Contacts of the strand formed by residues 276 - 280 (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 GLU 276 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LEU* 4.1 10.8 - - + +
182D ARG* 2.7 48.7 + - - -
184D HIS* 2.8 33.7 + - + +
247D THR 2.8 9.5 + - - +
248D ALA* 3.2 3.2 - - + -
249D LEU 2.9 24.3 + - - -
271D TYR* 4.6 3.6 - - + -
272D GLY* 3.5 26.4 - - - +
275D VAL* 1.3 75.9 - - - +
277D ILE* 1.3 65.9 + - - +
291D PRO* 4.4 14.2 - - + +
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Residues in contact with ILE 277 (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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179D LEU* 5.0 0.6 - - - +
249D LEU* 3.4 12.8 - - + +
251D THR* 3.5 27.6 - - + +
257D THR* 4.0 5.2 - - + -
260D ALA* 4.3 18.6 - - + -
261D MET* 3.7 31.6 - - + -
264D LEU* 4.2 11.7 - - + -
271D TYR* 4.0 15.3 + - + -
275D VAL* 4.4 9.0 - - + -
276D GLU* 1.3 83.9 - - - +
278D VAL* 1.3 65.6 + - - +
293D LEU* 3.3 31.0 - - + +
294D PRO* 3.3 22.9 - - - +
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Residues in contact with VAL 278 (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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175D ALA* 3.7 27.6 - - + +
176D VAL* 5.0 0.2 - - - -
178D TYR* 4.2 4.9 - - + -
179D LEU* 3.5 40.8 - - + +
249D LEU 3.1 3.0 + - - -
250D LEU* 3.4 25.1 - - + +
251D THR* 2.8 26.2 + - - +
277D ILE* 1.3 78.6 - - - +
279D SER* 1.3 62.6 + - - +
294D PRO* 3.3 30.3 - - + +
330D PHE* 4.6 1.8 - - + -
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Residues in contact with SER 279 (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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250D LEU* 5.3 0.9 - - - -
251D THR* 3.3 9.6 + - - -
253D SER 3.7 2.4 + - - -
257D THR* 2.7 29.4 + - - -
278D VAL* 1.3 74.2 - - - +
280D PHE* 1.3 74.3 + - - +
286D MET* 3.6 8.3 - - - +
293D LEU* 3.6 19.1 - - - -
294D PRO 3.0 6.5 + - - -
295D VAL* 3.1 11.4 - - - -
296D VAL* 2.8 35.9 + - - +
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Residues in contact with PHE 280 (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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167D GLU 5.1 0.7 - - - -
168D ASN* 3.5 35.4 - - - -
171D GLY* 4.2 0.9 - - - -
172D ALA* 3.6 22.2 - - + -
202D ARG* 3.3 49.8 - - + +
250D LEU* 4.4 8.3 - - + -
251D THR 3.2 17.7 + - - -
252D SER* 3.4 19.5 - - - +
254D HIS 3.3 5.5 + - - -
279D SER* 1.3 86.6 + - - +
281D ASP* 1.3 80.9 + - - +
296D VAL* 3.4 38.4 - - + -
298D GLN* 4.2 11.7 - - + -
328D THR* 5.3 2.5 - - + -
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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