Contacts of the strand formed by residues 235 - 242 (chain D) in PDB entry 2VGB
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D LEU* 4.0 7.6 - - - -
185D VAL 3.4 11.4 - - - -
186D THR* 5.0 0.7 - - - -
187D VAL* 6.4 0.2 - - - -
208D VAL* 4.1 15.5 - - - +
231D ILE* 3.9 2.5 - - - +
232D GLY* 2.8 35.8 + - - +
233D PRO 3.2 2.6 + - - -
234D GLU* 1.3 83.0 + - - +
236D LEU* 1.3 63.5 + - - -
237D VAL* 3.8 2.3 + - - +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 3.2 10.2 - - - -
185D VAL* 2.9 41.5 + - + -
207D ILE* 4.0 35.2 - - + +
208D VAL* 4.3 13.0 - - + -
211D VAL* 3.7 23.6 - - + +
217D ILE* 3.8 26.5 - - + -
228D VAL* 3.8 12.8 - - + -
230D LYS 3.9 1.3 - - - -
231D ILE* 3.7 24.0 - - + -
235D GLY* 1.3 71.3 - - - -
237D VAL* 1.3 61.4 + - - +
238D THR* 3.6 15.1 - - + +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D GLN* 4.4 13.9 - - + -
183D VAL 4.2 1.8 - - - -
184D LEU* 4.9 10.5 - - + +
228D VAL* 3.5 2.6 - - - -
229D GLN* 2.7 49.6 + - + +
230D LYS* 2.8 37.3 + - + +
232D GLY* 5.0 5.2 - - - +
234D GLU* 5.4 5.4 - - - +
235D GLY 4.8 4.5 - - - +
236D LEU* 1.3 70.4 - - - +
238D THR* 1.3 54.2 + - - +
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D GLN* 3.4 11.8 - - - +
183D VAL* 2.8 43.2 + - - +
185D VAL* 4.5 11.9 - - + -
217D ILE* 4.8 3.1 - - + -
226D LEU* 3.7 26.6 - - + +
227D VAL 3.1 15.0 - - - -
228D VAL* 4.0 13.9 - - + -
229D GLN* 3.8 5.2 - - - -
236D LEU* 3.6 26.7 - - + +
237D VAL* 1.3 80.1 - - - +
239D GLN* 1.3 59.6 + - - +
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Residues in contact with GLN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY* 2.9 38.9 + - - +
181D SER 3.4 4.0 - - - +
182D GLN* 4.0 4.8 - - - +
226D LEU* 4.4 0.2 - - - -
227D VAL* 2.9 37.1 + - + +
229D GLN* 3.4 30.2 + - + +
238D THR* 1.3 73.5 - - - +
240D VAL* 1.3 70.8 + - - +
241D GLU* 3.2 2.1 + - - +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU* 4.2 11.4 - - + +
178D VAL 3.3 24.7 - - - +
179D LYS* 3.9 6.4 - - - +
180D GLY* 2.9 25.1 + - - +
181D SER* 3.0 19.1 + - - +
183D VAL* 3.5 22.4 - - + -
224D ILE* 5.1 0.2 - - + -
225D SER 4.1 1.8 - - - +
226D LEU* 3.6 15.4 - - + +
238D THR 4.3 0.2 - - - -
239D GLN* 1.3 74.3 - - - +
241D GLU* 1.3 59.0 + - - +
242D ASN 3.2 31.0 - - - +
243D GLY* 3.6 12.6 - - - +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LYS* 3.2 27.3 - - - +
216D ARG* 2.8 41.7 + - - -
225D SER* 2.9 23.9 + - - +
227D VAL* 3.5 21.0 - - + +
239D GLN 3.2 1.2 + - - +
240D VAL* 1.3 73.9 - - - +
242D ASN* 1.3 70.8 + - - +
243D GLY 4.1 0.2 - - - -
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Residues in contact with ASN 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B PRO* 5.0 12.4 - - + +
382B ARG* 6.6 0.2 - - - -
179D LYS* 4.9 6.1 + - - +
218D TYR* 5.3 3.2 + - - -
222D GLY 5.8 0.8 + - - -
223D LEU 3.9 13.7 - - - +
224D ILE* 3.7 2.8 - - - +
225D SER* 3.1 52.3 + - - +
240D VAL* 3.2 11.9 - - - +
241D GLU* 1.3 90.5 - - - +
243D GLY* 1.3 63.3 + - - +
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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