Contacts of the strand formed by residues 250 - 253 (chain D) in PDB entry 1E3S
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 VAL 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B GLU* 4.0 6.6 - - - +
159D PHE* 4.3 20.9 - - + -
176D VAL* 4.2 30.5 - - + +
179D THR* 4.6 6.5 - - + +
195D THR* 3.2 31.2 - - + +
197D ALA* 4.1 22.0 - - + -
249D GLU* 1.3 97.2 + - - +
251D ILE* 1.3 64.0 + - - +
252D ARG* 5.1 1.1 - - + +
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Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 6.1 0.4 - - + -
246B LEU* 4.3 5.2 - - + -
249B GLU* 3.8 3.6 - - + +
251B ILE* 4.1 46.9 - - + -
194D VAL* 4.5 12.1 - - + -
195D THR 3.0 10.7 + - - +
196D ILE* 3.6 7.4 - - + +
197D ALA* 2.9 26.1 + - - -
236D LEU* 4.2 26.5 - - + -
239D MET* 6.0 1.8 - - - -
240D VAL* 4.4 22.2 - - + -
246D LEU* 4.6 12.6 - - + -
249D GLU* 4.3 6.3 - - + -
250D VAL* 1.3 79.0 - - - +
252D ARG* 1.3 70.9 + - - +
253D LEU 3.7 0.7 + - - -
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Residues in contact with ARG 252 (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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246B LEU* 3.4 19.8 - - - +
247B ASN 5.5 0.5 + - - -
249B GLU* 3.0 43.3 + - + +
156D VAL* 3.4 18.4 - - + +
159D PHE* 3.9 28.5 - - + +
160D GLU* 2.8 41.6 + - - -
197D ALA* 3.4 18.2 - - + +
250D VAL* 4.3 1.5 - - + -
251D ILE* 1.3 72.0 - - - +
253D LEU* 1.3 58.0 + - - +
254D ASP* 2.9 28.1 + - - +
257D ILE 3.3 19.8 + - - -
258D ARG* 3.5 22.9 - - - +
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Residues in contact with LEU 253 (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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243B ASN* 3.7 25.6 - - - +
245B PHE* 4.0 15.9 - - + -
246B LEU* 3.7 22.9 - - + -
196D ILE* 4.5 7.4 - - + -
197D ALA 3.1 8.2 + - - +
198D PRO* 3.5 3.6 - - + +
199D GLY 3.0 18.7 + - - -
201D PHE* 3.5 31.9 - - + -
232D GLU* 3.9 6.3 - - + +
233D TYR* 3.7 30.7 - - + +
236D LEU* 4.1 23.3 - - + -
251D ILE 3.7 0.4 + - - -
252D ARG* 1.3 71.3 - - - +
254D ASP* 1.3 59.7 + - - +
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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