Contacts of the helix formed by residues 22 - 29 (chain Y) in PDB entry 2Q4G
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 LEU 22 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5W GLN* 4.8 1.1 - - - +
7Y LEU* 4.1 18.2 - - + -
9Y ILE* 3.3 28.0 - - + -
14Y LEU* 4.4 10.3 - - + -
18Y ARG* 3.1 46.1 + - - +
19Y TRP* 2.6 45.3 + - + +
21Y GLU* 1.3 73.5 - - - +
23Y LEU* 1.3 54.4 + - + +
24Y PRO* 3.3 3.6 - - - -
25Y LEU* 2.7 47.7 + - + +
26Y LEU* 3.4 7.5 + - + +
34Y LEU* 4.6 3.4 - - + -
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Residues in contact with LEU 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y TRP* 2.8 60.3 - - + +
20Y ALA* 3.9 10.3 - - - +
22Y LEU* 1.3 75.2 - - + +
24Y PRO* 1.3 69.6 - - + +
26Y LEU* 2.7 29.9 + - + +
27Y GLN* 3.2 17.4 + - - +
46Y ASP* 4.2 36.3 - - + +
50Y ALA* 4.5 6.0 - - + +
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Residues in contact with PRO 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y ALA 3.8 11.2 - - - +
21Y GLU* 4.1 8.3 - - - +
22Y LEU 3.3 5.6 - - - -
23Y LEU* 1.3 92.3 - - + +
25Y LEU* 1.3 60.2 + - + +
27Y GLN* 3.0 29.2 + - + +
28Y GLN* 3.1 29.9 - - - +
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Residues in contact with LEU 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W GLN* 3.7 27.1 - - - +
25W LEU* 4.8 13.2 - - + -
5Y GLN* 5.4 2.9 - - - +
6Y SER 6.0 0.2 - - - +
7Y LEU* 3.6 28.0 - - + -
21Y GLU 3.5 20.2 - - - +
22Y LEU* 2.7 30.0 + - + +
24Y PRO* 1.3 74.6 - - + +
26Y LEU* 1.3 57.2 + - - +
27Y GLN 3.1 4.9 - - - -
28Y GLN* 4.4 8.1 - - - +
29Y CYS* 2.7 51.6 + - - +
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Residues in contact with LEU 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y LEU* 4.4 17.5 - - + -
19Y TRP* 4.1 28.5 - - + -
22Y LEU* 4.0 6.1 - - + +
23Y LEU* 2.7 30.8 + - + +
25Y LEU* 1.3 74.2 - - - +
27Y GLN* 1.3 59.1 + - - +
28Y GLN 3.4 0.2 - - - -
32Y VAL* 3.9 33.4 - - + -
34Y LEU* 4.4 10.8 - - + -
47Y ILE* 4.7 17.5 - - + -
50Y ALA* 3.7 19.4 - - + +
51Y LEU* 3.7 19.3 - - + +
54Y ASN* 3.0 18.4 + - - +
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Residues in contact with GLN 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y LEU* 3.6 14.8 - - - +
24Y PRO* 3.0 18.7 + - - +
26Y LEU* 1.3 80.1 - - - +
28Y GLN* 1.3 61.0 + - + +
50Y ALA* 3.5 32.6 - - - +
53Y VAL* 3.7 21.6 - - + +
54Y ASN* 3.0 25.2 - - - -
55Y PRO* 3.3 8.7 - - - +
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Residues in contact with GLN 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W ARG* 5.7 4.9 - - - +
21W GLU* 5.6 4.0 + - - -
25W LEU* 5.7 2.1 - - - +
3Y ASP* 4.6 5.6 + - - +
5Y GLN* 3.6 40.7 + - - +
24Y PRO* 3.1 28.4 - - - +
25Y LEU* 3.2 6.1 + - - +
27Y GLN* 1.3 86.2 - - + +
29Y CYS* 1.3 63.9 + - - +
30Y GLN* 3.6 2.3 + - - +
54Y ASN* 3.7 6.5 - - - +
55Y PRO* 4.9 4.5 - - - +
56Y ALA* 5.0 6.2 - - - +
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Residues in contact with CYS 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y GLN* 3.6 14.1 - - - +
6Y SER 3.8 30.3 - - - -
7Y LEU* 4.0 7.6 - - - -
25Y LEU* 2.7 44.0 + - - +
28Y GLN* 1.3 73.0 - - - +
30Y GLN* 1.3 63.0 + - - +
31Y VAL 3.5 14.8 - - - +
32Y VAL* 3.5 10.3 - - + -
54Y ASN* 2.9 24.5 + - - +
57Y LEU* 3.6 9.0 - - - +
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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