Contacts of the helix formed by residues 36 - 48 (chain Y) in PDB entry 5A31
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 ASN 36 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230X VAL* 3.5 26.3 - - + +
37Y VAL* 1.3 66.2 + - - +
38Y ILE* 3.3 3.7 - - - +
39Y ASP* 3.2 33.9 + - - +
40Y HIS* 2.9 52.7 + - - -
75Y GLN* 5.6 5.3 - - - +
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Residues in contact with VAL 37 (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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201X LEU* 4.9 2.8 - - + +
229X THR* 5.3 0.9 - - + -
230X VAL* 3.3 29.1 - - + +
232X ASN* 4.0 23.6 - - + +
233X LEU* 4.1 24.5 - - + -
36Y ASN* 1.3 75.5 - - - +
38Y ILE* 1.3 61.6 + - + +
40Y HIS* 3.2 10.0 + - - +
41Y VAL* 3.0 25.0 + - + +
56Y LEU* 5.9 1.1 - - + -
60Y LEU* 3.7 40.2 - - + -
71Y PHE* 4.7 8.7 - - + -
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Residues in contact with ILE 38 (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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36Y ASN* 3.3 2.3 - - - +
37Y VAL* 1.3 77.0 - - + +
39Y ASP* 1.3 64.7 + - - +
41Y VAL* 3.0 9.5 + - + +
42Y ARG* 2.8 28.3 + - + +
60Y LEU* 4.9 3.8 - - + -
71Y PHE* 4.0 29.2 - - + -
75Y GLN* 4.0 30.1 - - + +
78Y GLN* 3.8 36.8 - - + +
79Y LEU* 3.8 36.1 - - + +
82Y TYR* 6.3 0.4 - - + -
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Residues in contact with ASP 39 (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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36Y ASN* 3.4 39.4 + - - +
38Y ILE* 1.3 80.0 - - - +
40Y HIS* 1.3 56.8 + - - +
42Y ARG* 3.2 29.2 + - - +
43Y ASP* 3.0 37.4 + - - +
75Y GLN* 5.7 2.8 + - - +
78Y GLN* 5.8 1.6 + - - +
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Residues in contact with HIS 40 (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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199X CYS* 4.7 8.8 - - - -
200X PRO* 5.2 7.8 - - + +
201X LEU* 3.0 36.3 - - + -
229X THR* 6.3 4.6 - - + +
230X VAL* 5.0 4.0 - - + +
36Y ASN* 2.9 51.4 + - - -
37Y VAL* 3.3 8.6 - - - +
38Y ILE 3.1 0.4 - - - -
39Y ASP* 1.3 77.3 - - + +
41Y VAL* 1.3 55.1 + - - +
43Y ASP* 3.2 19.0 + - + +
44Y MET* 3.0 30.7 + - - +
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Residues in contact with VAL 41 (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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37Y VAL* 3.0 13.7 + - + +
38Y ILE* 3.0 15.4 + - + +
40Y HIS* 1.3 72.2 - - - +
42Y ARG* 1.3 59.5 + - - +
44Y MET* 3.3 7.6 + - - +
45Y ALA 2.9 24.1 + - - -
53Y VAL* 4.1 16.1 - - + +
56Y LEU* 3.7 28.9 - - + -
57Y SER* 5.0 11.2 - - - -
60Y LEU* 3.8 20.4 - - + -
79Y LEU* 5.5 6.3 - - + -
82Y TYR* 3.5 25.9 - - + -
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Residues in contact with ARG 42 (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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38Y ILE 2.8 11.8 + - - +
39Y ASP* 3.3 31.3 + - - +
41Y VAL* 1.3 74.7 - - - +
43Y ASP* 1.3 64.0 + - - +
45Y ALA* 3.1 4.5 + - - +
46Y ALA* 2.8 26.9 + - + +
78Y GLN* 4.4 17.8 + - - +
82Y TYR* 2.9 33.8 + - + +
132Y LEU* 5.0 19.5 - - - +
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Residues in contact with ASP 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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199X CYS* 5.9 3.1 - - + -
39Y ASP* 3.0 20.6 + - - +
40Y HIS* 3.4 25.9 + - + +
41Y VAL 3.2 0.2 - - - -
42Y ARG* 1.3 84.3 + - - +
44Y MET* 1.3 59.7 + - + +
46Y ALA* 3.3 10.9 + - - +
47Y ALA* 3.0 24.1 + - - +
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Residues in contact with MET 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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199X CYS* 3.6 28.9 - - + -
201X LEU* 4.2 5.6 - - - +
202X ALA* 3.7 17.0 - - - -
40Y HIS 3.0 17.9 + - - +
41Y VAL* 3.3 6.3 + - - +
43Y ASP* 1.3 74.4 - - - +
45Y ALA* 1.3 58.1 + - - +
47Y ALA* 3.0 8.3 + - - +
48Y GLY 2.9 22.2 + - - -
49Y LEU* 3.6 21.5 + - + +
52Y ASN* 3.3 46.2 - - + +
53Y VAL* 3.4 15.0 - - + +
56Y LEU* 3.9 24.7 - - + -
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Residues in contact with ALA 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 VAL 2.9 7.7 + - - -
42Y ARG 3.1 0.2 + - - -
44Y MET* 1.3 73.7 - - - +
46Y ALA* 1.3 64.7 + - - +
48Y GLY* 3.0 17.0 + - - +
49Y LEU 5.1 0.2 - - - +
53Y VAL* 3.8 12.7 - - + +
82Y TYR* 3.1 43.7 - - + -
85Y ASP* 5.3 7.0 - - + +
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Residues in contact with ALA 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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170X LYS* 5.1 5.2 + - - -
42Y ARG* 2.8 13.7 + - + +
43Y ASP* 3.3 13.9 + - - +
45Y ALA* 1.3 75.4 - - - +
47Y ALA* 1.3 62.0 + - - +
48Y GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 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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169X PRO* 4.4 20.9 - - + -
170X LYS* 3.2 40.0 + - + +
43Y ASP 3.0 11.7 + - - +
44Y MET* 3.0 11.7 + - - +
46Y ALA* 1.3 75.6 - - - +
48Y GLY* 1.3 59.9 + - - +
49Y LEU* 3.4 22.0 - - + -
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Residues in contact with GLY 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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140X TYR* 5.2 5.2 + - - -
170X LYS* 5.4 1.7 - - - +
44Y MET 2.9 5.6 + - - -
45Y ALA* 3.0 17.0 + - - -
46Y ALA 4.1 1.3 - - - -
47Y ALA* 1.3 79.5 - - - +
49Y LEU* 1.3 59.4 + - - +
50Y HIS* 3.3 27.0 + - - -
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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