Contacts of the strand formed by residues 152 - 159 (chain D) in PDB entry 6H25
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 PHE 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D THR* 4.1 14.6 - - + -
102D CYS* 4.2 19.7 - - - -
105D VAL* 3.6 29.6 - - + -
106D VAL* 6.2 0.2 - - + -
134D LEU* 3.5 43.2 - - + +
137D ALA* 4.3 2.7 - - + -
138D CYS* 3.3 40.3 - - + +
141D LEU* 5.6 2.0 - - + -
148D MET* 4.6 10.1 - - - -
150D ALA 4.5 2.5 - - - -
151D LEU* 1.3 79.9 - - - +
153D CYS* 1.3 65.0 + - - +
184D ALA* 5.3 2.0 - - + -
185D LEU 3.2 15.7 - - - +
193D LEU* 4.0 15.7 - - + -
221D PHE* 3.7 5.2 - - - -
224D TYR* 3.0 16.8 + - - -
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Residues in contact with CYS 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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134D LEU* 4.9 2.9 - - - -
135D ASN* 3.3 17.0 - - - +
152D PHE* 1.3 75.7 - - - +
154D GLY* 1.3 64.2 + - - +
155D VAL* 4.9 2.5 - - - -
183D PHE 4.0 0.5 - - - +
184D ALA* 3.3 5.3 - - - +
185D LEU* 2.8 34.2 + - - +
217D SER* 3.9 28.7 - - - -
220D VAL* 3.7 22.7 - - + -
221D PHE* 3.6 27.8 - - + -
224D TYR* 3.8 2.0 - - - +
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Residues in contact with GLY 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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49D GLN* 5.1 2.6 + - - -
131D ALA* 3.3 29.2 + - - +
134D LEU* 4.5 8.9 - - - +
135D ASN* 3.1 20.0 + - - +
153D CYS* 1.3 77.4 - - - +
155D VAL* 1.3 67.4 + - - +
182D THR* 5.9 0.2 - - - -
183D PHE 3.3 8.3 - - - -
184D ALA* 4.2 3.8 - - - -
220D VAL* 5.4 2.1 - - - +
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Residues in contact with VAL 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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28D LEU* 4.6 4.7 - - + -
131D ALA* 4.0 4.3 - - - -
153D CYS* 4.9 5.2 - - - -
154D GLY* 1.3 78.8 - - - +
156D ALA* 1.3 67.4 + - - +
167D LEU* 5.5 3.6 - - + -
168D ASP* 3.9 12.1 - - - +
182D THR* 3.5 5.5 - - - +
183D PHE* 2.9 34.1 + - + +
185D LEU* 4.2 5.2 - - + -
213D ALA* 3.7 37.7 - - + +
216D ALA* 3.7 31.2 - - + -
217D SER 4.6 1.3 - - - +
220D VAL* 4.6 12.3 - - + -
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Residues in contact with ALA 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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128D SER* 3.5 29.8 - - - +
131D ALA* 5.0 0.7 - - + -
155D VAL* 1.3 77.9 - - - +
157D CYS* 1.3 60.5 + - - +
167D LEU* 3.4 9.2 - - - +
168D ASP* 2.7 36.0 + - - +
169D PRO* 4.1 5.8 - - + -
180D VAL* 5.3 3.1 - - + -
181D LEU 3.1 14.6 - - - +
182D THR* 3.9 13.0 - - + +
183D PHE* 4.8 1.1 - - - +
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Residues in contact with CYS 157 (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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156D ALA* 1.3 74.3 - - - +
158D ALA* 1.3 61.7 + - - +
159D LEU* 4.2 2.2 - - + -
165D LEU* 4.4 7.9 - - + -
166D VAL 3.2 7.9 - - - +
167D LEU* 4.2 14.6 - - + -
169D PRO* 4.7 2.9 - - - -
179D ALA 4.7 0.2 - - - -
180D VAL* 3.6 4.9 - - - +
181D LEU* 2.9 51.7 + - - +
183D PHE* 4.4 6.0 - - - -
209D CYS* 3.0 49.4 - - + +
213D ALA* 6.3 0.2 - - - -
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Residues in contact with ALA 158 (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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157D CYS* 1.3 76.3 - - - +
159D LEU* 1.3 63.5 + - - +
160D ASP* 3.8 3.2 + - - +
164D THR 3.6 3.6 - - - +
165D LEU* 3.3 4.5 - - - -
166D VAL* 2.9 35.3 + - + +
169D PRO* 3.8 30.3 - - + -
173D GLN* 4.4 5.2 - - + +
177D ALA* 4.2 14.1 - - + -
179D ALA 3.4 8.5 - - - +
180D VAL* 4.8 3.8 - - + -
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Residues in contact with LEU 159 (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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157D CYS* 4.4 4.7 - - - -
158D ALA* 1.3 75.0 - - - +
160D ASP* 1.3 64.2 + - - +
163D GLY* 3.4 36.1 - - - +
164D THR 4.3 0.2 - - - -
165D LEU* 4.1 12.1 - - + -
177D ALA* 3.3 2.7 - - - +
178D ARG* 3.0 9.7 + - + +
179D ALA* 2.9 46.0 + - + -
181D LEU* 4.7 8.7 - - + -
201D TYR* 5.4 1.1 - - + -
205D GLU* 4.4 30.7 - - + +
209D CYS* 2.9 37.2 - - - -
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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