Contacts of the strand formed by residues 141 - 147 (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 SER 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ALA* 4.2 2.0 - - - +
77B THR 5.9 0.4 - - - +
140B HIS* 1.3 74.5 - - - +
142B ILE* 1.3 61.6 + - - +
143B ASP* 4.2 1.1 - - - -
154B VAL 4.3 0.4 - - - -
155B LEU* 3.1 7.5 - - - +
156B PHE* 2.9 39.4 + - - +
207B HIS* 2.5 34.2 + - - -
209B SER* 3.5 27.8 - - - -
218B ILE* 4.0 8.5 - - - +
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Residues in contact with ILE 142 (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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76B ALA* 4.0 20.5 - - + +
77B THR* 3.3 19.8 + - - +
78B CYS* 2.9 35.5 - - + +
92B ILE* 4.0 22.9 - - + +
94B HIS* 4.5 8.1 - - + -
107B ILE* 5.1 1.1 - - + -
141B SER* 1.3 75.0 - - - +
143B ASP* 1.3 75.8 + - - +
153B GLY* 5.1 0.9 - - - -
154B VAL 3.1 15.3 - - - +
155B LEU* 3.9 23.3 - - + -
185B ILE* 4.4 9.6 - - + -
187B PHE* 4.4 15.7 - - + -
209B SER* 4.6 0.5 + - - -
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Residues in contact with ASP 143 (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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78B CYS* 3.8 11.8 - - - +
141B SER* 4.2 1.0 - - - -
142B ILE* 1.3 84.5 + - - +
144B VAL* 1.3 64.7 + - - +
153B GLY* 3.4 4.5 - - - -
154B VAL* 2.9 33.2 + - - +
187B PHE* 5.7 0.2 - - - -
209B SER* 2.6 45.3 + - - +
211B ALA* 3.6 26.0 + - + +
216B VAL* 3.8 14.7 - - + +
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Residues in contact with VAL 144 (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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78B CYS* 4.1 18.5 - - - +
79B SER 4.1 15.4 + - - +
80B TYR* 4.2 16.2 - - + -
92B ILE* 4.3 1.3 - - + -
143B ASP* 1.3 78.4 - - - +
145B VAL* 1.3 69.6 + - - +
146B TYR* 3.7 40.4 - - + +
151B SER* 4.4 9.4 - - - -
152B MET 3.5 8.5 - - - +
187B PHE* 4.2 19.1 - - + -
211B ALA* 3.7 18.4 - - - +
213B ASN 4.6 1.0 - - - +
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Residues in contact with VAL 145 (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* 1.3 78.8 - - - +
146B TYR* 1.3 64.4 + - - +
147B SER* 5.7 0.2 - - - -
150B LYS 3.7 0.5 - - - +
151B SER* 3.4 4.5 - - - -
152B MET* 2.9 53.7 + - + +
154B VAL* 4.0 19.5 - - + -
213B ASN 3.3 12.6 - - - +
214B ASP* 4.0 20.6 - - - +
215B THR 4.0 4.0 - - - +
216B VAL* 3.7 27.8 - - + +
236B ILE 5.6 0.4 - - - +
238B VAL* 4.1 19.3 - - + -
240B LEU* 5.2 1.3 - - + +
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Residues in contact with TYR 146 (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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79B SER 5.4 0.3 + - - -
80B TYR* 3.8 5.6 - + - -
81B LYS* 3.6 36.0 + - + +
144B VAL* 3.7 30.1 - - + +
145B VAL* 1.3 74.3 - - - +
147B SER* 1.3 59.3 + - - +
149B GLY* 5.5 2.2 - - - +
150B LYS 3.1 10.1 - - - +
151B SER* 3.8 25.6 - - - -
213B ASN* 2.8 23.5 + - - +
214B ASP* 3.3 21.9 + - - +
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Residues in contact with SER 147 (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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145B VAL* 4.2 1.3 + - - -
146B TYR* 1.3 75.8 - - - +
148B ARG* 1.3 72.1 + - - +
149B GLY 3.3 1.1 - - - -
150B LYS* 2.9 26.3 + - - +
214B ASP* 3.9 7.3 + - - +
238B VAL* 3.4 20.7 + - - -
239B ASP* 3.0 28.8 + - - -
240B LEU* 3.0 22.1 + - - +
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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