Contacts of the strand formed by residues 172 - 183 (chain D) in PDB entry 6B0B
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 HIS 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D GLU* 4.3 7.1 - - - +
144D GLU* 3.3 39.5 + - + +
164D ARG* 3.3 59.5 + - + +
165D LEU 3.4 7.6 - - - +
166D LYS* 4.6 6.4 - - + +
167D LEU* 4.0 11.7 - - - +
171D GLY* 1.3 83.9 + - - -
173D TYR* 1.3 60.3 + - - +
174D ASP* 3.6 7.5 + - - +
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Residues in contact with TYR 173 (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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99D PHE* 3.1 36.5 - + + +
100D GLU* 3.5 31.6 - - + -
101D ASP* 2.4 35.7 + - + -
129D PHE* 4.5 0.9 - - - -
134D PRO* 3.5 28.7 - - + -
135D VAL* 3.5 23.2 - - + +
143D TRP* 4.5 2.1 - - - -
163D GLN 4.0 0.9 - - - +
164D ARG* 3.7 0.5 - - - -
165D LEU* 2.6 64.2 + - + +
167D LEU* 4.1 16.6 - - + -
172D HIS* 1.3 73.1 - - - +
174D ASP* 1.3 61.2 + - - +
175D ALA* 4.0 0.3 + - - +
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Residues in contact with ASP 174 (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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99D PHE* 4.1 1.2 - - - +
100D GLU* 2.7 49.5 + - + +
162D LYS* 5.2 13.5 + - - +
163D GLN 3.3 5.4 - - - +
164D ARG* 3.2 40.1 + - - +
172D HIS* 3.6 9.4 - - - +
173D TYR* 1.3 78.9 - - - +
175D ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 175 (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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97D MET* 5.3 0.4 - - + -
98D ASN 3.4 11.9 - - - +
99D PHE* 3.6 32.3 - - + -
100D GLU 4.7 0.4 - - - +
143D TRP* 4.7 10.3 - - + -
161D ILE 3.6 1.2 - - - +
162D LYS* 3.6 6.2 + - - +
163D GLN* 2.9 34.2 + - + +
173D TYR 5.1 0.2 - - - +
174D ASP* 1.3 78.3 - - - +
176D GLU* 1.3 64.3 + - - +
177D VAL* 4.0 11.2 + - + -
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D VAL 3.7 1.9 - - - +
97D MET* 3.5 1.4 - - - -
98D ASN* 2.9 47.2 + - + +
161D ILE 3.6 5.4 - - - +
162D LYS* 3.4 37.1 + - + +
175D ALA* 1.3 71.5 - - - +
177D VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 177 (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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63D PRO* 6.5 0.2 - - + -
95D ARG* 3.6 35.7 - - + +
96D VAL 3.5 2.7 - - - -
97D MET* 3.8 25.4 - - + -
159D GLY 3.8 0.4 - - - +
160D GLU* 3.3 6.1 - - - +
161D ILE* 2.9 53.9 + - + +
163D GLN* 3.5 29.2 - - + +
175D ALA* 4.6 4.7 - - + +
176D GLU* 1.3 77.6 - - - +
178D LYS* 1.3 64.8 + - - +
179D THR* 3.8 5.8 - - - +
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Residues in contact with LYS 178 (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 GLU 3.9 1.0 - - - +
95D ARG* 3.4 1.4 - - - -
96D VAL* 2.9 41.8 + - + +
158D LYS* 4.4 25.3 - - + +
159D GLY 3.4 4.5 - - - +
160D GLU* 4.2 30.4 - - + +
177D VAL* 1.3 75.1 - - - +
179D THR* 1.3 67.5 - - - +
180D THR* 5.4 2.0 - - - +
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Residues in contact with THR 179 (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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93D TRP* 3.7 9.4 - - + -
94D GLU 3.4 10.8 - - - +
95D ARG* 2.5 45.7 + - + +
148D GLU* 4.9 2.4 + - - -
157D LEU 3.8 0.7 - - - +
158D LYS* 3.5 5.0 - - - +
159D GLY 2.9 34.6 + - - -
161D ILE* 5.5 0.5 - - - +
177D VAL* 3.8 5.4 - - - +
178D LYS* 1.3 74.4 - - - +
180D THR* 1.3 65.0 + - - +
181D TYR* 3.4 39.5 + - + +
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Residues in contact with THR 180 (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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92D LYS 4.0 0.2 - - - +
93D TRP* 3.0 6.2 - - - +
94D GLU* 2.9 41.0 + - - +
156D ALA* 3.8 17.5 - - + -
157D LEU 3.4 3.8 - - - +
158D LYS* 3.3 41.5 + - - +
178D LYS* 5.4 2.8 - - - +
179D THR* 1.3 73.0 - - - +
181D TYR* 1.3 65.3 + - - +
182D LYS* 4.9 4.0 - - + +
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Residues in contact with TYR 181 (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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70D LYS* 4.0 32.0 - - + +
82D TYR* 4.3 4.3 + - + -
83D LEU* 4.6 18.8 - - + -
91D PHE* 4.7 9.2 - + + -
92D LYS 3.5 5.8 - - - +
93D TRP* 3.5 23.8 - + + -
95D ARG* 2.8 23.8 + - - -
148D GLU* 3.8 13.2 + - - -
150D MET* 3.8 27.6 - - + -
156D ALA* 3.5 2.6 - - - +
157D LEU* 2.9 54.4 + - + +
179D THR* 3.4 30.7 - - + +
180D THR* 1.3 72.5 - - - +
182D LYS* 1.3 58.4 + - - +
183D ALA 4.3 0.2 - - - -
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Residues in contact with LYS 182 (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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82D TYR* 4.2 3.8 - - - +
91D PHE* 3.5 3.5 - - - -
92D LYS* 2.9 41.0 + - + +
156D ALA* 3.8 29.8 - - + +
180D THR* 4.1 4.7 - - + -
181D TYR* 1.3 74.1 - - - +
183D ALA* 1.3 76.7 + - - +
184D LYS* 3.9 0.7 + - - +
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Residues in contact with ALA 183 (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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82D TYR* 3.2 34.9 + - + +
86D SER* 3.7 22.2 - - - -
91D PHE* 3.6 9.0 - - + -
182D LYS* 1.3 93.6 - - - +
184D LYS* 1.3 64.6 + - - +
185D LYS* 3.2 21.0 + - - +
187D VAL* 5.1 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