Contacts of the helix formed by residues 317 - 334 (chain w) in PDB entry 6AH0
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 ASN 317 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289w LYS 5.5 1.4 - - - -
290w GLY* 5.3 10.8 + - - -
313w ASP* 2.7 18.5 + - - +
314w THR* 5.3 0.4 - - - -
316w ARG* 1.3 71.6 - - - +
318w LYS* 1.3 61.7 + - - +
319w ASP 3.5 1.6 - - - -
320w ILE* 3.6 5.5 + - - +
321w ALA* 3.0 21.5 + - - -
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Residues in contact with LYS 318 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314w THR* 3.9 19.4 + - - +
315w GLU 4.8 0.6 - - - -
316w ARG 3.4 4.6 + - - +
317w ASN* 1.3 74.7 - - - +
319w ASP* 1.3 66.6 + - - +
321w ALA* 3.2 2.8 + - - +
322w PHE* 2.9 21.7 + - - -
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Residues in contact with ASP 319 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316w ARG 5.0 1.8 + - - -
317w ASN 3.5 0.2 - - - -
318w LYS* 1.3 74.6 - - - +
320w ILE* 1.3 56.3 + - - +
322w PHE* 3.4 1.4 + - - +
323w LEU* 2.9 25.8 + - - -
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Residues in contact with ILE 320 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234w SER* 5.9 2.9 - - - +
317w ASN* 3.6 7.0 + - - +
318w LYS 3.2 0.8 - - - -
319w ASP* 1.3 72.8 - - - +
321w ALA* 1.3 65.0 + - - +
323w LEU* 3.1 2.6 + - - +
324w GLU* 2.8 22.0 + - - -
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Residues in contact with ALA 321 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288w THR 5.4 3.1 - - - -
289w LYS* 5.0 15.7 - - - +
317w ASN 3.0 15.7 + - - -
318w LYS* 3.7 2.7 - - - +
320w ILE* 1.3 73.8 - - - +
322w PHE* 1.3 62.8 + - - +
324w GLU* 3.2 2.1 + - - +
325w ALA* 2.9 19.9 + - - -
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Residues in contact with PHE 322 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318w LYS 2.9 13.0 + - - -
319w ASP 3.8 3.1 - - - -
321w ALA* 1.3 74.6 - - - +
323w LEU* 1.3 56.7 + - - +
325w ALA* 3.3 2.6 + - - +
326w GLN* 2.9 25.1 + - - -
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Residues in contact with LEU 323 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237w LEU 5.4 4.4 - - - +
238w THR* 6.0 4.9 - - - +
241w GLY* 4.7 8.9 - - - -
319w ASP 2.9 15.2 + - - -
320w ILE* 3.1 4.4 + - - +
322w PHE* 1.3 72.7 - - - +
324w GLU* 1.3 65.7 + - - +
326w GLN* 3.3 2.3 + - - +
327w ILE* 2.9 20.6 + - - -
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Residues in contact with GLU 324 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237w LEU 6.0 2.2 - - - -
320w ILE 2.8 13.6 + - - -
321w ALA* 3.6 3.6 - - - +
323w LEU* 1.3 74.7 - - - +
325w ALA* 1.3 62.8 + - - +
327w ILE* 3.1 4.4 + - - +
328w TYR* 2.9 19.2 + - - -
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Residues in contact with ALA 325 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321w ALA 2.9 14.0 + - - -
322w PHE* 3.3 4.2 + - - +
324w GLU* 1.3 74.8 - - - +
326w GLN* 1.3 61.3 + - - +
328w TYR* 3.0 4.5 + - - +
329w GLU* 2.9 20.1 + - - -
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Residues in contact with GLN 326 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241w GLY 5.9 0.4 - - - -
322w PHE 2.9 14.4 + - - -
323w LEU* 3.3 3.8 + - - +
324w GLU 3.3 0.2 - - - -
325w ALA* 1.3 74.7 - - - +
327w ILE* 1.3 62.0 + - - +
329w GLU* 3.2 1.1 + - - +
330w TYR* 2.9 25.7 + - - +
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Residues in contact with ILE 327 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210w PHE* 4.8 1.7 - - - +
241w GLY* 4.5 19.1 - - - -
323w LEU 2.9 14.8 + - - -
324w GLU* 3.1 4.7 + - - +
326w GLN* 1.3 73.0 - - - +
328w TYR* 1.3 62.0 + - - +
330w TYR* 5.4 0.4 - - - +
331w VAL* 2.9 22.2 + - - +
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Residues in contact with TYR 328 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210w PHE* 3.5 26.5 - - - +
324w GLU 2.9 12.7 + - - -
325w ALA* 3.0 7.4 + - - +
327w ILE* 1.3 76.4 - - - +
329w GLU* 1.3 55.8 + - - +
331w VAL 3.3 0.2 + - - -
332w GLU* 2.9 24.4 + - - -
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Residues in contact with GLU 329 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325w ALA 2.9 15.2 + - - -
326w GLN* 3.9 1.3 - - - +
328w TYR* 1.3 72.6 - - - +
330w TYR* 1.3 57.0 + - - +
332w GLU* 3.3 3.0 + - - +
333w ILE* 2.9 23.7 + - - -
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Residues in contact with TYR 330 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244w LEU 5.9 7.0 - - - -
245w ASP* 6.1 3.1 - - - +
326w GLN 2.9 14.5 + - - -
327w ILE* 5.4 0.2 - - - +
329w GLU* 1.3 73.4 - - - +
331w VAL* 1.3 65.3 + - - +
333w ILE* 3.3 3.5 + - - +
334w LEU* 3.1 18.7 + - - -
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Residues in contact with VAL 331 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210w PHE 5.4 4.0 - - - -
327w ILE 2.9 18.7 + - - -
328w TYR 3.7 0.9 - - - -
330w TYR* 1.3 73.0 - - - +
332w GLU* 1.3 66.4 + - - +
334w LEU* 3.1 11.8 + - - +
335w GLY* 3.1 13.7 + - - -
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Residues in contact with GLU 332 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210w PHE 5.0 2.3 + - - -
328w TYR 2.9 15.3 + - - -
329w GLU* 3.3 5.1 + - - +
330w TYR 3.2 0.4 - - - -
331w VAL* 1.3 76.4 - - - +
333w ILE* 1.3 61.0 + - - +
334w LEU 3.1 1.0 + - - -
335w GLY* 3.2 12.2 + - - -
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Residues in contact with ILE 333 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42w ARG 6.1 1.6 - - - -
329w GLU 2.9 13.6 + - - -
330w TYR* 3.3 6.6 + - - +
332w GLU* 1.3 75.0 - - - +
334w LEU* 1.3 56.1 + - - +
335w GLY 3.5 0.4 + - - -
336w GLU 5.4 0.3 + - - -
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Residues in contact with LEU 334 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330w TYR 3.1 9.0 + - - -
331w VAL* 3.1 10.2 + - - +
332w GLU 3.0 1.0 - - - -
333w ILE* 1.3 79.1 - - - +
335w GLY* 1.3 64.2 + - - +
336w GLU 3.1 3.4 - - - -
337w GLN* 2.8 17.1 + - - +
338w ARG* 2.9 10.7 + - - -
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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