Contacts of the strand formed by residues 244 - 250 (chain B) in PDB entry 3V62
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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLU* 2.8 16.2 - - - -
53B GLY* 4.5 1.8 - - - -
241B LEU* 3.0 31.0 + - - +
242B LYS 3.5 1.6 + - - -
243B SER* 1.3 78.5 - - - +
245B PHE* 1.3 76.8 + - - -
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER 3.2 6.9 - - - +
50B LEU* 3.3 3.8 - - - -
51B GLU* 2.9 51.7 + - + +
238B GLN* 2.9 35.4 - - + -
239B PHE 3.7 8.3 - - - -
240B ASP* 2.8 40.4 - - - -
241B LEU* 4.5 3.7 - - - +
244B GLY* 1.3 87.8 - - - -
246B LEU* 1.3 61.0 + - - +
247B GLN* 4.1 14.4 - - + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.5 30.1 - - + -
49B SER 3.8 4.5 - - - +
50B LEU* 4.1 16.6 - - + -
218B GLY* 4.4 3.6 - - - -
221B LEU* 4.4 23.6 - - + -
238B GLN* 3.1 5.1 - - - +
239B PHE* 2.9 53.0 + - + +
241B LEU* 4.1 14.0 - - + +
245B PHE* 1.3 74.9 - - - +
247B GLN* 1.3 68.9 + - - +
248B PHE* 3.8 22.9 - - + -
301B NEQ 3.8 20.2 - - - -
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU 3.4 0.7 - - - +
48B VAL* 3.2 5.7 - - - +
49B SER* 2.8 50.6 + - - +
130B GLU* 3.8 26.2 + - - +
236B LEU* 3.9 10.0 - - + +
237B PHE 3.4 4.3 - - - -
238B GLN* 2.9 33.4 + - + +
245B PHE* 4.1 14.2 - - + +
246B LEU* 1.3 83.2 - - - +
248B PHE* 1.3 64.7 + - - +
249B PHE* 3.4 28.1 - - + -
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B CYS* 4.8 0.4 - - - -
46B LEU* 3.9 20.2 - - + -
47B LEU 3.1 3.8 - - - -
48B VAL* 3.9 26.7 - - + -
215B ILE* 3.7 55.9 - - + -
218B GLY* 5.2 1.6 - - - -
235B ALA 3.4 3.1 - - - +
236B LEU* 3.4 7.1 - - - +
237B PHE* 2.7 41.9 + - + +
239B PHE* 3.9 17.0 - + - -
246B LEU* 3.8 28.0 - - + -
247B GLN* 1.3 75.9 - - - +
249B PHE* 1.3 62.6 + - - +
250B LEU 4.0 0.4 - - - -
301B NEQ 3.9 35.0 - + - -
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL 3.5 1.2 - - - +
46B LEU* 3.4 2.5 - - - +
47B LEU* 2.8 63.2 + - + -
49B SER* 4.4 12.1 - - - -
126B LEU* 5.4 0.9 - - + -
128B ILE* 3.9 33.4 - - + -
130B GLU* 4.6 12.3 - - + -
131B LEU* 6.2 0.7 - - + -
133B TYR* 4.4 14.8 - - - -
234B PRO* 4.3 9.4 - - + -
235B ALA 3.3 8.7 - - - +
236B LEU* 3.1 32.1 - - + -
247B GLN* 3.4 26.9 - - + -
248B PHE* 1.3 73.4 - - - +
250B LEU* 1.3 61.7 + - - +
1152C ILE* 3.4 16.5 - - + +
1156C LEU* 6.2 0.9 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 3.7 23.8 - - + +
46B LEU* 4.1 7.4 - - + -
207B PHE* 3.7 28.8 - - + -
208B GLY 4.7 0.4 - - - +
211B TYR* 3.7 31.0 - - + -
212B LEU* 3.7 30.1 - - + -
215B ILE* 3.7 15.0 - - + -
234B PRO* 3.3 4.5 - - - +
235B ALA 2.9 29.9 + - - -
237B PHE* 3.9 16.2 - - + -
248B PHE 4.0 0.2 - - - -
249B PHE* 1.3 74.7 - - - +
251B ALA* 1.3 70.9 + - - +
252B PRO* 3.7 1.4 - - - +
1149C GLN* 5.7 0.2 - - - +
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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