Contacts of the strand formed by residues 235 - 242 (chain I) in PDB entry 6G2T
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 GLY 235 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193I LYS* 5.6 3.4 - - - -
233I PHE 3.4 2.9 + - - -
234I THR* 1.3 78.9 - - - +
236I SER* 1.3 60.6 + - - -
237I TYR* 3.9 6.6 + - - -
253I ASN* 3.6 6.1 - - - +
254I LEU* 3.0 33.2 + - - +
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Residues in contact with SER 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I LYS* 4.4 1.4 - - - +
194I GLY* 3.0 28.7 + - - -
235I GLY* 1.3 71.9 - - - -
237I TYR* 1.3 68.4 + - - +
251I ASN* 5.1 9.4 - - - +
252I PHE 4.0 1.6 + - - -
253I ASN* 3.3 19.6 + - - -
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Residues in contact with TYR 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I PHE* 5.0 0.2 - + - -
191I TRP* 6.0 0.2 - - + -
192I PHE 3.3 8.1 - - - +
193I LYS* 3.4 37.5 - - + +
199I LEU* 4.9 10.9 - - + +
202I LYS* 5.8 0.3 + - - -
207I LEU* 6.2 0.4 - - + -
224I LEU* 4.5 9.6 - - + -
226I ILE* 3.9 13.4 - - + +
233I PHE* 2.9 41.5 + - - +
235I GLY 3.9 6.0 + - - -
236I SER* 1.3 84.8 + - - +
238I ARG* 1.3 60.3 + - - +
251I ASN* 3.7 1.7 - - - -
252I PHE* 2.8 75.2 + + + +
254I LEU* 3.5 34.1 - - + +
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Residues in contact with ARG 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I LYS 3.9 1.0 - - - +
191I TRP* 3.8 1.6 - - - -
192I PHE* 2.8 62.4 + - + +
194I GLY 4.6 9.6 + - - +
195I LYS* 4.8 23.8 + - - +
236I SER 4.4 0.4 + - - -
237I TYR* 1.3 74.5 - - - +
239I CYS* 1.3 63.0 + - - +
240I GLU* 4.0 12.4 + - + +
249I CYS* 3.3 39.8 - - + +
250I SER 3.5 5.4 - - - +
251I ASN* 3.3 22.5 + - - +
252I PHE* 4.4 3.1 - - - -
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Residues in contact with CYS 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I PHE* 3.7 12.2 - - + -
161I PRO* 3.8 22.9 - - + -
176I ALA* 4.3 9.9 - - - -
189I VAL* 3.8 16.6 - - - -
190I LYS 3.7 2.9 - - - -
191I TRP* 3.6 44.9 - - + -
238I ARG* 1.3 72.7 - - - +
240I GLU* 1.3 60.8 + - - +
241I VAL* 4.4 0.2 - - - -
249I CYS* 3.1 4.2 - - - -
250I SER 2.9 36.9 + - - +
252I PHE* 4.0 3.2 - - + -
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Residues in contact with GLU 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I VAL 3.9 0.5 - - - +
189I VAL* 3.3 2.3 - - - +
190I LYS* 2.7 63.4 + - + +
192I PHE* 3.8 24.7 - - + -
238I ARG* 4.0 12.6 + - + +
239I CYS* 1.3 74.3 - - - +
241I VAL* 1.3 68.7 + - - +
242I SER* 5.1 4.2 - - - +
247I PHE* 4.2 20.7 - - + +
248I ASP 3.5 15.3 - - - +
249I CYS* 4.2 9.4 - - + -
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Residues in contact with VAL 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I LEU* 3.7 9.5 - - + +
157I PHE* 3.2 30.9 - - + -
176I ALA* 5.4 2.5 - - + -
178I VAL* 3.6 29.2 - - + -
187I PRO* 3.7 21.5 - - + -
188I VAL 3.3 6.5 - - - +
189I VAL* 3.6 21.3 - - + -
222I PHE* 4.1 7.9 - - + -
239I CYS* 4.4 3.6 - - - -
240I GLU* 1.3 79.3 - - - +
242I SER* 1.3 64.9 + - - +
243I THR* 4.7 2.2 - - + -
247I PHE* 4.4 0.2 - - - -
248I ASP 3.1 28.5 + - - +
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Residues in contact with SER 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I PRO* 3.3 5.7 - - - +
188I VAL* 2.7 55.6 + - - +
190I LYS* 5.8 3.7 - - - +
240I GLU* 5.3 5.4 - - - -
241I VAL* 1.3 74.3 - - - +
243I THR* 1.3 65.6 + - - +
246I LYS 4.0 3.4 - - - -
247I PHE* 4.6 23.3 - - - +
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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