Contacts of the strand formed by residues 210 - 216 (chain G) in PDB entry 5GJQ
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 VAL 210 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47G VAL* 4.5 2.9 - - + -
48G ALA 3.5 5.2 - - - +
50G LYS* 3.6 11.3 - - - +
192G LEU* 3.6 25.8 - - + -
195G LEU* 4.6 4.9 - - + -
205G LEU* 3.7 35.7 - - + -
206G THR 3.5 20.4 + - - +
207G THR 4.9 3.1 - - - +
208G LYS 3.7 1.4 - - - +
209G ASN* 1.3 90.1 - - - +
211G SER* 1.3 65.1 + - - +
212G ILE* 4.1 14.8 - - + -
225G ASP* 4.3 2.3 - - - +
226G ASP 4.8 1.0 + - - -
229G VAL* 3.7 24.5 - - + +
233G LEU* 4.9 1.3 - - + -
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Residues in contact with SER 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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47G VAL* 3.5 4.0 - - - +
48G ALA* 2.9 37.3 + - - +
50G LYS* 2.8 32.3 - - - +
61G LYS* 5.4 2.4 - - - +
62G LYS 5.2 4.1 + - - -
63G ILE* 3.6 22.2 - - - +
210G VAL* 1.3 72.7 - - - +
212G ILE* 1.3 65.4 + - - +
223G ILE* 4.9 3.4 - - - +
224G TYR 3.6 5.2 - - - -
225G ASP* 3.7 14.2 + - - +
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Residues in contact with ILE 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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45G VAL* 4.2 6.1 - - + -
46G LEU 3.5 8.7 - - - +
47G VAL* 4.7 6.1 - - + -
63G ILE* 3.5 7.1 - - - +
188G VAL* 3.7 30.3 - - + -
192G LEU* 4.5 5.8 - - + -
210G VAL* 4.1 11.4 - - + -
211G SER* 1.3 80.5 - - - +
213G GLY* 1.3 62.8 + - - +
214G ILE* 4.2 19.7 - - + -
223G ILE* 3.5 3.8 - - - +
224G TYR* 2.8 40.9 + - + +
229G VAL* 3.9 19.7 - - + -
232G PHE* 3.7 35.2 - - + -
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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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44G ALA 3.9 0.3 - - - +
45G VAL* 3.2 6.2 - - - +
46G LEU* 2.8 36.0 + - - +
63G ILE* 3.7 8.0 - - - +
212G ILE* 1.3 77.4 - - - +
214G ILE* 1.3 63.7 + - - +
221G PHE* 4.4 16.1 - - - -
222G THR 3.2 10.3 - - - -
223G ILE* 4.6 0.7 - - - -
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Residues in contact with ILE 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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43G HIS* 4.0 9.9 - - + -
44G ALA 3.5 8.1 - - - +
45G VAL* 4.2 6.3 - - + -
184G LEU* 3.6 32.3 - - + -
188G VAL* 3.9 21.3 - - + -
212G ILE* 4.2 8.7 - - + -
213G GLY* 1.3 80.2 - - - +
215G VAL* 1.3 63.5 + - - +
219G LEU* 4.0 20.1 - - + +
220G GLU 3.4 4.2 - - - +
221G PHE* 3.2 5.9 - - - -
222G THR* 2.9 31.1 + - - +
224G TYR* 3.6 27.8 - - + +
232G PHE* 4.1 16.4 - - + -
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Residues in contact with VAL 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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43G HIS* 3.5 5.6 - - - +
44G ALA* 2.8 45.8 + - + +
68G ASN 4.2 0.4 - - - +
69G HIS* 3.7 26.2 - - + +
135G ALA* 3.9 6.5 - - + +
136G GLY* 3.8 33.2 - - - +
137G TYR* 4.3 6.9 - - + +
214G ILE* 1.3 79.1 - - - +
216G GLY* 1.3 63.4 + - - +
219G LEU* 3.6 13.2 - - - +
220G GLU* 4.6 0.2 - - - -
221G PHE* 3.7 26.9 - - + +
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Residues in contact with GLY 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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42G THR 3.3 13.7 - - - -
43G HIS* 4.4 7.6 - - - -
137G TYR* 4.0 19.4 - - - +
215G VAL* 1.3 79.1 - - - +
217G LYS* 1.3 64.8 + - - -
218G ASP 3.2 3.5 + - - -
219G LEU* 2.8 24.6 + - - +
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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