Contacts of the strand formed by residues 210 - 215 (chain O) 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 ILE 210 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O THR 3.7 3.1 - - - +
51O GLU* 4.3 5.2 - - + -
52O LYS* 3.8 6.7 + - - -
194O LEU* 4.5 4.0 - - + -
197O LEU* 3.8 20.9 - - + -
202O VAL* 4.4 8.1 - - + -
206O PHE* 3.6 38.1 - - + -
207O ASN 3.3 20.4 + - - +
208O GLY 3.2 16.5 - - - +
209O THR* 1.3 95.7 - - - +
211O GLU* 1.3 61.3 + - - +
212O LEU* 3.7 28.0 - - + -
229O ILE* 3.5 24.8 - - + +
233O LEU* 5.7 0.7 - - + -
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Residues in contact with GLU 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O ALA* 3.3 4.0 - - - +
50O THR* 3.0 41.2 + - + +
52O LYS* 4.0 27.0 + - + +
62O GLU* 5.2 2.8 - - - +
64O LEU 3.5 15.9 - - - +
65O SER* 4.4 1.2 - - - -
66O LYS* 2.8 38.9 + - - +
67O VAL* 3.8 23.0 - - + +
209O THR 4.3 0.2 - - - -
210O ILE* 1.3 73.0 - - - +
212O LEU* 1.3 63.2 + - - +
223O LYS* 3.4 30.8 - - + +
229O ILE* 4.9 0.2 - - - -
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Residues in contact with LEU 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O VAL* 3.6 22.7 - - + -
48O ILE 3.4 5.4 - - - +
49O ALA* 3.3 29.6 - - + -
67O VAL* 4.8 2.5 - - - -
190O ILE* 4.0 21.8 - - + +
193O ALA* 5.0 3.1 - - + -
194O LEU* 4.1 17.3 - - + +
197O LEU* 4.6 2.0 - - + -
210O ILE* 3.7 27.0 + - + -
211O GLU* 1.3 72.4 - - - +
213O ALA* 1.3 60.5 + - - +
214O ILE* 5.5 0.4 - - + -
223O LYS* 3.7 6.2 - - - +
224O LEU* 2.9 53.7 + - + +
229O ILE* 4.5 11.0 - - + +
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Residues in contact with ALA 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O VAL* 3.5 4.8 - - - +
48O ILE* 2.9 38.1 + - + +
67O VAL* 3.4 29.1 - - + +
212O LEU* 1.3 74.6 - - - +
214O ILE* 1.3 64.9 + - - +
215O ILE* 6.1 0.2 - - + -
221O PHE* 3.9 17.7 - - + -
222O ARG 3.2 12.6 - - - +
223O LYS* 3.9 7.4 - - + -
224O LEU 4.4 0.4 - - - +
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Residues in contact with ILE 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O VAL 3.3 7.9 - - - +
47O VAL* 4.5 4.3 - - + -
186O LEU* 4.1 24.9 - - + -
190O ILE* 4.1 30.3 - - + -
213O ALA* 1.3 79.4 - - - +
215O ILE* 1.3 66.5 + - - +
216O GLY* 4.1 11.2 - - - +
217O ASN* 6.2 0.9 - - - -
220O ARG 4.6 0.4 - - - +
221O PHE* 3.3 4.5 - - - -
222O ARG* 2.8 74.7 + - + +
224O LEU* 4.4 16.6 - - + -
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Residues in contact with ILE 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O GLY* 3.2 6.2 - - - -
46O VAL* 2.8 37.2 + - + +
48O ILE* 5.8 3.4 - - + -
73O ASP 3.6 20.2 - - - +
75O GLY* 3.7 15.7 - - - +
139O ALA* 3.5 42.6 - - + +
140O GLY 3.9 1.8 - - - -
141O HIS* 3.9 25.6 - - + +
147O PHE* 3.5 6.4 - - + -
214O ILE* 1.3 78.4 - - - +
216O GLY* 1.3 59.4 + - - +
220O ARG* 3.6 13.5 - - + -
221O PHE* 3.7 20.2 - - + -
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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