Contacts of the strand formed by residues 188 - 193 (chain D) in PDB entry 4S10
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 CYS 188 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D VAL* 2.7 46.0 + - + +
187D ASP* 1.3 73.0 - - - +
189D PHE* 1.3 67.8 + - - +
200D TRP 3.1 3.8 - - - +
201D CYS* 2.1 45.3 - - - -
205D SER* 3.1 20.3 + - - -
209D GLU 4.1 1.6 - - - +
210D ARG* 3.9 17.3 - - - -
213D ALA* 3.9 18.4 - - + -
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Residues in contact with PHE 189 (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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162D LEU* 3.8 15.0 - - + -
163D PHE 3.2 17.0 - - - +
164D GLN* 3.7 28.9 - - + -
176D VAL* 4.8 1.1 - - + -
182D SER* 3.5 31.0 - - - -
183D PHE* 3.5 40.8 - + + -
184D ASN* 3.5 43.3 - - - -
187D ASP* 4.2 6.7 - - + -
188D CYS* 1.3 78.3 - - - +
190D ILE* 1.3 68.8 + - - +
191D LEU 4.0 0.2 - - - -
198D HIS 3.5 1.2 - - - +
200D TRP* 2.6 46.4 + + - +
213D ALA* 5.9 0.2 - - - +
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Residues in contact with ILE 190 (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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162D LEU* 3.5 6.7 - - - -
163D PHE* 3.0 40.9 + - + -
165D VAL* 4.0 16.4 - - + -
189D PHE* 1.3 78.2 - - - +
191D LEU* 1.3 60.7 - - - +
192D ASP 3.5 1.7 + - - -
197D ILE* 3.8 26.7 - - + -
198D HIS 3.3 3.1 - - - +
199D GLN* 4.4 6.7 - - + -
213D ALA* 3.2 31.2 - - + +
216D VAL* 3.3 29.2 - - + -
217D SER* 3.8 8.5 - - - +
220D ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 191 (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 ARG 3.3 16.6 - - - +
162D LEU* 4.0 15.7 - - + +
178D VAL* 3.9 24.5 - - + -
183D PHE* 5.3 1.8 - - + -
189D PHE 4.0 1.4 - - - -
190D ILE* 1.3 71.3 - - - +
192D ASP* 1.3 61.0 + - - +
193D LEU* 3.4 35.9 + - + +
196D ASN 4.0 0.3 - - - +
197D ILE* 3.7 0.5 - - - -
198D HIS* 2.8 46.0 + - + +
200D TRP* 6.3 0.7 - - + -
243D MET* 3.9 23.8 - - + -
246D VAL* 4.5 5.4 - - + -
247D LEU* 3.9 29.2 - - + -
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Residues in contact with ASP 192 (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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160D GLN* 3.2 9.7 - - - -
161D ARG* 2.8 66.8 + - + +
163D PHE* 4.5 7.9 - - + -
190D ILE 3.5 1.6 + - - -
191D LEU* 1.3 68.6 - - - +
193D LEU* 1.3 61.4 + - - +
194D GLY 3.2 5.7 + - - -
196D ASN 4.5 1.1 - - - -
197D ILE* 4.2 7.5 - - - +
220D ILE* 3.9 15.3 - - + +
225D ARG* 2.6 49.3 + - - -
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Residues in contact with LEU 193 (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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101B HIS* 4.3 12.7 - - + -
160D GLN* 3.6 27.1 - - + +
191D LEU* 3.7 34.1 - - + +
192D ASP* 1.3 79.6 + - - +
194D GLY* 1.3 58.2 + - - +
195D ASN* 3.0 14.7 + - - +
196D ASN* 2.9 26.7 + - + +
198D HIS* 3.8 23.8 - - + +
242D ALA 4.4 7.6 - - - +
246D VAL* 4.0 25.1 - - + -
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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