Contacts of the strand formed by residues 248 - 251 (chain F) in PDB entry 3EGC
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 ALA 248 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F LEU* 3.8 23.1 - - + -
184F HIS* 3.6 30.7 - - + -
186F ARG 3.5 1.0 + - - -
187F ILE* 3.4 6.6 - - + -
188F GLY 2.7 30.7 + - - -
246F PRO* 3.3 8.2 - - - +
247F THR* 1.3 83.8 + - - +
249F LEU* 1.3 59.0 + - - +
275F VAL* 4.3 1.3 - - - -
276F GLU 3.2 10.5 - - - +
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Residues in contact with LEU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LEU* 4.0 5.6 - - - +
188F GLY* 3.2 25.6 - - - -
189F ALA 4.2 0.9 - - - +
190F ILE* 4.0 19.7 - - + -
236F ALA* 5.3 0.2 - - + -
239F VAL* 4.0 13.2 - - + -
240F LEU* 3.8 24.9 - - + -
246F PRO* 3.7 16.4 - - + -
248F ALA* 1.3 84.0 - - - +
250F LEU* 1.3 64.4 + - - +
251F THR* 3.8 4.0 + - + -
260F ALA* 4.8 9.0 - - + -
264F LEU* 5.7 0.7 - - + -
275F VAL* 3.7 23.1 - - + -
276F GLU 2.9 9.2 + - - +
277F ILE* 3.5 15.8 - - + +
278F VAL* 3.1 25.1 + - - +
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ALA* 4.0 11.9 - - + -
175F ALA* 4.4 13.0 - - + -
176F VAL* 4.0 18.4 - - + -
179F LEU* 4.7 1.0 - - - +
187F ILE* 4.9 0.4 - - - +
188F GLY 2.8 13.4 + - - +
189F ALA* 3.3 8.7 - - + +
190F ILE 2.8 27.9 + - - +
191F VAL* 5.6 4.2 - - + +
202F ARG* 3.7 30.3 - - + +
203F LEU* 5.5 0.7 - - - -
206F PHE* 4.0 17.0 - - + -
249F LEU* 1.3 72.8 - - - +
251F THR* 1.3 70.7 + - - +
252F SER 5.0 0.4 - - - +
278F VAL* 3.4 28.0 - - + +
279F SER 5.0 0.2 - - - +
280F PHE* 4.5 13.9 - - + -
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Residues in contact with THR 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ILE* 3.4 10.8 - - + -
249F LEU* 3.8 4.7 + - + -
250F LEU* 1.3 85.4 - - - +
252F SER* 1.3 61.1 + - - +
253F SER 3.3 0.4 - - - -
256F ILE* 3.8 17.7 - - + +
257F THR* 2.5 29.0 + - - +
260F ALA* 3.8 29.2 - - + -
277F ILE* 3.5 11.6 - - + +
278F VAL 2.9 13.1 + - - +
279F SER* 3.3 5.9 - - - -
280F PHE* 3.2 21.7 + - - -
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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