Contacts of the strand formed by residues 210 - 216 (chain D) in PDB entry 3SDI
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 ALA 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D VAL 3.2 12.3 - - - +
52D LYS* 3.9 5.9 - - - +
194D LEU* 5.3 6.1 - - + -
197D LEU* 4.1 9.9 - - + -
201D MET* 4.5 4.0 - - - -
207D LEU* 3.8 29.4 - - + -
208D ASP 3.4 7.5 + - - +
209D ASN* 1.3 103.3 + - + +
211D GLN* 1.3 63.6 + - - +
226D ASN* 5.2 1.6 + - - -
229D THR* 4.7 8.7 - - + +
233D ILE* 6.3 0.2 - - + -
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Residues in contact with GLN 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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49D GLY* 3.1 5.9 - - - -
50D VAL* 2.9 40.8 + - + +
52D LYS* 3.7 23.8 + - + +
62D ASP 5.7 0.7 - - - +
64D ILE 4.1 15.6 + - - +
65D GLU* 5.2 0.4 - - - +
66D LYS 4.3 0.4 - - - +
67D ILE* 3.5 39.7 + - + +
197D LEU* 5.1 1.1 - - - +
210D ALA* 1.3 77.2 - - - +
212D LEU* 1.3 72.4 + - - +
223D ILE* 3.6 25.1 - - + +
224D TYR 4.9 4.5 - - - +
226D ASN* 5.7 4.8 + - - +
229D THR* 5.4 1.8 - - - -
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Residues in contact with LEU 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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47D VAL* 3.7 18.8 - - + -
48D LEU 3.6 0.7 - - - -
49D GLY* 3.8 7.6 - - - -
67D ILE* 4.4 1.8 - - - -
190D GLU* 4.3 9.0 - - + -
193D VAL* 3.4 33.2 - - + -
194D LEU* 3.3 41.7 - - + -
197D LEU* 5.5 0.9 - - + -
211D GLN* 1.3 78.3 - - - +
213D SER* 1.3 61.6 + - - +
223D ILE* 3.9 1.6 - - - -
224D TYR* 3.0 45.6 + - + +
229D THR* 4.4 16.1 + - + +
232D LEU* 4.2 18.8 - - + -
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Residues in contact with SER 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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47D VAL* 3.4 8.7 - - - +
48D LEU* 2.8 49.4 + - - +
67D ILE* 3.4 24.4 - - - +
212D LEU* 1.3 77.2 - - - +
214D CYS* 1.3 65.3 + - - +
221D PHE* 3.8 9.0 - - - -
222D LYS 3.1 17.7 - - - -
223D ILE* 3.9 6.3 - - - -
224D TYR* 4.0 8.0 + - - -
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Residues in contact with CYS 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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46D VAL 3.0 17.7 - - - +
47D VAL* 4.3 2.2 - - + -
48D LEU* 4.6 0.4 - - - +
186D LEU* 4.3 16.4 - - + -
213D SER* 1.3 77.0 - - - +
215D ILE* 1.3 69.0 + - - +
216D THR* 4.4 17.7 - - - -
220D GLY 3.5 1.3 - - - +
221D PHE* 3.4 4.0 - - - -
222D LYS* 2.9 35.6 + - - +
224D TYR* 3.2 32.8 - - - +
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Residues in contact with ILE 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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45D GLY* 3.3 4.7 - - - -
46D VAL* 3.0 30.7 + - + +
48D LEU* 6.2 0.9 - - + -
73D HIS* 3.5 19.5 - - + +
75D GLY* 4.3 2.0 - - - +
139D ALA* 4.1 19.7 - - + +
140D GLY* 3.5 16.8 - - - +
141D HIS* 3.4 35.9 - - + +
146D TYR* 3.5 3.8 - - + -
214D CYS* 1.3 74.2 - - - +
216D THR* 1.3 70.6 + - - +
217D LYS* 5.3 0.4 - - - -
220D GLY* 3.1 10.1 - - - +
221D PHE* 3.2 37.9 - - + -
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Residues in contact with THR 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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44D GLU 3.4 22.0 - - - +
45D GLY* 4.3 1.3 - - - -
146D TYR* 3.7 8.5 - - - -
186D LEU* 4.0 21.1 - - + -
214D CYS* 4.2 8.6 - - - -
215D ILE* 1.3 80.8 - - - +
217D LYS* 1.3 59.4 + - - +
218D GLN* 4.1 6.2 - - - -
219D ASP* 3.3 29.3 + - - +
220D GLY* 2.7 38.0 + - - -
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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