Contacts of the strand formed by residues 208 - 215 (chain D) in PDB entry 5DST
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 LEU 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D LYS* 3.7 11.1 - - - -
179D VAL* 3.7 15.5 - - - +
180D ASP 3.8 17.7 - - - +
181D ILE 4.3 0.4 - - - +
182D ILE* 4.1 17.9 - - + +
203D ALA 3.7 1.4 + - - -
204D ARG* 2.9 51.6 + - + +
205D ASP 4.9 1.6 - - - +
207D TRP* 1.3 72.0 - - - +
209D LYS* 1.3 73.6 + - - +
210D PRO* 4.4 0.2 - - - +
212D GLY* 3.9 17.9 - - - +
213D LEU 3.9 10.3 - - - +
214D MET* 3.9 20.9 - - + -
281D TYR* 4.7 4.9 - - + -
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Residues in contact with LYS 209 (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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113D LYS* 3.9 18.0 - - - +
178D LYS* 3.5 19.1 - - + -
179D VAL 3.1 18.4 + - - +
180D ASP* 2.7 37.2 + - - +
207D TRP 3.4 1.8 + - - -
208D LEU* 1.3 82.9 - - - +
210D PRO* 1.3 87.3 - - + +
211D GLY 3.4 3.7 + - - -
212D GLY* 3.1 29.1 + - - +
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Residues in contact with PRO 210 (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 LYS* 4.8 9.2 - - + -
208D LEU 3.8 1.3 - - - +
209D LYS* 1.3 99.5 - - + +
211D GLY* 1.3 58.6 + - - +
212D GLY 3.1 3.3 + - - -
210K PRO* 5.2 15.0 - - + -
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Residues in contact with GLY 211 (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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209D LYS* 3.4 5.9 + - - -
210D PRO* 1.3 71.6 - - - +
212D GLY* 1.3 67.6 + - - +
213D LEU* 3.8 12.6 - - - +
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Residues in contact with GLY 212 (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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180D ASP 3.4 14.8 - - - -
208D LEU* 3.9 14.2 - - - +
209D LYS* 3.1 27.2 + - - -
210D PRO 3.1 2.2 + - - -
211D GLY* 1.3 86.4 - - - +
213D LEU* 1.3 61.2 + - - +
281D TYR* 3.7 14.7 - - - -
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Residues in contact with LEU 213 (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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109D VAL* 3.3 35.7 - - + -
113D LYS* 6.5 1.1 - - + -
180D ASP 3.3 6.0 + - - +
181D ILE* 3.4 14.0 - - + -
182D ILE 3.1 23.6 + - - -
208D LEU* 3.9 1.9 - - - +
211D GLY 3.8 13.9 - - - +
212D GLY* 1.3 75.2 - - - +
214D MET* 1.3 67.6 + - - +
215D PHE* 4.3 11.7 - - + -
281D TYR* 3.8 3.8 - - - +
317D LYS* 3.7 43.5 - - + -
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Residues in contact with MET 214 (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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182D ILE* 3.4 25.1 - - + +
200D VAL* 3.6 31.2 - - + -
204D ARG* 3.8 33.7 - - + -
208D LEU* 3.9 10.3 - - + -
213D LEU* 1.3 81.5 - - - +
215D PHE* 1.3 69.4 + - - +
216D PRO* 3.4 16.6 - - - +
217D ASP* 3.3 23.8 - - + +
280D ILE* 3.6 28.3 - - + +
281D TYR* 3.1 24.3 + - + -
315D PHE* 5.3 1.2 - - - +
317D LYS* 5.1 0.7 - - - +
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Residues in contact with PHE 215 (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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99D TYR* 4.0 3.9 - - + -
102D SER* 3.5 44.2 - - - +
103D MET* 4.8 3.4 - - + -
106D ASN* 5.5 1.3 - - + -
109D VAL* 4.2 22.0 - - + -
110D PHE* 3.7 30.1 - + - -
181D ILE* 3.9 15.7 - - + -
182D ILE 3.0 5.5 + - - -
183D ILE* 3.4 16.4 - - + -
184D SER* 3.1 25.6 + - - +
213D LEU* 4.3 14.4 - - + -
214D MET* 1.3 80.7 - - - +
216D PRO* 1.3 62.2 - - - +
315D PHE* 3.6 16.2 - + + -
317D LYS* 4.7 13.7 - - + -
318D CYS* 4.1 10.8 - - - -
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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