Contacts of the strand formed by residues 278 - 282 (chain D) in PDB entry 4PE5
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 ILE 278 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ILE* 4.5 10.8 - - + -
166D TRP* 3.6 31.0 - - + -
255D THR* 3.6 15.7 - - + -
256D TRP 3.1 11.5 + - - +
257D ILE* 4.2 19.5 - - + -
258D VAL* 3.1 21.6 + - - +
276D GLY 3.7 8.1 - - - +
277D LEU* 1.3 82.7 - - - +
279D SER* 1.3 67.9 + - - +
364D ILE* 3.9 20.2 - - + -
365D ILE 3.5 8.5 - - - +
366D LEU* 3.8 1.1 - - + -
391D TRP* 3.5 35.7 - - + -
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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
----------------------------------------------------------
257D ILE* 5.3 0.9 - - - -
258D VAL* 3.2 15.6 + - - -
259D PRO 3.5 5.0 + - - -
263D ALA* 3.2 18.4 + - - +
277D LEU* 5.4 0.7 - - - -
278D ILE* 1.3 81.4 - - - +
280D VAL* 1.3 77.6 + - - +
364D ILE* 3.6 5.9 - - - +
365D ILE* 2.9 48.7 + - - +
373D TRP* 3.8 16.2 - - - -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D PRO* 4.9 1.3 - - + -
153D GLN* 4.0 33.2 - - + +
156D VAL* 4.7 14.1 - - + -
157D MET* 3.9 28.3 - - + -
160D ILE* 5.3 6.1 - - + -
257D ILE* 5.6 0.7 - - + -
258D VAL 3.1 8.4 + - - +
259D PRO* 4.8 0.4 - - + -
260D SER* 3.4 13.0 - - - -
263D ALA* 4.4 0.7 - - - +
279D SER* 1.3 89.6 + - - +
281D SER* 1.3 72.2 + - - +
362D LEU* 3.7 36.6 - - + -
363D VAL 3.8 4.9 - - - +
364D ILE* 4.8 3.6 - - + +
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D PRO* 5.9 0.4 - - - -
260D SER* 4.3 8.5 - - - +
263D ALA* 5.4 1.6 - - - -
266D THR* 5.2 5.2 - - - -
280D VAL* 1.3 84.3 - - - +
282D TYR* 1.3 66.3 + - - +
362D LEU* 3.8 5.7 - - - -
363D VAL* 2.9 41.7 + - - -
365D ILE* 3.6 28.5 - - - -
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Residues in contact with TYR 282 (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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131D SER* 5.6 2.0 - - - +
146D PHE* 3.4 58.9 - + + +
147D GLY* 4.5 8.7 - - - -
148D PRO* 4.9 6.8 - - + +
260D SER* 4.2 13.8 + - - +
281D SER* 1.3 74.7 - - - +
283D ASP* 1.3 62.0 + - + +
284D GLU* 2.6 23.0 + - - +
287D TYR* 5.3 10.3 - - + +
292D ARG* 3.4 41.0 + - + +
360D PRO* 4.3 16.2 - - + +
361D LYS* 3.8 18.8 - - + -
362D LEU* 4.5 8.2 - - + +
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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