Contacts of the helix formed by residues 332 - 337 (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 LYS 332 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C ASP* 3.2 27.5 + - - +
308C ASP* 5.7 0.6 + - - -
312C THR* 3.1 14.4 + - - +
330C LEU* 3.6 22.4 - - + +
331C ILE* 1.3 72.9 - - - +
333C PRO* 1.3 64.9 - - - +
334C ASN* 3.2 2.7 - - - +
335C GLN* 2.8 58.5 + - + +
359C SER* 3.8 14.1 - - - +
360C HIS 3.8 14.4 - - - +
361C ARG* 3.5 38.6 - - - +
383C LYS* 5.6 2.1 - - - +
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Residues in contact with PRO 333 (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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38C PRO* 6.3 2.9 - - + -
111C LEU* 4.0 22.6 - - + +
115C MET* 5.9 1.6 - - - -
331C ILE 3.5 11.0 - - - +
332C LYS* 1.3 83.3 - - - +
334C ASN* 1.3 59.5 + - - +
336C ILE* 3.1 7.5 + - + +
337C GLY* 2.9 25.8 + - - -
339C ILE* 5.2 1.3 - - + -
342C THR* 3.4 33.6 + - + +
358C MET* 4.3 2.7 - - - -
359C SER 4.2 9.0 - - - +
369C PHE* 6.1 0.9 - - + -
370C ILE* 4.3 15.9 - - + -
373C PHE* 4.2 20.0 - - + -
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 4.1 12.2 - - + +
38C PRO* 3.1 31.5 + - + +
39C SER 3.5 0.6 - - - -
40C GLY* 3.4 23.2 - - - +
48C ALA* 4.4 2.4 - - - +
50C GLU* 4.8 3.0 + - - +
107C ALA* 3.7 23.7 - - - +
108C ASN* 6.2 0.4 - - - +
111C LEU* 3.5 25.3 - - + +
332C LYS* 3.2 2.4 - - - +
333C PRO* 1.3 80.7 - - - +
335C GLN* 1.3 59.6 + - - +
336C ILE 3.4 0.9 + - - -
337C GLY 4.1 1.6 - - - +
361C ARG* 2.6 39.2 + - - +
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Residues in contact with GLN 335 (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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47C GLU* 3.1 40.8 - - + +
48C ALA* 3.0 31.4 + - - +
307C ASP* 4.5 8.4 + - - +
308C ASP* 5.4 2.4 - - - +
311C VAL* 3.3 37.3 - - - +
312C THR* 2.8 28.8 + - - +
330C LEU 5.1 1.2 + - - -
332C LYS* 2.8 42.4 + - + +
334C ASN* 1.3 81.5 + - - +
336C ILE* 1.3 59.1 - - - +
361C ARG* 4.2 7.3 + - - +
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Residues in contact with ILE 336 (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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48C ALA* 4.0 8.2 - - + +
100C ASN 6.1 0.7 - - - +
102C TYR* 3.2 22.3 - - - -
311C VAL 4.7 1.1 - - - +
312C THR* 3.8 24.0 - - + +
313C ASN* 3.9 38.8 - - + +
314C GLU 5.0 1.6 - - - +
333C PRO 3.1 4.7 + - - +
335C GLN* 1.3 85.6 - - - +
337C GLY* 1.3 57.7 + - - +
338C THR 3.7 3.0 + - - +
341C GLN* 3.9 24.4 + - + +
342C THR* 3.3 40.8 - - - +
345C THR* 4.9 0.9 - - - +
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Residues in contact with GLY 337 (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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102C TYR* 4.1 6.1 - - - -
107C ALA* 4.2 12.6 - - - -
110C THR* 2.9 26.2 + - - -
111C LEU* 2.9 26.3 + - - -
333C PRO 2.9 12.2 + - - -
334C ASN 4.0 2.0 + - - -
335C GLN 3.9 0.2 - - - -
336C ILE* 1.3 76.8 - - - +
338C THR* 1.3 63.0 + - - +
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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