Contacts of the strand formed by residues 248 - 251 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LEU* 3.7 25.4 - - + -
184E HIS* 3.6 29.6 - - + -
186E ARG 3.4 1.8 + - - -
187E ILE* 3.5 7.3 - - + -
188E GLY 2.9 22.8 + - - -
246E PRO* 3.4 3.9 - - - +
247E THR* 1.3 83.1 - - - +
249E LEU* 1.4 68.5 + - - +
275E VAL* 4.5 2.0 - - - +
276E GLU 3.2 10.1 - - - +
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Residues in contact with LEU 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E LEU* 3.9 6.3 - - - +
188E GLY* 3.1 18.6 - - - +
189E ALA 4.4 0.7 - - - +
190E ILE* 3.9 21.8 - - + -
236E ALA* 5.4 0.2 - - + -
239E VAL* 4.1 11.7 - - + -
240E LEU* 3.8 24.5 - - + -
246E PRO* 3.8 22.7 - - + -
248E ALA* 1.4 83.2 - - - +
250E LEU* 1.3 65.5 + - - +
251E THR* 4.0 4.4 + - + -
260E ALA* 5.0 9.4 - - + +
264E LEU* 6.3 0.2 - - + -
275E VAL* 3.7 24.0 - - + -
276E GLU 2.8 8.8 + - - +
277E ILE* 3.4 14.3 - - + +
278E VAL* 3.1 25.8 + - - +
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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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172E ALA* 4.0 11.0 - - + +
175E ALA* 4.2 13.9 - - + -
176E VAL* 4.0 19.5 - - + -
179E LEU* 4.7 1.0 - - - +
187E ILE* 4.9 0.2 - - - +
188E GLY 2.8 11.6 + - - +
189E ALA* 3.3 8.9 - - + +
190E ILE 2.8 26.5 + - - +
191E VAL* 5.5 3.8 - - + +
202E ARG* 3.8 28.0 - - + +
203E LEU* 5.5 0.2 - - - -
206E PHE* 3.9 17.9 - - + -
249E LEU* 1.3 73.6 - - - +
251E THR* 1.3 71.0 + - - +
252E SER* 5.4 0.2 - - - -
278E VAL* 3.5 27.1 - - + +
279E SER 5.4 0.2 - - - -
280E PHE* 4.5 15.3 - - + -
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Residues in contact with THR 251 (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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190E ILE* 3.4 11.9 - - + -
249E LEU* 4.6 4.3 - - + -
250E LEU* 1.3 82.3 - - - +
252E SER* 1.3 62.7 + - - +
253E SER 3.4 0.7 - - - -
256E ILE* 4.0 18.2 - - + +
257E THR* 2.6 27.4 + - - +
260E ALA* 3.9 29.2 - - + -
277E ILE* 3.6 12.8 - - + +
278E VAL 2.9 6.4 + - - +
279E SER* 3.2 12.8 - - - -
280E PHE* 3.4 19.6 + - - -
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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