Contacts of the helix formed by residues 326 - 336 (chain A) in PDB entry 6F3T
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLY* 5.0 9.4 - - - -
320A HIS* 2.9 61.6 + - + +
321A LEU* 3.9 5.5 - - - +
323A GLU* 2.9 26.6 + - - +
325A GLN* 1.3 89.2 + - - +
327A ASN* 1.3 63.0 + - - +
328A GLN 3.2 4.0 + - - -
329A ILE* 3.3 24.5 - - + +
330A TRP* 3.4 8.3 + - - +
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Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 4.6 1.3 - - - -
323A GLU 3.5 5.3 + - - +
324A LYS* 3.4 22.1 + - - +
325A GLN 3.4 3.4 + - - -
326A ASN* 1.3 77.3 - - - +
328A GLN* 1.3 79.5 + - + +
330A TRP* 3.6 25.0 + - - +
331A ASN* 3.3 34.3 + - - -
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Residues in contact with GLN 328 (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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208A GLN* 3.7 24.3 + - - +
209A GLY* 4.4 4.4 - - - -
217A TYR* 3.7 48.0 - - + +
325A GLN 5.8 2.0 - - - +
326A ASN 3.2 1.4 + - - -
327A ASN* 1.3 96.6 + - + +
329A ILE* 1.3 64.9 + - - +
331A ASN* 3.3 24.0 + - - +
332A ILE* 3.5 17.4 + - - +
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Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.9 32.8 - - + +
218A TYR* 4.4 3.6 - - + +
221A LEU* 4.4 23.8 - - + +
243A LEU* 4.6 14.1 - - + -
247A MET* 3.7 35.2 - - + -
320A HIS* 5.2 0.7 - - + -
321A LEU* 3.6 20.0 - - + -
326A ASN* 3.3 22.8 + - + +
328A GLN* 1.3 77.4 - - - +
330A TRP* 1.3 62.9 + - - +
332A ILE* 3.3 8.9 + - + +
333A VAL* 3.0 28.9 + - + +
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Residues in contact with TRP 330 (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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318A LYS* 5.3 6.6 - - + +
321A LEU* 3.6 46.6 - - + +
322A GLN* 3.8 40.8 - - + -
326A ASN 3.4 9.8 + - - +
327A ASN* 3.7 26.0 - - - +
328A GLN 3.2 0.6 - - - -
329A ILE* 1.3 81.2 - - - +
331A ASN* 1.3 61.1 + - - +
333A VAL* 3.3 7.9 + - + +
334A GLN* 2.9 60.8 + - + +
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Residues in contact with ASN 331 (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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208A GLN* 5.2 10.1 + - - +
327A ASN* 3.3 33.3 + - - +
328A GLN* 3.3 20.7 + - - +
329A ILE 3.3 0.6 - - - -
330A TRP* 1.3 79.7 - - - +
332A ILE* 1.3 59.8 + - + +
334A GLN* 3.4 16.9 + - - +
335A GLU* 3.0 30.7 + - - +
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Residues in contact with ILE 332 (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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214A TYR* 4.4 21.5 - - + +
217A TYR* 4.9 4.7 - - + -
243A LEU* 3.7 22.4 - - + -
246A HIS* 5.0 4.5 - - + -
247A MET* 4.0 40.8 - - + -
250A GLU* 5.0 6.1 - - - +
328A GLN 3.5 15.5 + - - +
329A ILE* 3.3 14.3 + - + +
330A TRP 3.3 0.4 - - - -
331A ASN* 1.3 76.5 - - + +
333A VAL* 1.3 62.4 + - - +
335A GLU* 4.5 0.9 - - - -
336A HIS* 3.0 43.8 + - + +
337A LEU* 4.8 0.9 - - - +
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Residues in contact with VAL 333 (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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221A LEU* 5.4 2.2 - - + -
239A LEU* 4.9 4.7 - - + -
243A LEU* 4.0 24.5 - - + -
321A LEU* 4.4 24.0 - - + -
329A ILE* 3.0 21.7 + - + +
330A TRP* 3.6 13.5 - - + +
332A ILE* 1.3 74.7 - - - +
334A GLN* 1.3 65.7 + - + +
337A LEU* 3.1 48.7 + - + +
339A ILE* 4.2 21.8 - - + -
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Residues in contact with GLN 334 (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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304A LYS* 2.6 32.9 + - - -
330A TRP* 2.9 66.1 + - + +
331A ASN* 3.8 16.7 - - - +
333A VAL* 1.3 79.1 - - + +
335A GLU* 1.3 51.8 + - - +
337A LEU 4.1 1.6 - - - +
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Residues in contact with GLU 335 (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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207A GLN* 5.1 10.3 - - - +
304A LYS* 3.3 23.2 - - - +
331A ASN 3.0 18.3 + - - +
332A ILE* 4.4 0.7 - - - -
333A VAL 3.2 0.2 - - - -
334A GLN* 1.3 78.3 - - - +
336A HIS* 1.3 90.1 + - + +
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Residues in contact with HIS 336 (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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207A GLN* 5.8 3.6 + - - -
243A LEU* 6.1 0.2 - - + -
246A HIS* 3.1 49.4 + + + +
250A GLU* 4.0 16.8 + - - -
301A ARG* 3.6 33.7 + - + -
303A SER 4.9 2.2 - - - -
304A LYS* 3.4 7.2 - - - +
305A PHE 3.0 20.9 + - - -
332A ILE* 3.0 33.9 + - + +
335A GLU* 1.3 100.2 + - + +
337A LEU* 1.3 67.2 + - + +
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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