Contacts of the strand formed by residues 196 - 204 (chain D) in PDB entry 3HB8
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 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D PHE* 5.8 3.4 - + - -
135D TYR* 3.2 31.1 + + + -
181D ALA* 3.6 17.1 - - + +
194D PRO* 4.2 5.2 - - - +
195D CYS* 1.3 77.5 - - + +
197D ALA* 1.3 67.5 + - - +
198D LEU* 3.5 2.4 - - - -
212D LEU* 3.7 13.1 - - + +
213D TYR 3.5 4.7 - - - -
214D GLN* 3.7 17.6 - - - +
226D ASN* 3.7 24.5 + - + +
229D SER* 6.0 1.2 - - - -
230D TYR* 3.4 37.1 - + - +
565D UMP 3.2 28.8 + + - -
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Residues in contact with ALA 197 (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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180D CYS* 3.8 0.5 - - - -
181D ALA 3.0 21.8 + - - -
182D TRP* 3.4 22.8 + - + +
195D CYS 3.4 4.6 + - - +
196D HIS* 1.3 76.2 - - - +
198D LEU* 1.3 62.5 + - - +
213D TYR* 2.9 38.8 + - + -
215D ARG* 5.0 1.7 - - + +
178E ILE* 5.0 8.7 - - + -
198E LEU* 3.7 21.8 - - + -
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Residues in contact with LEU 198 (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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178D ILE* 4.2 16.2 - - + -
179D MET 3.1 17.0 - - - +
180D CYS* 3.6 18.8 - - + -
181D ALA* 5.7 0.2 - - - -
196D HIS* 3.5 1.9 - - - -
197D ALA* 1.3 83.1 - - + +
199D CYS* 1.3 67.5 + - - +
212D LEU* 3.8 4.4 - - - +
213D TYR* 2.9 30.0 + - + +
182E TRP* 4.7 6.1 - - + -
197E ALA* 3.7 20.0 - - + -
198E LEU* 3.6 27.4 - - + -
213E TYR* 3.7 36.6 - - + -
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Residues in contact with CYS 199 (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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139D TRP* 5.8 0.9 - - - -
178D ILE* 3.3 8.1 - - - +
179D MET* 2.9 61.9 + - - -
198D LEU* 1.3 77.4 - - - +
200D GLN* 1.3 61.9 + - - +
201D PHE* 4.1 20.3 - - - -
210D CYS* 4.1 11.0 - - - -
211D GLN 3.0 13.7 - - - +
212D LEU* 4.2 6.1 - - + -
230D TYR* 4.1 26.5 - - + -
233D LEU* 5.0 0.7 - - - -
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Residues in contact with GLN 200 (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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175D ARG* 3.8 19.4 + - - +
177D ILE 3.2 14.6 - - - +
178D ILE* 3.4 17.9 - - + -
199D CYS* 1.3 74.7 - - - +
201D PHE* 1.3 70.5 + - - +
202D TYR* 5.5 1.0 - - - +
210D CYS* 3.4 1.2 - - - -
211D GLN 2.8 33.8 + - - +
59E PHE* 3.1 28.5 - - + -
213E TYR* 2.7 34.7 + - + +
215E ARG* 3.2 26.9 + - - +
253E GLY* 3.2 15.4 - - - -
254E ASP* 4.3 5.9 - - - +
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Residues in contact with PHE 201 (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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161D LEU* 6.1 1.6 - - + -
164D VAL* 3.3 37.5 - - + -
168D ILE* 4.5 4.5 - - + -
174D ASP 4.8 1.7 - - - +
177D ILE* 2.9 47.7 + - + +
179D MET* 4.8 5.4 - - + -
199D CYS* 4.1 17.9 - - - -
200D GLN* 1.3 79.7 + - - +
202D TYR* 1.3 60.6 + - - +
208D LEU* 4.1 20.9 - - + -
209D SER 3.4 4.9 - - - +
210D CYS* 3.1 41.3 - - + -
233D LEU* 4.1 26.0 - - + -
234D THR* 4.5 9.2 - - - -
237D ILE* 4.6 14.1 - - + -
59E PHE* 4.4 1.3 - - - -
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Residues in contact with TYR 202 (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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174D ASP 5.9 1.1 - - - -
177D ILE* 5.3 0.4 - - - -
200D GLN* 4.0 1.5 + - - +
201D PHE* 1.3 72.3 - - - +
203D VAL* 1.3 68.3 + - - +
204D VAL* 3.5 28.2 - - + +
208D LEU* 3.2 8.5 - - - +
209D SER* 2.8 42.7 + - - +
45E VAL* 4.0 10.0 - - - +
47E LYS* 3.3 31.8 - - + +
57E SER* 2.9 34.0 + - - -
59E PHE* 3.2 61.5 - + + -
254E ASP* 3.6 18.6 - - + -
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Residues in contact with VAL 203 (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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168D ILE* 3.9 23.8 - - + -
172D PRO* 3.3 44.6 + - + +
173D ASP* 5.1 0.9 - - - +
177D ILE* 4.8 4.7 - - + +
201D PHE 4.4 0.2 + - - -
202D TYR* 1.3 86.1 - - - +
204D VAL* 1.3 71.6 + - - +
206D SER* 5.2 2.0 - - - +
207D GLU 3.2 13.2 - - - +
208D LEU* 3.6 18.6 - - + -
243D LEU* 3.8 17.3 - - + -
47E LYS* 3.7 21.8 - - - +
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Residues in contact with VAL 204 (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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202D TYR* 3.5 31.4 - - + +
203D VAL* 1.3 81.8 - - - +
205D ASN* 1.3 86.2 + - - +
206D SER 3.2 1.8 - - - -
207D GLU* 3.0 25.6 + - + +
209D SER* 5.8 1.3 - - - +
45E VAL* 3.2 32.5 - - + -
46E ARG 4.5 8.3 - - - +
47E LYS* 4.7 9.0 - - + -
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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