Contacts of the helix formed by residues 264 - 268 (chain D) in PDB entry 3CB4
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 ASP 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D PHE* 5.7 1.3 - - - -
206D VAL* 3.6 9.0 - - - -
262D ILE* 3.4 12.2 - - - +
263D LYS* 1.3 86.8 - - - +
265D ILE* 1.3 60.2 + - + +
266D HIS* 3.5 33.8 - - + +
267D GLY* 2.9 24.1 + - - -
319D LEU* 5.9 8.3 - - + -
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Residues in contact with ILE 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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198D SER* 3.7 16.5 - - - +
199D TRP 3.6 42.6 - - - +
200D PHE 4.1 0.2 - - - +
206D VAL* 3.7 15.0 - - + +
264D ASP* 1.3 72.2 - - + +
266D HIS* 1.3 68.9 + - + +
267D GLY 3.2 0.2 - - - -
268D ALA 3.1 28.0 + - - +
269D PRO* 3.8 1.9 - - - +
318D SER 4.3 2.7 - - - +
319D LEU* 3.4 26.4 + - - +
320D ASN* 3.7 25.1 - - - +
321D ASP 4.1 0.7 - - - -
322D ALA* 3.8 27.8 - - + +
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Residues in contact with HIS 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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264D ASP* 3.0 25.5 + - + +
265D ILE* 1.3 87.1 - - + +
267D GLY* 1.3 59.6 + - - +
268D ALA 3.2 0.9 - - - -
269D PRO* 3.4 19.7 - - - +
290D LYS* 5.2 10.0 - - - -
318D SER* 4.2 21.2 + - - -
321D ASP 4.7 1.9 + - - -
322D ALA* 3.5 31.3 + - - +
324D LEU 5.9 2.9 - - - -
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Residues in contact with GLY 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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225D VAL* 3.5 30.1 - - - +
228D THR* 4.4 10.0 - - - +
232D TYR* 4.8 5.1 + - - -
262D ILE* 3.7 16.5 - - - +
264D ASP* 2.9 15.8 + - - -
266D HIS* 1.3 76.8 - - - +
268D ALA* 1.3 57.1 + - - +
269D PRO* 3.4 2.9 - - - -
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Residues in contact with ALA 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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195D ILE* 3.9 9.8 - - + +
198D SER* 2.9 22.2 + - - +
206D VAL* 4.7 5.6 - - + -
208D SER* 3.4 24.5 - - - +
225D VAL* 4.8 3.1 - - + -
262D ILE* 3.9 20.4 - - + -
264D ASP 4.0 0.8 + - - -
265D ILE 3.1 13.5 + - - +
267D GLY* 1.3 80.0 - - - +
269D PRO* 1.3 66.2 - - - +
270D VAL 3.5 1.4 + - - -
274D LEU* 6.3 1.3 - - + -
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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