Contacts of the helix formed by residues 315 - 321 (chain A) in PDB entry 5AJO
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 LYS 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A ALA* 4.1 12.3 - - + +
215A ALA* 3.0 26.0 + - + +
216A GLN* 3.9 6.7 + - - +
217A ALA 2.8 26.8 + - - +
218A LYS 2.9 25.1 + - - +
219A VAL 4.2 0.2 - - - +
220A LEU* 3.9 32.5 - - + -
313A MET 3.3 3.0 + - - -
314A ASP* 1.3 71.2 - - - +
316A PHE* 1.3 83.1 + - + +
318A PHE* 3.3 3.3 + - + +
319A GLU* 3.0 47.5 + - + +
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.9 42.2 - - + -
245A ARG* 3.8 14.4 - - - +
314A ASP* 3.0 13.9 + - - +
315A LYS* 1.3 99.0 - - - +
317A TYR* 1.3 58.6 + - - +
319A GLU* 3.3 19.8 + - - +
320A GLU* 2.8 38.8 + - + +
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Residues in contact with TYR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 3.2 49.0 - - - +
246A THR* 3.6 35.8 - - + +
248A VAL* 4.4 5.4 - - + -
313A MET* 3.6 24.0 - - + -
314A ASP* 3.0 18.7 + - + +
316A PHE* 1.3 74.8 - - - +
318A PHE* 1.3 65.5 + - - +
320A GLU* 4.2 7.0 - - + -
321A LEU* 2.9 69.0 + - + +
342A VAL* 5.0 0.7 - - + -
345A CYS 4.4 1.8 + - - -
346A GLY 4.0 1.9 - - - -
347A GLY* 3.2 29.4 + - - -
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 4.5 7.0 - - + -
212A ALA* 3.6 26.0 - - + -
220A LEU* 3.6 22.9 - - + -
222A PHE* 4.2 14.8 - + - -
313A MET* 3.7 30.8 - - + +
314A ASP 2.9 14.2 + - - +
315A LYS* 3.4 7.4 - - + +
317A TYR* 1.3 76.8 - - - +
319A GLU* 1.3 68.5 + - + +
321A LEU* 4.1 1.7 - - - +
322A GLY 3.5 2.9 + - - -
323A LYS* 2.8 76.0 + - + +
324A TYR* 4.0 26.7 - + - -
338A ILE* 4.8 4.0 - - + -
341A ARG* 4.9 0.3 + - - -
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA 4.9 4.9 - - - +
213A ASP* 5.3 4.2 - - - +
315A LYS* 3.0 43.9 + - + +
316A PHE* 3.6 23.1 - - - +
318A PHE* 1.3 81.2 - - + +
320A GLU* 1.3 67.6 + - + +
322A GLY* 3.1 13.7 + - - -
323A LYS* 3.9 33.0 + - - +
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 2.7 45.2 + - - -
316A PHE* 2.8 26.1 + - - +
317A TYR* 3.8 8.5 - - + +
319A GLU* 1.3 73.9 - - + +
321A LEU* 1.3 62.0 + - + +
322A GLY* 3.4 1.0 + - - -
417A LEU* 4.6 4.2 - - - +
420A LYS* 5.2 3.6 - - - -
421A LEU* 3.7 18.0 - - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A MET* 4.2 5.4 - - + -
317A TYR* 2.9 62.1 + - + +
318A PHE 4.2 1.8 - - - +
320A GLU* 1.3 77.7 - - + +
322A GLY* 1.3 56.4 + - - +
323A LYS 3.8 0.2 - - - -
341A ARG* 2.9 48.6 + - + +
342A VAL* 3.9 33.0 - - + +
345A CYS* 4.1 21.5 - - + +
417A LEU* 3.6 5.5 - - - +
421A LEU* 3.7 20.1 - - + +
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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