Contacts of the strand formed by residues 264 - 268 (chain D) in PDB entry 5DO7
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 LEU 264 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN 5.1 1.1 - - - +
35D SER* 5.0 1.6 - - - -
36D LEU* 4.0 23.6 - - + +
95D VAL* 3.3 31.9 - - + +
96D ARG 3.2 31.2 - - - +
97D SER* 3.5 8.3 - - - +
99D GLN 3.9 4.3 - - - +
232D GLY 2.8 18.7 + - - +
233D ILE* 3.4 32.2 - - + -
234D LEU* 2.8 31.6 + - - +
262D ASN 3.9 0.2 + - - -
263D ARG* 1.3 73.3 - - - +
265D VAL* 1.3 62.0 + - - +
266D LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 265 (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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95D VAL* 5.2 0.2 - - - +
99D GLN 3.3 7.3 + - - +
100D MET* 3.4 23.2 - - + -
101D LEU 2.8 29.6 + - - -
234D LEU* 3.4 13.0 - - + +
236D LEU* 4.2 24.5 - - + -
255D LEU* 4.0 11.4 - - + +
258D LEU* 5.1 2.0 - - + -
259D ALA* 3.4 40.8 - - + +
263D ARG* 4.1 7.0 - - + +
264D LEU* 1.3 79.9 - - - +
266D LEU* 1.3 68.8 + - - +
267D ILE* 4.3 4.0 - - + -
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.5 16.4 - - + -
93D PHE* 4.5 8.5 - - + -
95D VAL* 4.6 5.4 - - + -
101D LEU* 3.5 31.2 - - + +
103D ILE* 4.1 20.2 - - + -
115D LEU* 4.8 6.3 - - + -
118D ILE* 5.2 4.9 - - + -
233D ILE* 5.5 0.2 - - + -
234D LEU 2.8 15.4 + - - +
235D ILE* 3.6 25.5 - - + -
236D LEU* 2.8 31.8 + - - +
264D LEU* 4.0 26.7 - - + -
265D VAL* 1.3 86.5 - - - +
267D ILE* 1.3 64.3 + - - +
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Residues in contact with ILE 267 (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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100D MET* 3.4 36.1 - - + -
101D LEU 2.8 13.5 + - - +
102D ALA* 4.1 11.4 - - + -
103D ILE* 2.8 32.0 + - - +
115D LEU* 4.7 2.2 - - - -
236D LEU* 3.6 10.1 - - + -
239D PRO* 4.0 16.2 - - + -
252D VAL* 4.2 10.5 - - + -
255D LEU* 4.1 19.5 - - + -
265D VAL* 4.3 5.6 - - + -
266D LEU* 1.3 80.0 - - - +
268D SER* 1.3 70.3 + - - +
269D LEU* 3.1 31.0 - - + -
280D PHE* 5.1 2.0 - - + -
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Residues in contact with SER 268 (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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103D ILE* 3.2 14.8 - - - -
111D ARG* 4.0 23.7 + - - -
115D LEU* 3.4 26.5 - - - +
236D LEU 3.5 4.4 + - - -
237D ASP* 3.4 14.9 + - - -
238D GLU* 3.1 26.8 + - - +
267D ILE* 1.3 77.9 - - - +
269D LEU* 1.3 64.9 + - - +
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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