Contacts of the helix formed by residues 300 - 307 (chain D) in PDB entry 4O9U
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 GLY 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299D PRO* 1.3 74.5 - - - +
301D TYR* 1.3 65.1 + - - -
302D GLY 3.2 4.2 + - - -
303D MET* 3.3 13.2 + - - +
304D ALA 3.7 1.6 + - - -
334D ALA* 4.4 1.1 - - - -
341D MET* 3.4 23.0 - - - +
374D ILE 2.9 9.7 + - - -
375D GLY 3.2 9.2 - - - -
376D ALA* 3.9 4.0 - - - -
500D NAP 3.9 13.7 - - - -
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Residues in contact with TYR 301 (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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144D LYS* 5.1 8.5 + - - -
300D GLY* 1.3 71.6 - - - -
302D GLY* 1.3 56.2 + - - +
304D ALA* 3.0 16.9 + - + +
305D LEU* 2.9 72.5 + - + +
335D GLY* 4.2 10.2 - - - -
336D ARG* 3.4 65.0 + - + +
340D HIS* 5.1 4.0 - + - -
375D GLY 3.1 3.2 + - - -
500D NAP 3.8 35.5 + + - +
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Residues in contact with GLY 302 (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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301D TYR* 1.3 75.5 - - - +
303D MET* 1.3 62.7 + - - +
306D SER 3.4 17.5 + - - -
375D GLY* 2.9 16.6 + - - -
436D ALA* 3.7 9.6 - - - +
500D NAP 3.3 47.0 + - - -
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Residues in contact with MET 303 (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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299D PRO* 3.8 8.7 - - + -
300D GLY 3.3 8.3 + - - +
301D TYR 3.3 0.4 - - - -
302D GLY* 1.3 75.8 - - - +
304D ALA* 1.3 57.6 + - - +
307D GLN* 3.1 6.2 + - - -
308D ALA* 2.8 40.5 + - + -
309D GLN* 3.6 27.6 - - + +
312D LEU* 3.7 28.7 - - + -
341D MET* 3.8 30.3 - - + -
344D LEU* 3.8 35.4 - - + -
345D LEU* 4.9 7.6 - - + -
374D ILE* 3.9 21.7 - - + +
375D GLY* 4.2 4.2 - - - -
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Residues in contact with ALA 304 (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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79D THR* 4.9 1.8 - - - +
300D GLY 3.7 2.1 + - - +
301D TYR* 3.0 24.8 + - + +
303D MET* 1.3 77.4 - - - +
305D LEU* 1.3 67.0 + - - +
307D GLN* 2.7 34.1 + - - +
340D HIS* 4.0 26.5 - - + +
341D MET* 5.3 1.6 - - + -
344D LEU* 4.0 14.4 - - + -
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Residues in contact with LEU 305 (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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301D TYR* 2.9 61.2 + - + +
302D GLY 3.6 0.2 + - - -
304D ALA* 1.3 72.5 - - - +
306D SER* 1.3 59.1 + - - +
307D GLN* 4.9 2.4 - - - +
410D ARG* 5.8 3.6 - - - +
500D NAP 3.6 32.8 - - + +
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Residues in contact with SER 306 (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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302D GLY 3.4 2.9 + - - -
304D ALA 3.2 0.2 - - - -
305D LEU* 1.3 78.5 - - - +
307D GLN* 1.3 66.8 + - - +
308D ALA 4.5 1.1 - - - -
435D ASP* 2.8 32.1 + - - -
436D ALA* 3.6 22.2 + - - -
437D GLN* 3.0 23.5 + - - +
500D NAP 3.1 19.5 - - - -
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Residues in contact with GLN 307 (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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79D THR* 4.2 24.4 + - - +
303D MET 3.1 2.1 + - - -
304D ALA* 2.7 34.9 + - - +
305D LEU 4.9 1.8 - - - +
306D SER* 1.3 81.7 - - - +
308D ALA* 1.3 60.8 + - - +
309D GLN* 2.7 45.9 + - - +
310D HIS* 4.6 4.2 + - - +
311D LYS* 5.4 0.5 + - - +
344D LEU* 4.2 9.4 - - - +
347D GLU* 5.2 4.5 - - - +
437D GLN* 2.9 15.9 - - - +
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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