Contacts of the helix formed by residues 52 - 60 (chain C) in PDB entry 1QNN
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 ASP 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 4.8 10.3 - - - -
50C ASN 4.2 0.8 + - - -
51C ALA* 1.3 76.3 - - - +
53C LEU* 1.3 65.2 + - - +
54C ASN* 3.2 27.2 + - - +
55C THR* 2.5 40.5 + - - -
56C ILE* 3.2 10.0 + - - +
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Residues in contact with LEU 53 (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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1C MET* 5.2 1.4 - - - -
3C HIS* 4.0 19.8 + - + +
39C LEU* 3.6 30.7 - - + -
51C ALA 3.9 1.2 + - - -
52C ASP* 1.3 72.5 + - - +
54C ASN* 1.3 64.9 + - - +
56C ILE* 3.3 9.6 + - + +
57C VAL* 3.0 26.9 + - - +
68C ALA* 4.0 17.9 - - + +
71C THR* 4.0 13.2 - - + -
72C LEU* 3.7 42.8 - - + +
75C ASN* 4.1 11.4 - - - +
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Residues in contact with ASN 54 (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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52C ASP* 3.1 15.0 + - - +
53C LEU* 1.3 81.4 - - - +
55C THR* 1.3 62.4 + - - +
57C VAL* 3.3 6.8 + - - +
58C GLN* 3.0 37.0 + - - +
72C LEU* 3.6 32.6 - - - +
146C VAL* 4.3 15.9 - - - +
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Residues in contact with THR 55 (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 PHE* 5.2 3.1 - - + -
51C ALA* 4.2 15.9 - - + -
52C ASP* 2.5 29.9 + - - -
54C ASN* 1.3 74.7 - - - +
56C ILE* 1.3 67.3 + - - +
58C GLN* 3.1 13.1 + - - +
59C LYS* 2.9 47.2 + - + +
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Residues in contact with ILE 56 (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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3C HIS* 3.8 25.6 - - + +
39C LEU* 4.5 3.1 - - + -
43C ILE* 4.7 5.2 - - + -
48C PHE* 3.8 36.3 - - + +
51C ALA* 3.7 24.0 - - + +
52C ASP 3.2 8.8 + - - +
53C LEU* 3.5 11.0 - - + +
55C THR* 1.3 76.9 - - - +
57C VAL* 1.3 53.8 + - - +
60C SER* 2.7 39.8 + - - +
64C ILE* 3.6 24.9 - - + -
68C ALA* 3.4 24.7 - - + -
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Residues in contact with VAL 57 (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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53C LEU* 3.0 20.9 + - + +
54C ASN 3.7 4.7 - - - +
55C THR 3.2 0.2 - - - -
56C ILE* 1.3 76.5 - - - +
58C GLN* 1.3 51.7 + - - +
60C SER* 4.5 0.7 - - - -
65C PHE* 3.4 21.6 - - + -
68C ALA* 3.7 33.7 - - + +
69C GLY* 3.9 4.0 - - - +
72C LEU* 3.8 18.8 - - + -
144C ASN* 4.5 11.0 - - + -
146C VAL* 3.3 27.6 - - + -
147C ARG* 2.6 33.6 + - + +
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Residues in contact with GLN 58 (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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54C ASN* 3.0 28.6 + - - +
55C THR* 3.1 13.7 + - - +
57C VAL* 1.3 79.0 - - - +
59C LYS* 1.3 63.7 + - + +
146C VAL* 3.3 36.4 + - + +
147C ARG* 3.2 26.2 + - - +
149C GLY* 4.7 9.1 - - - -
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Residues in contact with LYS 59 (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* 4.2 18.4 + - - +
48C PHE* 3.9 17.3 - - + -
55C THR* 2.9 33.1 + - + +
58C GLN* 1.3 86.9 - - + +
60C SER* 1.3 64.3 + - - +
61C GLU* 4.7 6.9 - - - +
147C ARG* 4.3 2.8 + - - +
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Residues in contact with SER 60 (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 PHE* 3.7 18.6 - - - -
56C ILE* 2.7 30.5 + - - +
58C GLN 3.9 0.2 - - - -
59C LYS* 1.3 74.2 - - - +
61C GLU* 1.3 63.6 + - - +
64C ILE* 3.5 26.3 - - - +
65C PHE* 3.1 27.6 + - - +
147C ARG* 2.9 30.1 + - - -
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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