Contacts of the strand formed by residues 264 - 270 (chain D) in PDB entry 4CEV
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D PHE* 3.6 19.9 - - + -
119D ILE* 4.1 14.8 - - + -
221D VAL* 3.4 28.0 - - + +
223D LEU* 4.1 16.6 - - + -
258D LEU* 4.1 22.0 - - + +
262D GLN* 3.8 1.5 - - - +
263D ILE* 1.3 83.4 - - + +
265D THR* 1.3 59.6 + - - +
266D SER 3.3 27.1 - - - +
267D ALA* 4.4 1.3 - - + -
293D LEU* 4.1 27.8 - - + -
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Residues in contact with THR 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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91D PHE* 3.3 18.7 - - - -
92D PRO* 3.8 8.3 - - - +
113D TYR* 3.2 30.6 + - + +
116D LEU* 4.2 2.9 - - - +
219D ASP 5.0 1.3 - - - +
220D GLY* 3.4 16.8 - - - -
221D VAL 2.7 29.8 + - - -
263D ILE 3.7 10.5 - - - +
264D ILE* 1.3 75.6 - - - +
266D SER* 1.3 59.7 + - - -
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Residues in contact with SER 266 (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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91D PHE* 3.4 11.5 - - - -
92D PRO* 3.6 23.8 - - - -
105D THR* 5.6 0.4 - - - -
109D VAL* 3.8 20.8 - - - +
221D VAL 3.5 0.8 + - - -
222D HIS* 2.7 36.7 + - - +
223D LEU 2.9 21.7 + - - -
264D ILE* 3.3 5.5 - - - +
265D THR* 1.3 80.1 + - - +
267D ALA* 1.3 65.4 + - - +
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Residues in contact with ALA 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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91D PHE* 3.5 16.0 - - + -
92D PRO 3.2 12.4 + - - +
93D LEU* 3.4 5.0 - - + -
94D VAL* 2.9 24.6 + - - +
105D THR* 5.0 0.3 - - - +
222D HIS* 3.8 5.4 + - - -
223D LEU* 3.2 22.4 - - + +
264D ILE* 4.4 0.2 - - + -
266D SER* 1.3 80.2 + - - +
268D GLU* 1.3 63.5 + - - +
269D PHE* 4.3 9.4 - - + -
293D LEU* 4.1 15.5 - - + -
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Residues in contact with GLU 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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94D VAL* 3.0 23.1 - - + +
101D ILE* 3.9 7.3 - - - +
102D ALA* 3.3 26.5 + - - +
105D THR* 2.7 26.2 + - - -
222D HIS* 2.8 25.0 + - + +
223D LEU 3.0 5.7 + - - +
224D SER* 2.8 29.5 + - - +
225D LEU* 2.9 28.2 + - - +
267D ALA* 1.3 75.5 - - - +
269D PHE* 1.3 68.0 + - - +
270D VAL* 4.2 13.9 - - + -
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Residues in contact with PHE 269 (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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27D MET* 3.6 14.3 - - - +
93D LEU* 4.0 19.1 - - + -
94D VAL 3.0 7.2 + - - -
95D LEU* 3.8 1.7 - - + -
96D GLY 3.0 21.5 + - - -
223D LEU* 4.3 10.5 - - + -
225D LEU* 3.3 37.9 - - + -
227D LEU* 4.3 14.1 - - + -
255D MET* 4.6 1.6 - - - -
267D ALA* 4.3 5.8 - - + -
268D GLU* 1.3 78.1 - - - +
270D VAL* 1.3 62.0 + - - +
286D ALA* 4.0 17.0 - - + -
289D LEU* 4.1 11.4 - - + -
290D MET* 3.4 50.0 - - + -
293D LEU* 4.2 20.6 - - + -
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Residues in contact with VAL 270 (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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96D GLY* 4.4 0.7 - - - -
97D GLY 3.3 9.4 - - - +
98D ASP 4.3 1.1 - - - +
99D HIS* 3.5 38.4 - - + +
101D ILE* 3.8 33.7 - - + -
224D SER* 5.5 0.2 - - - +
225D LEU 3.0 5.3 + - - +
226D ASP* 3.7 17.9 - - - -
227D LEU* 3.1 25.5 + - - +
268D GLU* 4.2 17.0 - - + -
269D PHE* 1.3 79.2 - - - +
271D GLU* 1.3 72.9 + - + +
272D VAL 3.3 5.0 + - - -
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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