Contacts of the strand formed by residues 211 - 216 (chain D) in PDB entry 3S52
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 LYS 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D TRP* 3.5 37.8 - - + +
8D GLN* 4.0 7.1 - - - +
134D ILE* 3.3 40.4 - - + -
206D ILE 3.6 0.9 - - - +
207D MSE 3.2 4.2 - - - -
208D LEU 2.9 35.6 + - - +
209D ASN* 3.1 7.0 + - + +
210D GLY* 1.3 74.7 - - - +
212D THR* 1.3 60.1 + - - +
220D CL 3.3 29.3 - - - +
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Residues in contact with THR 212 (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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7D TRP* 4.2 9.6 + - - +
205D LYS* 3.7 33.9 - - + +
206D ILE 3.3 4.0 - - - +
207D MSE 3.0 29.3 - - - +
210D GLY 3.3 2.9 + - - -
211D LYS* 1.3 73.2 - - - +
213D VAL* 1.3 63.8 + - - +
214D ASN* 4.0 17.8 + - - +
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Residues in contact with VAL 213 (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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7D TRP* 4.5 19.1 - - + -
54D ILE* 4.1 23.6 - - + +
55D ARG* 3.8 30.1 - - + -
98D VAL* 5.0 2.2 - - + -
131D SER* 5.2 1.3 - - - -
204D LEU 4.1 0.2 - - - +
205D LYS* 3.7 1.7 - - - -
206D ILE* 2.8 61.8 + - + +
211D LYS 4.1 0.2 + - - -
212D THR* 1.3 75.6 - - - +
214D ASN* 1.3 73.1 + - - +
215D THR 4.4 0.2 + - - -
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Residues in contact with ASN 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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55D ARG* 4.2 9.5 - - - +
203D MSE 6.3 3.1 - - + -
204D LEU 3.3 6.0 - - - +
205D LYS* 3.5 31.0 - - - +
212D THR* 4.0 12.4 + - - +
213D VAL* 1.3 85.7 - - - +
215D THR* 1.3 66.7 + - - +
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Residues in contact with THR 215 (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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54D ILE* 3.0 21.8 + - + +
55D ARG 4.1 2.1 - - - -
56D GLN 2.9 30.5 + - - -
57D PRO* 3.9 0.2 - - - +
58D VAL* 4.0 11.1 - - + +
100D LEU* 5.8 0.2 - - + -
203D MSE 3.7 8.5 - - - +
204D LEU* 2.8 54.9 + - + +
206D ILE* 4.3 13.0 - - + -
213D VAL* 5.8 0.2 - - - -
214D ASN* 1.3 75.9 - - - +
216D ARG* 1.3 70.5 + - - +
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Residues in contact with ARG 216 (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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57D PRO* 3.5 29.6 - - + +
58D VAL* 2.8 28.8 + - - +
201D GLY* 5.1 2.9 - - - +
202D ASP 3.2 12.8 - - - +
203D MSE 3.7 24.2 - - + -
204D LEU* 4.4 2.0 - - - +
215D THR* 1.3 82.4 + - - +
217D ILE* 1.3 69.6 + - - +
218D ILE* 3.8 26.7 - - - +
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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