Contacts of the strand formed by residues 248 - 251 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LEU* 3.8 27.8 - - + -
184D HIS* 3.6 25.6 - - + +
186D ARG 3.5 1.4 + - - -
187D ILE* 3.4 9.7 - - + -
188D GLY 2.8 28.7 + - - -
246D PRO* 3.3 8.9 - - - +
247D THR* 1.3 81.0 + - - +
249D LEU* 1.3 59.3 + - - +
275D VAL* 4.5 0.2 - - - -
276D GLU 3.2 9.2 - - - +
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Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D LEU* 4.1 6.2 - - - +
188D GLY* 3.1 26.0 - - - +
189D ALA 4.1 1.6 - - - +
190D ILE* 3.8 22.0 - - + -
236D ALA* 5.4 0.4 - - + -
239D VAL* 4.0 12.6 - - + -
240D LEU* 3.8 23.6 - - + -
246D PRO* 3.8 17.3 - - + -
248D ALA* 1.3 82.4 - - - +
250D LEU* 1.3 64.7 + - - +
251D THR* 3.9 7.1 + - + -
260D ALA* 5.0 8.3 - - + -
264D LEU* 6.2 0.2 - - + -
275D VAL* 3.5 26.7 - - + -
276D GLU 2.9 8.2 + - - +
277D ILE* 3.4 10.3 - - + -
278D VAL* 3.1 24.9 + - - +
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Residues in contact with LEU 250 (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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172D ALA* 4.0 9.9 - - + +
175D ALA* 4.1 15.0 - - + -
176D VAL* 4.0 16.6 - - + -
179D LEU* 4.8 1.0 - - + +
187D ILE* 4.8 0.4 - - + +
188D GLY 2.7 14.0 + - - +
189D ALA* 3.2 8.7 - - + +
190D ILE 2.9 27.0 + - - +
191D VAL* 5.4 3.9 - - + +
202D ARG* 3.8 28.9 - - + +
203D LEU* 5.5 0.2 - - - -
206D PHE* 3.9 18.8 - - + -
249D LEU* 1.3 72.8 - - - +
251D THR* 1.3 70.0 + - - +
252D SER* 5.4 0.7 - - - -
278D VAL* 3.4 28.5 - - + +
279D SER 5.0 0.7 - - - +
280D PHE* 4.4 14.6 - - + -
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Residues in contact with THR 251 (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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190D ILE* 3.4 13.7 - - + -
249D LEU* 3.9 5.1 + - + -
250D LEU* 1.3 80.9 - - - +
252D SER* 1.3 59.6 + - - +
253D SER 3.4 0.2 - - - -
256D ILE* 3.9 17.9 - - + -
257D THR* 2.6 29.1 + - - +
260D ALA* 3.9 28.0 - - + -
277D ILE* 3.5 11.9 - - + +
278D VAL 2.8 13.3 + - - +
279D SER* 3.3 5.5 - - - -
280D PHE* 3.2 24.3 + - - -
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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