Contacts of the helix formed by residues 42 - 53 (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 ALA 42 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40Y THR* 3.2 6.1 + - - +
41Y GLU* 1.3 72.8 - - - +
43Y ARG* 1.3 56.4 + - + +
44Y CYS 2.7 15.7 + - - -
45Y LYS* 3.1 27.2 + - + +
46Y ASP* 4.0 2.4 + - - +
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Residues in contact with ARG 43 (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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14Y LEU* 4.2 22.0 + - - +
15Y SER 4.3 0.2 + - - -
16Y ASP* 3.2 25.5 + - - -
19Y TRP* 3.8 62.9 - - + +
37Y CYS 4.8 7.5 + - - -
38Y GLY 4.7 9.9 + - - -
39Y LEU* 4.9 6.0 - - + +
40Y THR* 2.8 45.0 + - - +
42Y ALA* 1.3 75.8 - - + +
44Y CYS* 1.3 60.3 + - - +
45Y LYS 3.4 0.2 - - - -
46Y ASP* 3.3 14.9 + - - +
47Y ILE* 3.0 30.4 + - + +
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Residues in contact with CYS 44 (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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40Y THR 3.3 5.7 + - - -
41Y GLU* 2.8 22.1 + - - +
42Y ALA 2.7 2.4 + - - -
43Y ARG* 1.3 75.7 - - - +
45Y LYS* 1.3 55.7 + - - +
47Y ILE* 2.7 30.3 + - - +
48Y SER* 2.8 14.4 + - - -
67Y LEU* 4.3 15.3 - - - -
71Y GLY* 2.9 39.0 - - - -
74Y CYS* 3.3 21.1 - - + -
75Y VAL* 3.8 13.9 - - + +
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Residues in contact with LYS 45 (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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41Y GLU 5.2 0.4 - - - +
42Y ALA* 3.1 15.6 + - - +
44Y CYS* 1.3 74.8 - - - +
46Y ASP* 1.3 62.6 + - - +
48Y SER* 3.2 8.4 + - - -
49Y SER* 3.0 26.3 + - - -
70Y VAL* 6.5 0.4 - - - -
74Y CYS* 3.8 23.1 - - - -
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Residues in contact with ASP 46 (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* 3.9 25.9 + - + +
23Y LEU* 4.2 22.7 - - + +
26Y LEU* 5.2 0.2 - - - +
42Y ALA 4.0 1.3 + - - -
43Y ARG* 3.3 18.1 + - - +
45Y LYS* 1.3 79.1 - - - +
47Y ILE* 1.3 61.8 + - - +
49Y SER* 3.6 7.4 + - - -
50Y ALA* 3.3 23.4 + - - +
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Residues in contact with ILE 47 (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* 4.1 21.5 - - + -
26Y LEU* 4.7 10.8 - - + -
34Y LEU* 5.1 2.9 - - + -
39Y LEU* 4.2 28.5 - - + -
40Y THR 5.6 0.2 - - - +
43Y ARG* 3.0 18.6 - - + +
44Y CYS* 2.7 17.5 + - - +
46Y ASP* 1.3 77.1 - - - +
48Y SER* 1.3 59.8 + - - +
50Y ALA* 3.3 4.3 + - - +
51Y LEU* 2.9 58.3 + - + +
60Y LEU* 5.5 1.1 - - + -
62Y LEU* 4.9 13.5 - - + -
67Y LEU* 5.5 1.1 - - + -
75Y VAL* 4.0 20.2 - - + -
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Residues in contact with SER 48 (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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44Y CYS 2.8 10.4 + - - -
45Y LYS* 3.4 12.1 - - - -
47Y ILE* 1.3 76.0 - - - +
49Y SER* 1.3 58.5 + - - +
51Y LEU* 3.1 3.9 + - - -
52Y ARG* 2.8 28.9 + - - +
74Y CYS* 3.0 20.1 + - - -
75Y VAL* 4.5 4.7 - - - +
77Y GLN* 3.7 5.8 + - - +
78Y GLY* 2.7 38.4 + - - -
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Residues in contact with SER 49 (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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45Y LYS 3.0 10.7 + - - -
46Y ASP* 3.6 12.9 + - - -
48Y SER* 1.3 79.2 + - - +
50Y ALA* 1.3 68.3 + - - +
52Y ARG* 3.1 28.5 + - - +
53Y VAL* 3.5 10.7 + - - +
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Residues in contact with ALA 50 (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* 4.5 9.6 - - + +
26Y LEU* 4.0 27.6 - - + -
27Y GLN* 3.5 28.5 - - + +
46Y ASP 3.3 17.0 + - - +
47Y ILE* 3.3 4.9 + - - +
48Y SER 3.2 0.6 - - - -
49Y SER* 1.3 81.0 + - - +
51Y LEU* 1.3 62.2 + - - +
53Y VAL* 3.2 19.8 + - - +
54Y ASN 3.5 4.2 + - - -
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Residues in contact with LEU 51 (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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26Y LEU* 3.7 26.2 - - + +
32Y VAL* 5.1 3.6 - - + -
47Y ILE* 2.9 45.1 + - + +
48Y SER* 3.7 3.8 - - - +
50Y ALA* 1.3 73.8 - - + +
52Y ARG* 1.3 66.7 + - - +
54Y ASN* 3.0 19.9 + - - +
57Y LEU* 3.9 30.7 - - + +
60Y LEU* 3.5 38.1 - - + -
75Y VAL* 4.1 11.2 - - + +
78Y GLY 4.3 10.0 - - - +
79Y LEU* 4.6 5.7 - - + +
81Y THR* 5.5 0.5 + - - -
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Residues in contact with ARG 52 (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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48Y SER 2.8 12.9 + - - +
49Y SER* 3.1 22.4 + - - +
51Y LEU* 1.3 78.8 - - - +
53Y VAL* 1.3 74.6 + - - +
54Y ASN 4.8 1.6 - - - +
78Y GLY* 3.7 13.2 + - - +
81Y THR* 3.4 32.1 + - + +
83Y SER* 5.2 5.2 + - - +
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Residues in contact with VAL 53 (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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27Y GLN* 3.7 31.8 - - + +
49Y SER 4.0 9.9 - - - +
50Y ALA 3.2 14.6 - - - +
52Y ARG* 1.3 101.2 - - - +
54Y ASN* 1.3 63.9 + - - +
55Y PRO* 3.1 12.8 - - - +
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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