Contacts of the strand formed by residues 216 - 221 (chain G) in PDB entry 5T0J
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 GLU 216 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE 4.0 0.5 - - - +
51G VAL* 3.7 0.3 - - - -
52G THR* 2.7 43.4 + - - +
53G GLN* 3.3 19.9 + - - +
54G LYS* 2.9 40.0 + - - +
67G THR* 4.2 27.1 + - + +
68G HIS* 5.0 6.6 - - + +
69G LEU* 3.6 25.8 - - + +
213G SER 4.3 1.1 - - - +
214G GLU 2.9 16.1 - - - +
215G ILE* 1.3 74.5 - - - +
217G VAL* 1.3 58.5 + - - +
218G GLY 4.2 0.4 + - - -
229G ILE* 5.9 1.3 - - + -
235G ILE* 5.5 0.9 - - - -
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Residues in contact with VAL 217 (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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49G VAL* 3.7 22.9 - - + -
50G ILE 3.3 9.6 - - - +
51G VAL* 4.2 19.5 - - + -
69G LEU* 4.3 3.9 - - - +
195G VAL* 5.5 6.5 - - + -
198G ALA* 5.3 6.1 - - + -
199G ILE* 6.1 3.6 - - + -
215G ILE* 3.8 24.1 + - + -
216G GLU* 1.3 79.2 - - - +
218G GLY* 1.3 60.8 + - - +
229G ILE* 4.0 4.6 - - - +
230G LEU* 3.2 44.5 + - + +
235G ILE* 4.5 17.0 - - + +
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Residues in contact with GLY 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G VAL* 3.3 12.6 - - - +
50G ILE* 2.8 34.2 + - - +
69G LEU* 4.3 9.1 - - - +
216G GLU 4.2 0.6 - - - -
217G VAL* 1.3 74.5 - - - +
219G VAL* 1.3 61.8 + - - +
227G PHE* 4.2 19.1 - - - -
228G ARG 4.3 3.1 - - - -
229G ILE* 4.5 3.6 - - - -
230G LEU* 3.5 3.4 - - - -
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Residues in contact with VAL 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G CYS* 4.7 2.0 - - + -
48G ALA 3.4 12.1 - - - +
49G VAL* 3.7 12.3 - - + -
50G ILE* 5.9 0.2 - - - -
191G PHE* 3.6 27.4 - - + -
218G GLY* 1.3 75.8 - - - +
220G VAL* 1.3 63.7 + - - +
221G THR* 3.4 22.0 - - - +
227G PHE* 3.1 22.1 - - - -
228G ARG* 3.2 30.2 + - + +
230G LEU* 3.6 21.8 - - + -
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Residues in contact with VAL 220 (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 ASP 4.3 0.3 - - - +
47G CYS* 3.3 2.4 - - - -
48G ALA* 2.8 57.5 + - + +
50G ILE* 5.7 1.3 - - + -
75G ASN 5.0 3.6 - - - +
141G ILE* 3.8 39.7 - - + -
142G GLY 4.0 7.2 - - - +
143G ILE* 3.7 33.7 - - + -
149G PRO* 4.3 3.8 - - + +
150G GLN 4.8 2.5 - - - +
219G VAL* 1.3 74.0 - - - +
221G THR* 1.3 63.9 + - - +
225G PRO 5.2 3.1 - - - +
226G LYS 5.9 0.7 - - - -
227G PHE* 4.2 7.9 - - + +
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Residues in contact with THR 221 (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 ASP* 3.5 24.5 - - + +
47G CYS* 3.2 21.0 - - + +
143G ILE* 4.8 3.2 - - - +
191G PHE* 4.8 5.3 - - + -
219G VAL* 3.4 16.7 - - - +
220G VAL* 1.3 77.3 - - - +
222G VAL* 1.3 80.7 + - - +
223G GLU* 3.6 5.5 + - + -
224G ASN 3.7 13.0 - - - +
225G PRO* 4.2 8.3 - - - +
226G LYS 5.0 2.2 + - - +
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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