Contacts of the strand formed by residues 210 - 216 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49G ILE* 3.6 28.3 - - + -
50G SER 3.7 9.9 - - - +
51G GLN* 4.5 2.7 - - - +
52G LYS* 3.9 14.4 - - - +
194G ILE* 3.7 45.3 - - + -
197G MET* 5.1 1.1 - - - -
205G PHE* 4.0 36.1 - - + -
206G SER 3.9 3.1 + - - +
207G LYS 3.9 6.1 + - - +
208G ASN* 3.4 0.4 - - - -
209G ASP* 1.3 86.0 - - - +
211G GLU* 1.3 61.3 + - - +
212G VAL* 4.8 3.1 - - + -
229G ILE* 3.8 30.6 - - + +
233G LEU* 4.3 7.2 - - + -
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Residues in contact with GLU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G VAL 4.1 0.2 - - - +
49G ILE* 3.5 2.4 - - - +
50G SER* 3.0 44.1 + - - +
51G GLN 5.0 1.7 - - - +
52G LYS* 4.2 17.4 + - + +
64G VAL 3.4 7.7 - - - +
65G SER* 2.9 34.7 + - - +
66G TYR* 3.1 25.5 + - - +
67G ILE* 3.6 22.8 - - + +
210G LEU* 1.3 77.9 - - - +
212G VAL* 1.3 68.0 + - - +
223G THR* 6.2 2.2 - - - -
224G LEU 5.8 0.7 - - - -
229G ILE* 4.4 2.9 - - - -
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Residues in contact with VAL 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G VAL* 4.4 3.4 - - + -
48G VAL 3.5 9.4 - - - +
49G ILE* 4.2 12.1 - - + -
67G ILE* 3.9 4.8 - - - +
190G VAL* 3.9 28.0 - - + -
194G ILE* 4.9 4.7 - - + -
210G LEU* 4.8 3.8 - - + -
211G GLU* 1.3 84.5 - - - +
213G GLY* 1.3 65.3 + - - +
214G VAL* 4.2 2.0 - - + -
223G THR* 3.2 9.0 - - - -
224G LEU* 3.0 55.8 + - + +
229G ILE* 3.9 28.3 - - + +
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Residues in contact with GLY 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G THR 4.0 0.3 - - - +
47G VAL* 3.5 4.9 - - - +
48G VAL* 2.9 45.9 + - - +
67G ILE* 3.8 5.3 - - - +
212G VAL* 1.3 74.5 - - - +
214G VAL* 1.3 64.3 + - - +
221G PHE* 3.9 16.2 - - - -
222G PHE 3.4 7.6 - - - -
223G THR* 4.3 1.8 - - - -
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Residues in contact with VAL 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G CYS* 4.7 0.7 - - + -
46G THR 3.6 8.1 - - - +
47G VAL* 4.3 5.2 - - + -
186G TRP* 3.8 43.1 - - + -
190G VAL* 3.8 23.8 - - + -
212G VAL* 4.2 7.4 - - + -
213G GLY* 1.3 79.1 - - - +
215G ALA* 1.3 64.5 + - - +
216G THR* 4.1 7.9 - - + -
221G PHE* 3.3 4.6 - - - -
222G PHE* 2.7 66.8 + - + +
224G LEU* 4.4 5.4 - - + -
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Residues in contact with ALA 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G CYS* 3.2 8.1 - - - +
46G THR* 2.8 41.3 + - - +
73G THR 4.6 0.9 - - - +
139G VAL* 4.4 1.8 - - + -
140G SER* 3.7 33.9 - - - +
141G VAL* 3.3 2.8 - - - +
214G VAL* 1.3 73.6 - - - +
216G THR* 1.3 63.0 + - - +
220G LYS 3.6 4.5 - - - +
221G PHE* 3.6 22.4 - - + -
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Residues in contact with THR 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ASP* 4.2 4.5 - - - +
45G CYS* 4.2 11.2 - - + -
73G THR* 5.4 3.1 - - - +
141G VAL* 3.7 14.8 + - - +
186G TRP* 4.1 25.8 - - + +
214G VAL* 4.1 3.1 - - + -
215G ALA* 1.3 78.4 - - - +
217G LYS* 1.3 72.2 + - - +
218G ASP 2.9 3.3 + - - -
220G LYS* 2.7 31.6 + - - +
222G PHE* 4.2 18.0 - - + -
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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