Contacts of the strand formed by residues 167 - 173 (chain D) in PDB entry 3H3B
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 167 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 4.7 3.6 - - - -
166B ARG* 4.3 6.7 - - + -
167B SER 3.8 21.8 - - - -
168B ARG* 3.4 29.8 - - - -
169B ALA* 3.4 13.0 - - + -
165D GLY 5.3 0.4 - - - -
166D TYR* 1.3 76.5 - - - +
168D ILE* 1.3 68.6 + - - +
169D ASN* 4.0 3.4 - - - +
184D HIS* 4.9 18.8 - + + -
185D ILE 3.4 7.4 - - - +
186D SER* 3.7 26.0 - - - -
187D SER* 4.1 0.2 - - - -
232D ARG* 3.4 9.0 - - - +
233D SER* 2.8 50.7 + - - +
234D GLY* 3.6 23.6 - - - -
235D ASN* 4.2 10.5 - - - -
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 4.2 22.4 - - + -
156D CYS* 4.8 1.6 - - - -
161D TYR* 3.8 22.2 - - - +
163D PHE* 4.3 6.7 - - + -
166D TYR* 5.9 0.4 - - + -
167D PHE* 1.3 79.7 - - - +
169D ASN* 1.3 68.0 + - - +
170D TRP* 3.5 24.1 - - - +
184D HIS* 3.2 3.6 - - - -
185D ILE* 3.0 40.8 + - + +
187D SER* 3.6 17.3 - - - +
206D VAL* 5.2 0.2 - - + -
213D ALA* 3.8 28.3 - - + -
230D CYS* 3.9 13.9 - - + -
231D VAL 3.6 2.5 - - - +
232D ARG* 4.7 1.1 - - - -
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Residues in contact with ASN 169 (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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102D TRP* 3.3 13.1 - - - -
167D PHE 4.2 0.7 - - - +
168D ILE* 1.3 76.5 - - - +
170D TRP* 1.3 64.3 + - - +
171D VAL* 4.3 0.4 - - + -
181D TRP* 3.0 26.3 - - + +
183D GLY 3.3 6.5 - - - +
184D HIS* 3.2 26.4 - - - +
230D CYS* 3.2 6.4 - - - -
231D VAL* 2.7 45.0 + - + +
233D SER* 2.9 25.1 + - - -
241D MET* 3.7 24.3 - - - +
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Residues in contact with TRP 170 (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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140D GLN* 4.7 2.9 - - - -
154D ILE* 4.0 29.2 - - + -
156D CYS* 3.8 18.4 - - + -
168D ILE* 3.5 25.4 + - + +
169D ASN* 1.3 78.2 - - - +
171D VAL* 1.3 58.1 + - - +
181D TRP* 3.7 1.9 - - - -
182D ILE* 2.7 35.5 + - + +
183D GLY 2.8 12.3 + - - +
185D ILE* 4.8 3.0 - - - +
204D PHE* 3.4 44.6 - + + -
213D ALA* 4.0 6.5 - - - +
214D PHE 3.8 20.6 + - - -
215D MET* 3.7 42.0 - - + -
228D TYR* 5.1 0.2 - - + -
229D TYR* 3.3 20.6 - - - -
230D CYS* 3.8 25.1 - - + -
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Residues in contact with VAL 171 (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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104D PHE* 4.3 13.5 - - + -
170D TRP* 1.3 79.9 - - - +
172D LYS* 1.3 66.3 + - - +
173D LYS* 5.1 0.4 - - + -
179D PRO* 3.7 28.5 - - + -
180D GLU 3.2 11.9 - - - +
181D TRP* 4.5 4.3 - - + -
182D ILE* 3.8 4.2 - - - +
227D VAL 3.8 0.5 - - - +
228D TYR* 3.3 7.4 - - - +
229D TYR* 2.8 44.2 + - + +
231D VAL* 3.9 19.7 - - + -
241D MET* 4.5 9.4 - - - -
244D TRP* 3.8 27.1 - - + -
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Residues in contact with LYS 172 (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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171D VAL* 1.3 72.9 - - - +
173D LYS* 1.3 62.8 + - - +
174D ASN* 3.6 24.4 - - - +
178D SER 4.3 1.2 - - - +
179D PRO* 3.4 4.0 - - - +
180D GLU* 2.8 55.6 + - + +
182D ILE* 3.8 10.2 - - + +
197D LYS* 4.8 9.5 - - - +
198D PHE* 3.7 27.6 - - + -
223D GLU 3.0 26.8 + - - -
224D ASP* 3.9 12.1 + - - +
226D ALA* 3.7 14.4 - - + -
227D VAL 3.8 3.1 - - - -
228D TYR* 3.7 31.3 + - + +
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLN* 3.4 27.6 - - - +
50D PRO* 5.9 2.2 - - + -
93D TYR* 3.3 25.5 + - - -
171D VAL* 5.1 0.7 - - + -
172D LYS* 1.3 75.5 - - - +
174D ASN* 1.3 80.5 + - - +
175D SER* 4.1 6.4 + - - +
176D GLY 4.2 1.6 - - - +
177D LYS 2.6 26.6 + - - +
179D PRO* 3.8 26.0 - - + -
226D ALA* 3.6 2.1 - - - +
227D VAL* 2.9 37.2 + - + +
229D TYR* 3.7 30.3 - - + +
244D TRP* 6.3 0.4 - - + -
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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