Contacts of the strand formed by residues 244 - 250 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E GLU* 2.9 15.3 - - - -
53E GLY* 4.5 1.6 - - - -
240E ASP* 4.2 0.2 - - - -
241E LEU* 3.1 30.9 + - - +
242E LYS 3.5 1.4 + - - -
243E SER* 1.3 79.3 - - - +
245E PHE* 1.3 77.1 + - - -
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Residues in contact with PHE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E SER 3.3 6.6 - - - +
50E LEU* 3.4 0.3 - - - -
51E GLU* 2.9 47.9 + - + +
238E GLN* 2.9 35.2 - - + -
239E PHE 3.6 9.6 - - - -
240E ASP* 2.6 32.8 - - - -
241E LEU* 4.2 6.7 - - - +
244E GLY* 1.3 86.2 - - - -
246E LEU* 1.3 59.8 + - - +
247E GLN* 4.3 12.5 - - + +
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Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 3.5 29.8 - - + -
49E SER 3.8 8.1 - - - +
50E LEU* 4.0 21.8 - - + -
218E GLY* 4.5 4.0 - - - -
221E LEU* 4.5 18.8 - - + -
237E PHE 4.6 0.2 - - - -
238E GLN* 3.1 7.6 - - - +
239E PHE* 2.9 50.0 + - + +
241E LEU* 4.2 7.7 - - + +
245E PHE* 1.3 74.1 - - - +
247E GLN* 1.3 68.6 + - - +
248E PHE* 3.6 25.6 - - + -
301E NEQ 3.7 21.1 - - - -
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Residues in contact with GLN 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU 3.5 1.1 - - - +
48E VAL* 3.3 5.2 - - - +
49E SER* 2.8 48.1 + - - +
130E GLU* 3.3 27.8 + - - +
236E LEU* 3.9 10.5 - - + +
237E PHE 3.4 3.6 - - - -
238E GLN* 3.0 34.6 + - + +
245E PHE* 4.3 13.7 - - + +
246E LEU* 1.3 81.7 - - - +
248E PHE* 1.3 64.8 + - - +
249E PHE* 3.4 28.3 - - + -
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Residues in contact with PHE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E CYS* 4.7 0.7 - - - -
46E LEU* 4.0 17.9 - - + -
47E LEU 3.1 4.7 - - - -
48E VAL* 3.9 22.4 - - + -
215E ILE* 3.7 59.0 - - + -
218E GLY* 5.1 0.9 - - - -
236E LEU* 3.4 9.5 - - - +
237E PHE* 2.8 36.6 + - + +
239E PHE* 3.8 20.2 - + - -
246E LEU* 3.6 35.2 - - + -
247E GLN* 1.3 74.2 - - - +
249E PHE* 1.3 61.8 + - - +
250E LEU 4.1 0.4 - - - -
301E NEQ 4.0 31.0 - + - -
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Residues in contact with PHE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL 3.5 1.9 - - - +
46E LEU* 3.6 1.8 - - - -
47E LEU* 2.8 53.0 + - + +
49E SER* 4.6 9.6 - - - -
128E ILE* 3.7 39.0 - - + -
130E GLU* 4.3 15.3 - - + -
131E LEU* 6.0 0.4 - - + -
133E TYR* 4.1 16.8 - - - -
234E PRO* 4.4 9.4 - - + -
235E ALA 3.3 9.4 - - - +
236E LEU* 3.2 30.3 - - + -
247E GLN* 3.4 29.8 - - + -
248E PHE* 1.3 75.6 - - - +
250E LEU* 1.3 61.0 + - - +
1152F ILE* 3.3 19.2 - - + +
1156F LEU* 6.2 0.7 - - + -
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Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 3.7 27.4 - - + +
46E LEU* 4.0 13.0 - - + -
207E PHE* 3.7 38.8 - - + -
208E GLY 4.6 1.1 - - - +
211E TYR* 3.6 33.9 - - + -
212E LEU* 4.1 11.4 - - + -
215E ILE* 3.9 17.3 - - + -
234E PRO* 3.2 0.5 - - - +
235E ALA* 2.8 31.8 + - - +
237E PHE* 4.0 15.5 - - + -
248E PHE 4.1 0.2 - - - -
249E PHE* 1.3 74.8 - - - +
251E ALA* 1.3 64.1 + - - +
252E PRO* 3.7 1.4 - - - +
1149F GLN* 5.7 0.4 - - - +
1152F ILE* 4.0 3.3 - - - +
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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