Contacts of the helix formed by residues 52 - 59 (chain A) in PDB entry 2QCU
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A HIS* 3.4 20.0 - - - -
51A GLY* 1.3 77.8 - - - +
53A LEU* 1.3 68.5 + - - +
54A ARG* 3.1 4.5 - - - -
55A TYR* 2.8 42.0 + - - +
56A LEU 3.9 2.3 + - - -
64A VAL* 4.0 3.1 - - - +
108A TYR* 3.2 7.5 + - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 4.8 2.0 - - - -
52A GLY* 1.3 74.1 - - - +
54A ARG* 1.3 62.2 + - - +
55A TYR 3.2 0.3 + - - -
56A LEU* 3.3 16.4 + - + +
89A LEU* 5.0 3.8 - - + -
104A GLY 4.5 4.0 - - - +
105A LEU* 4.2 8.3 - - + -
108A TYR* 3.2 52.4 + - + +
141A TYR* 3.7 35.9 - - + +
247A ILE* 4.5 11.4 - - + -
801A BOG 3.5 59.2 + - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 2.9 2.3 + - - -
53A LEU* 1.3 78.2 - - - +
55A TYR* 1.3 79.5 + - + +
56A LEU 3.2 0.2 - - - -
57A GLU* 3.6 4.9 + - - +
58A HIS* 3.4 29.7 + - - -
96A ARG* 6.1 0.4 - - - +
247A ILE* 6.1 0.4 - - + -
253A LYS 5.8 2.5 + - - +
254A ARG* 5.6 8.4 - - - +
255A ILE* 3.7 38.1 - - + +
272A ASP* 4.2 3.0 + - - -
328A GLN* 3.1 41.5 + - - +
332A ARG* 3.1 24.9 - - - +
801A BOG 3.0 32.7 + - - +
804A PO4 2.9 31.6 + - - -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 4.4 1.5 + - - -
51A GLY 4.1 5.2 - - - -
52A GLY* 2.8 31.8 + - - +
54A ARG* 1.3 102.4 - - + +
56A LEU* 1.3 60.4 + - - +
58A HIS* 3.0 24.4 + + - -
59A TYR 3.2 8.5 + - - -
60A GLU* 3.2 24.6 + - + +
63A LEU* 3.8 21.1 - - + -
64A VAL* 3.7 11.4 - - + -
332A ARG* 3.4 21.5 - - + +
354A LYS* 2.9 41.0 + - + -
804A PO4 2.7 29.3 + - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.3 15.4 + - + +
54A ARG 3.2 0.6 - - - -
55A TYR* 1.3 74.1 - - - +
57A GLU* 1.3 57.1 + - - +
58A HIS 3.0 4.7 - - - -
59A TYR* 2.9 27.1 + - - +
60A GLU 4.8 0.9 - - - +
61A PHE* 3.9 27.9 - - + -
64A VAL* 4.1 17.0 - - + -
104A GLY 3.9 21.1 - - - +
107A MET* 4.0 21.1 - - + -
108A TYR* 4.3 18.4 - - + +
111A LEU* 3.8 23.1 - - + -
801A BOG 3.5 26.9 - - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.7 6.5 - - - +
56A LEU* 1.3 75.6 - - - +
58A HIS* 1.3 68.0 + - + +
59A TYR* 3.4 16.7 - - - -
96A ARG* 2.6 49.0 + - - +
100A MET* 4.2 9.1 - - - +
253A LYS* 4.6 9.7 - - - +
801A BOG 3.2 53.3 + - + +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.4 35.6 + - - -
55A TYR* 3.0 15.0 + + - +
57A GLU* 1.3 84.2 + - + +
59A TYR* 1.3 79.3 + - - +
60A GLU* 3.4 26.9 - - + +
328A GLN* 4.1 14.1 + - + +
329A ALA* 3.8 35.4 + - + +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 2.9 16.6 + - - -
57A GLU 4.0 14.7 + - - -
58A HIS* 1.3 87.1 - - - +
60A GLU* 1.3 56.1 + - - +
61A PHE* 2.8 48.5 + + + -
801A BOG 3.4 39.5 - - + +
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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