Contacts of the strand formed by residues 210 - 216 (chain P) 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 LEU 210 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P ALA 3.6 9.9 - - - +
51P GLU* 4.7 2.2 - - - -
52P ARG* 3.8 4.6 + - - -
61P GLN* 3.2 23.2 + - - -
194P LEU* 4.1 11.7 - - + -
197P LEU* 3.8 28.5 - - + -
205P LEU* 4.0 26.5 - - + -
206P THR 3.4 19.7 - - - +
207P TYR 3.1 7.2 + - - +
208P ASP 3.4 0.8 + - - -
209P ARG* 1.3 84.3 - - - +
211P GLU* 1.3 66.1 + - - +
212P PHE* 5.1 3.6 - - + -
229P ILE* 3.4 22.8 - - + +
233P LEU* 3.9 26.2 - - + -
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Residues in contact with GLU 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P ALA* 3.4 3.5 - - - -
50P ALA* 3.0 35.5 + - + +
52P ARG* 3.9 21.1 + - - +
61P GLN* 5.3 0.7 - - - +
63P SER 4.4 1.3 - - - +
64P THR* 3.4 14.0 - - - +
65P GLU* 3.1 25.9 + - - +
66P LYS* 2.9 35.5 + - - +
67P LEU* 3.7 28.6 + - + +
210P LEU* 1.3 77.7 - - - +
212P PHE* 1.3 66.4 + - - +
223P ILE* 6.2 4.0 - - + -
229P ILE* 4.2 2.7 - - + -
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Residues in contact with PHE 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P VAL* 3.5 28.3 - - + -
48P LEU 3.4 4.5 - - - -
49P ALA* 3.4 20.0 - - + -
67P LEU* 3.5 4.6 - - - +
190P ILE* 3.7 31.4 - - + -
193P ALA* 4.1 1.1 - - + -
194P LEU* 3.5 41.5 - - + -
197P LEU* 5.4 1.3 - - + -
210P LEU* 5.1 4.7 - - + -
211P GLU* 1.3 81.3 - - - +
213P ALA* 1.3 69.2 + - - +
214P THR* 5.0 0.2 - - + -
223P ILE* 3.8 4.4 - - - +
224P PHE* 2.9 51.0 + + + +
229P ILE* 3.9 30.9 - - + +
232P ILE* 5.2 4.5 - - + -
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Residues in contact with ALA 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P VAL* 3.6 0.9 - - - +
48P LEU* 2.7 51.0 + - + +
67P LEU* 3.5 18.4 - - + +
75P ALA* 5.6 5.2 - - + -
212P PHE* 1.3 76.5 - - - +
214P THR* 1.3 68.5 + - - +
215P ILE* 6.4 0.7 - - + -
222P LYS 3.2 13.2 - - - +
223P ILE* 4.1 13.5 - - + -
224P PHE* 3.9 1.8 - - - -
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Residues in contact with THR 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ILE 3.2 12.3 - - - +
47P VAL* 4.3 8.3 - - + -
186P VAL* 4.7 6.3 - - + -
190P ILE* 4.2 24.2 - - + -
212P PHE* 5.0 0.2 - - + -
213P ALA* 1.3 80.9 - - - +
215P ILE* 1.3 69.3 + - - +
216P ARG* 4.1 15.4 + - - +
220P TYR 3.8 1.2 - - - +
221P GLN* 3.7 0.5 - - - +
222P LYS* 3.0 42.1 + - - +
224P PHE* 3.3 29.7 - - + -
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Residues in contact with ILE 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P GLY* 3.2 7.1 - - - -
46P ILE* 3.0 36.1 + - + +
48P LEU* 5.9 0.7 - - + -
73P LYS* 4.1 12.1 - - - +
75P ALA* 4.2 12.6 - - + +
139P ALA* 3.2 44.9 - - + +
140P GLY 4.2 0.9 - - - +
141P TYR* 4.6 10.1 - - + +
146P TYR* 3.4 12.3 - - + -
213P ALA* 6.4 0.7 - - + -
214P THR* 1.3 76.3 - - - +
216P ARG* 1.3 62.4 + - - +
219P VAL* 3.7 23.3 - - - -
220P TYR 3.5 4.3 - - - +
221P GLN* 3.8 20.6 - - + +
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Residues in contact with ARG 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ASP* 3.4 26.2 + - - +
146P TYR* 3.6 3.1 - - - -
185P LYS* 5.5 2.2 - - - +
186P VAL* 3.5 27.9 - - + +
187P ASP* 2.9 28.5 + - - -
190P ILE* 4.4 10.9 - - - +
214P THR* 4.1 16.2 + - - +
215P ILE* 1.3 76.3 - - - +
216P LYS* 1.3 67.1 + - - +
219P VAL* 4.1 2.5 - - - -
220P TYR* 2.9 39.5 + - + +
222P LYS* 5.8 4.6 - - - +
224P PHE* 5.3 4.2 - - - -
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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