Contacts of the strand formed by residues 141 - 147 (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 SER 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.8 3.1 - - - +
140D HIS* 1.3 76.5 - - - +
142D ILE* 1.3 62.0 + - - +
143D ASP* 4.3 2.0 - - - -
154D VAL 4.5 0.7 - - - -
155D LEU* 3.3 6.9 - - - +
156D PHE* 3.0 41.2 + - - +
207D HIS* 2.4 39.1 + - - -
209D SER* 3.8 23.6 - - - -
218D ILE* 5.2 1.9 - - - +
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Residues in contact with ILE 142 (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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76D ALA* 3.7 36.1 - - + +
77D THR 3.5 12.9 + - - +
78D CYS* 3.2 17.9 - - - +
92D ILE* 4.0 22.9 - - + -
94D HIS* 4.4 14.1 - - + -
107D ILE* 4.7 1.3 - - + -
141D SER* 1.3 76.5 - - - +
143D ASP* 1.3 77.6 + - - +
154D VAL 3.2 16.2 - - - +
155D LEU* 3.8 17.5 - - + -
185D ILE* 4.5 7.0 - - + -
187D PHE* 4.1 17.7 - - + -
209D SER* 4.8 1.2 + - - -
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Residues in contact with ASP 143 (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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77D THR 5.3 0.7 - - - +
78D CYS* 4.0 11.7 - - - +
141D SER* 4.3 1.9 - - - -
142D ILE* 1.3 85.0 + - - +
144D VAL* 1.3 65.0 + - - +
145D VAL 4.2 0.2 - - - -
153D GLY* 3.3 5.4 - - - -
154D VAL* 2.8 33.9 + - - +
187D PHE* 5.1 0.2 - - - -
209D SER* 3.1 40.3 + - - +
211D ALA* 3.6 27.9 + - + +
216D VAL* 4.1 14.6 - - + +
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Residues in contact with VAL 144 (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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78D CYS* 4.0 15.8 - - - +
79D SER 4.3 8.7 + - - +
80D TYR* 4.0 25.1 - - + -
143D ASP* 1.3 79.1 - - - +
145D VAL* 1.3 69.3 + - - +
146D TYR* 3.6 41.6 - - + +
151D SER* 4.4 4.5 - - - -
152D MET 3.5 10.1 - - - +
187D PHE* 3.8 26.5 - - + -
211D ALA* 3.9 14.3 - - - +
213D ASN 4.6 1.4 + - - +
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Residues in contact with VAL 145 (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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143D ASP 4.2 0.4 + - - -
144D VAL* 1.3 76.0 - - - +
146D TYR* 1.3 65.2 + - - +
147D SER 4.3 0.2 - - - -
150D LYS 3.9 0.3 - - - +
151D SER* 3.5 3.6 - - - -
152D MET* 2.8 50.6 + - + +
154D VAL* 3.8 23.3 - - + -
184D LEU* 5.5 0.2 - - + -
211D ALA* 5.1 0.2 - - + -
213D ASN 3.4 12.8 - - - +
214D ASP* 4.2 13.7 - - - +
215D THR 4.2 5.8 - - - +
216D VAL* 3.5 33.4 - - + -
238D VAL* 4.2 18.8 - - + +
240D LEU* 4.7 4.4 - - + +
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Residues in contact with TYR 146 (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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79D SER 5.2 0.9 + - - -
80D TYR* 3.9 6.4 - + - -
81D LYS* 3.7 32.6 + - + +
144D VAL* 3.6 32.6 - - + +
145D VAL* 1.3 75.3 - - - +
147D SER* 1.3 60.3 + - - +
149D GLY* 5.5 2.5 - - - +
150D LYS 3.2 8.7 - - - +
151D SER* 3.9 26.5 - - - -
213D ASN* 3.0 22.0 + - - +
214D ASP* 3.4 23.4 + - - +
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Residues in contact with SER 147 (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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145D VAL* 6.0 0.9 - - - -
146D TYR* 1.3 74.6 - - - +
148D ARG* 1.3 81.0 + - - +
149D GLY 3.2 2.0 - - - -
150D LYS* 2.9 25.3 + - - +
214D ASP* 4.2 5.5 + - - +
238D VAL 3.5 19.7 + - - -
239D ASP* 3.4 8.0 - - - +
240D LEU* 3.0 36.5 + - - +
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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