Contacts of the helix formed by residues 317 - 323 (chain D) in PDB entry 3AP3
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 ALA 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D LEU* 4.8 7.4 - - + +
214D TRP* 4.0 20.2 - - + -
215D ASN* 3.7 5.4 - - + +
313D MET* 2.8 22.2 + - - +
314D ALA* 4.1 3.5 - - - +
316D ILE* 1.3 80.1 - - + +
318D PRO* 1.4 60.7 - - - +
319D MET 3.1 6.2 + - - -
320D LEU* 3.3 41.3 + - + +
321D ALA* 4.3 0.9 + - - +
327D PRO* 5.1 1.2 - - - +
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Residues in contact with PRO 318 (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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215D ASN* 3.6 13.7 - - - +
314D ALA* 3.6 17.3 - - + +
315D GLN 3.1 22.7 - - - +
316D ILE 3.5 2.5 - - - +
317D ALA* 1.4 80.2 - - - +
319D MET* 1.3 63.8 + - + +
321D ALA* 3.7 10.5 + - + +
322D GLN* 3.3 28.5 + - - +
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Residues in contact with MET 319 (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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214D TRP* 4.1 5.2 - - + -
215D ASN* 3.2 28.9 - - - +
218D ILE* 3.8 24.7 - - + -
219D GLU* 3.8 37.9 - - + +
222D TYR* 4.4 22.0 - - + -
317D ALA 3.1 0.8 - - - -
318D PRO* 1.3 76.5 - - + +
320D LEU* 1.3 67.7 + - - +
322D GLN* 2.9 24.7 + - + +
323D LEU* 2.8 44.8 + - + +
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Residues in contact with LEU 320 (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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184D ASP* 3.1 27.8 - - - +
185D GLY* 4.3 3.1 - - - +
186D ARG* 4.1 13.9 - - + +
211D LEU* 5.8 1.3 - - + -
214D TRP* 4.2 20.0 - - + -
313D MET* 3.9 29.2 - - + -
317D ALA* 3.3 33.4 + - + +
319D MET* 1.3 78.8 - - - +
321D ALA* 1.3 59.6 + - - +
323D LEU* 3.2 5.9 + - - +
325D TYR* 2.8 56.7 + - + +
327D PRO* 4.2 11.2 - - + -
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Residues in contact with ALA 321 (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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314D ALA* 6.4 0.7 - - + -
317D ALA 4.3 0.4 + - - -
318D PRO* 3.7 13.5 + - + +
319D MET 3.2 0.6 - - - -
320D LEU* 1.3 77.5 - - - +
322D GLN* 1.3 56.4 + - + +
324D GLY* 2.7 28.1 + - - -
325D TYR 3.2 9.8 + - - -
327D PRO* 4.4 18.1 - - + +
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Residues in contact with GLN 322 (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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222D TYR* 5.5 3.7 + - - -
318D PRO* 3.3 20.4 + - - +
319D MET* 2.9 28.8 + - + +
321D ALA* 1.3 73.9 - - + +
323D LEU* 1.3 59.9 + - - +
324D GLY 3.1 0.9 + - - -
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Residues in contact with LEU 323 (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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182D VAL* 3.7 22.4 - - + -
214D TRP* 4.3 21.5 - - + -
218D ILE* 3.6 28.3 - - + -
222D TYR* 3.6 39.5 - - + -
237D TYR* 3.5 36.2 + - - +
319D MET* 2.8 28.4 + - + +
322D GLN* 1.3 72.1 - - - +
324D GLY* 1.3 59.6 + - - +
325D TYR* 3.4 18.0 + - + -
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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