Contacts of the helix formed by residues 252 - 262 (chain D) in PDB entry 5HVO
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 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D SER* 4.8 8.0 + - - +
48D LEU* 5.7 5.5 - - - +
251D ILE* 1.3 76.5 - - - +
253D PRO* 1.3 66.7 - - - +
254D ASP* 3.1 26.8 + - - +
255D LYS* 3.3 26.8 + - + +
256D PHE* 3.4 14.7 - - - -
462D THR* 5.2 1.1 - - - -
463D SER* 3.8 9.3 + - - +
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Residues in contact with PRO 253 (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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251D ILE* 3.4 23.1 - - + +
252D ASP* 1.3 85.2 - - - +
254D ASP* 1.3 71.7 + - - +
255D LYS 3.2 0.2 - - - -
256D PHE* 3.1 8.8 + - + +
257D THR* 3.0 24.4 + - - +
397D ALA* 4.5 4.1 - - + +
455D TYR* 4.9 10.8 - - - +
458D ILE* 3.9 35.0 - - + +
459D SER* 4.1 15.0 - - - +
462D THR* 4.0 13.9 - - + -
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Residues in contact with ASP 254 (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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252D ASP* 3.1 15.8 + - - +
253D PRO* 1.3 83.5 - - - +
255D LYS* 1.3 54.1 + - - +
257D THR* 2.9 11.7 + - - +
258D ASP* 2.8 47.8 + - - +
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Residues in contact with LYS 255 (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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44D GLY 5.4 7.9 - - - +
252D ASP* 3.3 25.6 + - + +
253D PRO 3.2 0.2 - - - -
254D ASP* 1.3 77.3 - - - +
256D PHE* 1.3 65.7 + - + +
258D ASP* 3.8 7.0 - - - +
259D GLY* 2.9 24.8 + - - -
366D PHE* 3.5 47.1 - - + -
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Residues in contact with PHE 256 (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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251D ILE* 3.8 26.5 - - + -
252D ASP 3.4 17.7 - - - -
253D PRO* 3.1 6.6 + - + +
254D ASP 3.1 0.4 - - - -
255D LYS* 1.3 85.6 - - + +
257D THR* 1.3 65.4 + - - +
258D ASP 3.2 0.2 - - - -
260D LEU* 3.2 30.6 + - - +
366D PHE* 3.6 30.3 - + - -
369D LEU* 4.8 2.0 - - + -
370D ILE* 3.3 8.6 - - + +
373D TYR* 4.5 8.7 - + - -
394D GLU* 3.4 45.5 - - + -
397D ALA* 3.6 20.6 - - + +
398D THR* 3.9 20.4 - - + -
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Residues in contact with THR 257 (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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253D PRO 3.0 9.5 + - - +
254D ASP* 2.9 29.3 + - - -
256D PHE* 1.3 76.1 - - - +
258D ASP* 1.3 64.7 + - - +
260D LEU* 3.6 19.4 + - + +
261D LYS* 3.7 15.0 + - - +
397D ALA 4.4 9.9 - - - +
400D GLN* 4.1 13.2 - - - +
455D TYR* 3.6 23.6 - - + +
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Residues in contact with ASP 258 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D ASP* 2.8 33.8 + - - +
255D LYS* 3.8 6.7 - - - +
257D THR* 1.3 75.0 + - - +
259D GLY* 1.3 64.8 + - - +
261D LYS* 3.0 42.5 + - + +
262D SER 4.0 1.6 + - - -
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D LYS 2.9 18.2 + - - -
256D PHE 3.4 0.4 + - - -
258D ASP* 1.3 75.4 - - - +
260D LEU* 1.3 61.5 + - - +
262D SER* 3.2 24.3 + - - -
265D VAL* 3.3 10.1 - - - +
366D PHE* 4.4 9.0 - - - -
367D ASP* 5.2 3.1 - - - -
370D ILE* 3.7 16.6 - - - -
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Residues in contact with LEU 260 (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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256D PHE 3.2 18.9 + - - +
257D THR* 3.7 11.7 - - + +
258D ASP 3.1 1.0 - - - -
259D GLY* 1.3 75.4 - - - +
261D LYS* 1.3 61.2 + - - +
262D SER 3.2 1.9 + - - +
265D VAL* 4.1 7.2 - - + +
266D GLN* 2.2 37.1 + - - +
269D ILE* 4.1 26.0 - - + -
370D ILE* 4.0 19.3 - - + +
374D ALA* 4.2 11.0 - - + -
397D ALA 4.5 3.4 - - - +
398D THR* 3.9 31.0 - - - +
400D GLN* 6.1 1.1 - - + +
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Residues in contact with LYS 261 (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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257D THR* 3.8 15.0 - - - +
258D ASP* 3.0 29.9 + - + +
260D LEU* 1.3 75.5 - - + +
262D SER* 1.3 65.8 + - - +
263D PRO* 3.3 6.9 - - - +
266D GLN* 4.3 5.2 - - - +
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Residues in contact with SER 262 (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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258D ASP 4.0 1.2 + - - -
259D GLY* 3.2 17.3 + - - -
260D LEU 3.1 1.5 - - - +
261D LYS* 1.3 75.8 - - - +
263D PRO* 1.3 66.1 - - - +
264D LYS* 3.1 13.5 + - - +
265D VAL* 2.8 28.3 + - - +
266D GLN* 2.9 32.7 + - - +
367D ASP* 4.9 4.7 + - - -
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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