Contacts of the strand formed by residues 180 - 186 (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 GLU 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PHE* 4.6 0.7 - - - -
171D VAL* 3.2 8.5 - - - -
172D LYS* 2.8 57.4 + - + +
174D ASN* 4.9 5.9 + - - -
178D SER* 4.1 9.6 - - - +
179D PRO* 1.3 76.6 - - - +
181D TRP* 1.3 60.8 + - - +
182D ILE 3.3 0.5 + - - -
195D ASN* 5.7 1.9 + - - +
197D LYS* 4.2 18.3 + - - +
198D PHE* 3.8 37.4 - - + -
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Residues in contact with TRP 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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100D TYR* 3.5 26.0 - + + -
101D PRO* 3.7 25.8 - - + -
102D TRP* 3.2 55.0 + + + +
103D THR* 5.8 0.4 - - - +
104D PHE* 4.2 9.4 - - + -
169D ASN* 3.0 31.3 - - + +
170D TRP 3.8 4.3 - - - -
171D VAL* 4.5 5.4 - - + -
179D PRO 4.2 1.4 + - - -
180D GLU* 1.3 70.0 - - - +
182D ILE* 1.3 61.2 + - - +
183D GLY* 3.6 26.2 + - - -
184D HIS* 3.4 33.7 - + - -
193D THR* 3.9 11.0 - - + -
194D TYR 4.5 1.6 - - - -
195D ASN* 2.8 47.6 + - + +
198D PHE* 4.2 1.9 - - - -
241D MET* 4.5 9.9 - - + -
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Residues in contact with ILE 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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170D TRP* 2.7 17.7 + - + +
171D VAL 3.8 5.2 - - - -
172D LYS* 3.8 19.1 - - + +
180D GLU 4.2 0.9 - - - +
181D TRP* 1.3 73.2 - - - +
183D GLY* 1.3 53.2 + - - +
194D TYR* 3.7 4.4 - - + +
195D ASN* 2.8 32.0 + - - +
198D PHE* 3.7 36.3 - - + +
202D ALA* 3.6 30.3 - - + -
204D PHE* 3.8 11.6 - - + -
215D MET* 3.9 13.7 - - + -
217D LEU* 5.3 1.3 - - + -
228D TYR* 3.6 36.6 - - + -
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Residues in contact with GLY 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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169D ASN* 3.3 2.8 - - - -
170D TRP* 2.8 25.6 + - - +
181D TRP* 3.5 22.2 + - - -
182D ILE* 1.3 83.7 - - - +
184D HIS* 1.3 59.7 + - - +
193D THR 3.1 14.4 - - - -
204D PHE* 3.5 10.1 - - - -
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Residues in contact with HIS 184 (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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102B ASN* 5.0 2.0 - - + -
103B ASN* 3.8 14.7 + - - -
167B SER 5.9 1.3 - - - -
100D TYR* 3.0 41.6 + + - -
102D TRP* 4.1 11.8 - + - -
167D PHE* 4.9 16.2 - + + -
168D ILE 3.2 16.4 - - - +
169D ASN* 3.2 34.1 - - - +
181D TRP* 3.4 10.4 - + - -
183D GLY* 1.3 70.3 - - - +
185D ILE* 1.3 64.4 + - - +
191D THR 3.6 2.1 + - - +
192D SER* 3.4 2.9 - - - -
193D THR* 2.9 41.0 + - - +
204D PHE* 3.6 6.7 - - - -
233D SER* 5.0 2.9 - - - -
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Residues in contact with ILE 185 (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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161A LEU* 4.6 0.4 - - + -
167D PHE* 3.4 7.6 - - - +
168D ILE* 3.0 48.1 + - + +
170D TRP* 4.8 3.8 - - - +
184D HIS* 1.3 75.6 - - - +
186D SER* 1.3 75.2 + - - +
187D SER 3.4 1.1 + - - +
190D ALA* 3.7 22.0 - - + +
191D THR 3.1 9.9 - - - +
192D SER* 3.5 18.8 - - - +
204D PHE* 3.8 36.1 - - + +
205D THR* 4.2 4.7 - - - +
206D VAL* 3.9 30.3 - - + -
213D ALA* 5.2 0.4 - - + -
214D PHE 5.8 0.2 - - - +
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Residues in contact with SER 186 (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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166B ARG 2.6 28.3 + - - -
167B SER* 3.8 20.9 - - - -
167D PHE* 3.7 14.2 - - - -
184D HIS* 5.2 0.6 + - - -
185D ILE* 1.3 72.3 - - - +
187D SER* 1.3 60.2 + - - +
188D SER* 3.6 1.2 + - - -
189D TYR* 3.0 15.4 + - - +
190D ALA* 2.8 30.7 + - - -
191D THR* 2.9 22.9 + - - -
206D VAL* 4.3 0.3 - - - +
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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