Contacts of the helix formed by residues 313 - 323 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LYS 4.7 9.3 + - - -
100C ASN 5.4 5.7 + - - -
310C PHE* 2.7 21.6 + - - +
311C VAL* 3.9 7.9 - - + +
312C THR* 1.3 70.9 - - - +
314C GLU* 1.3 59.2 + - - +
315C ASP* 2.8 40.8 + - - +
316C ILE* 3.1 28.1 + - + +
317C LEU* 2.8 30.6 + - - +
336C ILE* 3.9 20.5 - - + +
345C THR* 4.0 0.4 - - - -
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Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ASN* 1.3 73.5 + - - +
315C ASP* 1.3 61.3 + - - +
317C LEU* 3.3 3.1 + - - -
318C ARG* 2.8 46.6 + - - +
336C ILE* 5.0 2.0 - - - +
341C GLN* 5.4 0.8 - - - +
344C ARG* 2.7 67.6 + - + +
345C THR* 3.3 20.8 + - - +
348C LEU* 3.2 30.3 - - + +
351C ARG* 5.0 4.3 + - - -
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Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ASN* 2.8 19.0 + - - +
314C GLU* 1.3 74.9 - - - +
316C ILE* 1.3 64.5 + - + +
318C ARG* 3.5 18.5 + - - +
319C GLU* 3.3 27.4 + - - +
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Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 3.9 33.2 - - + +
288C PHE* 6.6 0.4 - - + -
309C LEU* 3.3 24.2 - - + +
310C PHE* 3.9 12.3 - - + +
311C VAL* 3.9 11.2 - - + -
313C ASN* 3.1 34.8 + - + +
315C ASP* 1.3 74.2 - - + +
317C LEU* 1.3 65.9 + - - +
319C GLU* 3.3 7.6 + - + +
320C GLY* 3.0 18.9 + - - -
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C PHE* 3.8 43.2 - - + -
313C ASN 2.8 18.8 + - - +
314C GLU 3.6 3.6 - - - +
316C ILE* 1.3 77.0 - - - +
318C ARG* 1.3 56.0 + - - +
320C GLY* 3.1 2.8 + - - -
321C ILE* 2.8 31.9 + - + +
329C VAL* 4.4 6.3 - - + -
345C THR* 3.6 37.9 - - + +
348C LEU* 3.8 15.5 - - + -
349C ALA* 3.9 18.6 - - + +
354C TYR* 3.9 21.5 - - + -
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Residues in contact with ARG 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 6.0 0.2 - - - +
413B LYS* 4.1 18.5 - - - +
414B LEU* 3.3 46.4 + - + +
314C GLU* 2.8 55.9 + - - +
315C ASP* 3.8 17.0 + - - +
316C ILE 3.2 0.2 - - - -
317C LEU* 1.3 73.6 - - - +
319C GLU* 1.3 69.2 + - - +
321C ILE* 3.3 8.1 + - - +
322C ILE* 3.1 37.8 + - + +
344C ARG* 4.6 3.4 - - - +
348C LEU* 3.7 17.7 - - + +
351C ARG* 4.9 1.4 - - - +
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP 3.3 12.1 + - - +
316C ILE* 3.3 9.3 + - - +
317C LEU 3.2 0.6 - - - -
318C ARG* 1.3 79.8 - - - +
320C GLY* 1.3 61.0 + - - +
322C ILE* 3.3 22.1 + - - +
323C LYS* 2.9 51.4 + - + +
325C MET* 5.8 0.9 - - - -
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C PHE* 4.1 14.8 - - - -
316C ILE 3.0 13.2 + - - -
317C LEU 3.1 4.9 + - - -
319C GLU* 1.3 76.5 - - - +
321C ILE* 1.3 59.7 + - - +
323C LYS 3.5 0.6 + - - -
324C LYS 3.0 3.8 + - - -
325C MET* 2.9 44.9 + - - -
354C TYR* 3.3 6.7 + - - -
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Residues in contact with ILE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 4.1 13.9 - - + -
317C LEU* 2.8 32.2 + - + +
318C ARG* 3.5 7.6 - - - +
319C GLU 3.3 0.2 - - - -
320C GLY* 1.3 71.9 - - - +
322C ILE* 1.3 64.0 + - - +
324C LYS* 3.2 16.8 + - - +
348C LEU* 3.8 33.7 - - + +
349C ALA* 4.8 0.7 - - - -
352C ASN* 3.7 40.4 - - + +
354C TYR* 3.5 33.3 + - + -
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Residues in contact with ILE 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 3.4 23.8 - - + -
318C ARG* 3.1 27.8 + - + +
319C GLU* 3.3 21.3 + - - +
321C ILE* 1.3 77.3 - - - +
323C LYS* 1.3 76.0 + - + +
324C LYS* 3.5 7.6 + - - +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ILE* 3.4 26.0 - - + +
319C GLU* 2.9 33.8 + - + +
322C ILE* 1.3 89.3 - - + +
324C LYS* 1.3 68.8 + - - +
325C MET* 3.4 32.5 - - + -
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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