Contacts of the helix formed by residues 313 - 323 (chain B) in PDB entry 3QN3
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 313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B LYS 4.7 9.3 + - - -
100B ASN 5.4 5.1 + - - -
310B PHE* 2.8 16.9 + - - +
311B VAL* 3.7 8.5 - - + +
312B THR* 1.3 77.0 - - - +
314B GLU* 1.3 58.8 + - - +
315B ASP* 2.9 29.6 + - - +
316B ILE* 3.1 27.2 + - + +
317B LEU* 2.9 31.1 + - - +
336B ILE* 3.9 20.2 - - + +
345B THR* 3.9 0.9 - - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ASN* 1.3 71.7 + - - +
315B ASP* 1.3 62.9 + - - +
317B LEU* 3.3 2.0 + - - -
318B ARG* 2.8 44.3 + - - +
336B ILE* 5.1 1.8 - - - +
341B GLN 5.4 0.7 - - - +
344B ARG* 2.7 68.7 + - + +
345B THR* 3.2 21.2 + - - +
348B LEU* 3.2 31.6 - - + +
351B ARG* 5.1 3.1 + - - -
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASN* 2.9 17.8 + - - +
314B GLU* 1.3 75.3 - - - +
316B ILE* 1.3 68.6 + - + +
318B ARG* 3.1 29.3 + - - +
319B GLU* 3.3 25.5 + - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 4.1 23.3 - - + +
288B PHE* 6.6 0.2 - - + -
309B LEU* 3.3 24.9 - - + +
310B PHE* 3.9 11.1 - - + +
311B VAL* 3.9 27.1 - - + -
313B ASN* 3.1 25.0 + - + +
315B ASP* 1.3 78.1 - - + +
317B LEU* 1.3 62.7 + - - +
319B GLU* 3.3 7.2 + - - +
320B GLY* 3.1 18.5 + - - -
325B MET* 5.6 1.9 - - + +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 3.7 43.4 - - + -
313B ASN 2.9 17.7 + - - +
314B GLU 3.6 3.1 - - - +
316B ILE* 1.3 75.1 - - - +
318B ARG* 1.3 59.2 + - - +
320B GLY* 3.2 1.2 + - - -
321B ILE* 2.8 38.6 + - + +
329B VAL* 4.3 7.4 - - + -
345B THR* 3.6 37.2 - - + +
348B LEU* 4.0 11.9 - - + -
349B ALA* 3.7 18.4 - - + +
354B TYR* 4.1 18.6 - - + -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU* 2.8 33.4 + - - +
315B ASP* 3.1 37.9 + - - +
316B ILE 3.2 0.2 - - - -
317B LEU* 1.3 75.7 - - - +
319B GLU* 1.3 68.2 + - - +
321B ILE* 3.1 8.8 + - - +
322B ILE* 3.0 39.1 + - + +
344B ARG* 5.7 0.2 - - - +
348B LEU* 3.7 29.0 - - + +
351B ARG* 5.6 0.6 - - - +
413C LYS* 5.8 5.2 - - - +
414C LEU* 4.2 28.1 + - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ASP 3.3 12.5 + - - +
316B ILE* 3.8 8.7 - - + +
317B LEU 3.3 0.4 - - - -
318B ARG* 1.3 82.1 + - - +
320B GLY* 1.3 62.6 + - - +
322B ILE* 3.3 20.7 + - - +
323B LYS* 3.0 53.5 + - + +
325B MET* 4.7 2.7 - - + -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 4.0 11.0 - - - -
316B ILE 3.1 14.3 + - - -
317B LEU 3.5 3.6 - - - -
319B GLU* 1.3 77.6 - - - +
321B ILE* 1.3 60.9 + - - +
323B LYS 3.4 0.7 + - - -
324B LYS 2.9 18.4 + - - -
325B MET* 3.0 37.4 + - - +
354B TYR* 3.4 5.6 + - - -
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B LEU* 2.8 33.4 + - + +
318B ARG* 3.4 7.6 - - - +
320B GLY* 1.3 71.4 - - - +
322B ILE* 1.3 65.3 + - - +
324B LYS* 3.2 16.8 + - - +
348B LEU* 3.7 35.7 - - + +
349B ALA* 4.7 0.7 - - - -
352B ASN* 3.9 39.0 - - + +
354B TYR* 3.6 33.1 + - + -
414C LEU* 4.2 12.3 - - + -
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ARG* 3.0 32.3 + - + +
319B GLU* 3.7 28.3 - - - +
320B GLY 3.3 0.2 - - - -
321B ILE* 1.3 79.8 - - - +
323B LYS* 1.3 76.1 + - + +
324B LYS* 3.5 9.2 + - - +
414C LEU* 3.6 20.2 - - + -
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ILE* 3.6 28.5 - - + +
319B GLU* 3.0 37.8 + - + +
320B GLY 4.3 1.6 - - - +
322B ILE* 1.3 86.3 - - + +
324B LYS* 1.3 72.3 + - - +
325B MET* 3.5 17.0 - - + -
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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