER* 3.0 42.0 + - - +
154D VAL* 5.3 4.0 - - + -
155D LEU* 1.3 78.4 - - - +
157D GLY* 1.3 69.4 + - - +
180D PRO* 3.7 36.3 - - + -
181D HIS 3.8 19.1 - - - +
182D VAL* 4.5 9.2 - - + -
200D LEU* 3.9 27.8 - - + -
202D ASP 4.9 2.2 - - - -
204D LEU* 4.1 34.5 - - + -
207D HIS* 3.5 15.9 - + - -
218D ILE* 3.4 32.1 - - + -
236D ILE* 5.5 0.9 - - + -
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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