Contacts of the helix formed by residues 49 - 58 (chain B) in PDB entry 2QA5
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 GLY 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B GLY 3.5 0.4 - - - -
48B LEU* 1.3 78.6 - - - +
50B LYS* 1.3 59.7 + - - +
51B SER 3.5 0.9 - - - -
52B THR* 3.2 5.4 - - - +
53B LEU* 3.0 32.4 + - - +
152B PHE* 4.8 2.7 - - - -
241B GLY* 5.5 0.3 + - - -
316B GDP 3.0 45.0 + - - -
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Residues in contact with LYS 50 (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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42B VAL* 3.9 23.2 - - + +
43B VAL* 5.2 0.4 - - - -
44B GLY* 3.7 21.8 - - - +
45B GLU 3.3 36.8 + - - +
46B SER* 4.0 10.1 - - - +
48B LEU* 4.8 1.1 - - - -
49B GLY* 1.3 80.4 - - - +
51B SER* 1.3 57.2 + - - +
53B LEU* 3.9 1.6 - - - +
54B ILE* 3.1 30.9 + - - +
99B VAL* 5.5 8.8 - - + +
100B VAL 5.6 4.3 + - - +
152B PHE* 3.6 36.0 - - + -
316B GDP 2.6 40.1 + - - +
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Residues in contact with SER 51 (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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50B LYS* 1.3 76.1 - - - +
52B THR* 1.3 63.0 + - - +
53B LEU 3.4 0.4 - - - -
54B ILE* 4.2 10.1 - - - +
55B ASN* 3.4 30.1 + - - +
99B VAL* 5.4 12.8 - - - -
316B GDP 2.4 36.6 + - - -
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Residues in contact with THR 52 (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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49B GLY 3.2 14.6 - - - +
51B SER* 1.3 80.8 - - - +
53B LEU* 1.3 56.3 + - - +
55B ASN* 3.7 6.2 - - - +
56B SER* 3.2 24.4 + - - -
241B GLY* 4.2 6.7 - - - +
242B SER* 3.8 20.8 + - - -
243B ASN* 4.3 5.7 + - - +
316B GDP 2.8 63.0 + - + +
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Residues in contact with LEU 53 (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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49B GLY 3.0 20.5 + - - +
50B LYS* 3.9 2.5 - - - +
52B THR* 1.3 76.6 - - - +
54B ILE* 1.3 61.7 + - + +
55B ASN 3.2 1.8 - - - -
56B SER* 3.1 2.3 + - - +
57B LEU* 2.9 37.2 + - + +
150B PHE* 5.5 2.2 - - + -
152B PHE* 3.7 30.1 - - + -
180B VAL* 4.7 2.9 - - + -
239B VAL* 4.0 29.2 - - + -
240B VAL 3.7 31.2 - - - +
241B GLY* 3.7 7.2 - - - +
273B PHE* 4.1 14.1 - - + -
276B LEU* 5.2 7.9 - - + -
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Residues in contact with ILE 54 (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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40B LEU* 4.0 13.0 - - + -
42B VAL* 3.7 30.3 - - + -
50B LYS 3.1 17.5 + - - +
51B SER* 4.2 11.2 - - - +
53B LEU* 1.3 80.2 - - + +
55B ASN* 1.3 66.8 + - - +
57B LEU* 3.5 9.3 - - + +
58B PHE* 3.2 34.8 - - + +
62B LEU* 5.6 1.8 - - + -
97B LEU* 3.3 42.2 - - + +
99B VAL* 5.8 6.7 - - + -
150B PHE* 4.2 17.5 - - + -
152B PHE* 5.4 2.9 - - + -
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Residues in contact with ASN 55 (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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51B SER* 3.4 20.1 + - - +
52B THR* 3.7 7.5 - - - +
54B ILE* 1.3 85.0 - - - +
56B SER* 1.3 63.0 + - - +
58B PHE 3.6 0.9 + - - -
59B LEU* 3.4 12.3 + - - -
60B THR 2.8 24.0 + - - +
61B ASP* 3.3 22.8 + - + +
62B LEU* 2.9 46.7 + - - +
243B ASN* 6.1 5.8 - - + -
254B ARG* 5.3 0.6 + - - -
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Residues in contact with SER 56 (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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52B THR 3.2 13.7 + - - -
53B LEU* 3.1 8.5 + - - -
55B ASN* 1.3 76.1 - - - +
57B LEU* 1.3 69.1 + - - +
58B PHE 3.0 0.9 + - - -
59B LEU* 3.2 20.3 - - - +
241B GLY* 4.6 1.3 - - - -
242B SER 3.8 15.6 + - - -
254B ARG* 3.2 34.5 + - - +
265B VAL* 4.8 6.1 - - - +
273B PHE* 3.5 21.8 - - - -
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Residues in contact with LEU 57 (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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53B LEU* 2.9 18.3 + - + +
54B ILE* 3.5 15.7 - - + +
55B ASN 3.2 0.2 - - - -
56B SER* 1.3 77.1 - - - +
58B PHE* 1.3 86.2 + - + +
150B PHE* 4.1 9.6 - - + -
273B PHE* 3.6 24.5 - - + -
276B LEU* 4.0 21.8 - - + -
277B ARG* 3.1 51.1 + - + +
280B LEU* 3.7 28.0 - - + -
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Residues in contact with PHE 58 (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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40B LEU* 4.4 5.8 - - + -
54B ILE* 3.2 33.4 - - + +
55B ASN 3.6 2.5 + - - +
56B SER 3.1 0.4 - - - -
57B LEU* 1.3 99.2 - - + +
59B LEU* 1.3 74.3 + - - +
60B THR* 3.2 15.7 + - - +
86B VAL* 4.7 22.7 - - + +
93B VAL* 6.3 2.0 - - + -
95B LEU* 3.6 35.4 - - + -
97B LEU* 4.4 6.7 - - + -
277B ARG* 5.5 0.4 - - - +
280B LEU* 3.9 28.0 - - + -
281B ILE* 4.8 16.8 - - + -
284B MSE 5.0 8.7 - - + -
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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