Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 1YV5
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 ILE 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP* 6.3 2.2 - - + -
49A HIS* 3.3 14.6 + - + +
50A PRO 3.3 0.2 + - - -
51A GLU* 1.3 82.3 - - + +
53A GLY* 1.3 63.3 + - - +
54A ASP 3.4 1.3 - - - -
55A ALA* 3.1 12.0 + - + +
56A ILE* 3.0 35.9 + - + +
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Residues in contact with GLY 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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46A GLU* 3.3 26.2 - - - +
49A HIS 4.1 0.4 + - - -
50A PRO* 2.7 25.8 + - - -
51A GLU 2.9 3.8 + - - -
52A ILE* 1.3 71.2 - - - +
54A ASP* 1.3 64.7 + - - -
56A ILE 3.1 1.6 + - - -
57A ALA* 3.0 22.0 + - - +
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Residues in contact with ASP 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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51A GLU 4.4 3.4 + - - +
52A ILE 3.4 0.6 - - - -
53A GLY* 1.3 81.2 - - - +
55A ALA* 1.3 59.2 - - - +
57A ALA* 3.4 9.1 - - - +
58A ARG* 3.2 21.0 + - - +
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Residues in contact with ALA 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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52A ILE* 3.1 14.3 + - + +
53A GLY 3.0 0.4 - - - -
54A ASP* 1.3 78.9 - - - +
56A ILE* 1.4 64.3 + - + +
58A ARG* 3.3 9.2 + - - +
59A LEU* 2.8 27.7 + - - +
148A LEU* 5.4 4.6 - - + +
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Residues in contact with ILE 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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42A LEU 4.4 3.8 - - - +
43A THR* 3.5 44.9 - - + +
45A ASP* 4.9 12.3 - - + -
46A GLU* 3.7 27.6 - - + +
52A ILE* 3.0 28.5 + - + +
53A GLY 3.1 4.9 + - - +
55A ALA* 1.4 78.0 - - + +
57A ALA* 1.3 58.6 + - - +
59A LEU* 2.7 37.0 + - + +
60A LYS* 2.9 12.9 + - - +
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Residues in contact with ALA 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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46A GLU* 3.9 6.6 + - - +
53A GLY 3.0 12.2 + - - +
54A ASP* 3.4 14.8 - - - +
56A ILE* 1.3 73.4 - - - +
58A ARG* 1.3 65.5 + - - +
59A LEU 3.0 0.9 + - - -
60A LYS* 3.0 21.2 + - - +
61A GLU* 3.1 12.9 + - - +
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Residues in contact with ARG 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 ASP 3.2 12.6 + - - +
55A ALA* 3.3 10.3 + - - +
56A ILE 3.3 0.4 - - - -
57A ALA* 1.3 80.3 - - - +
59A LEU* 1.3 58.6 + - - +
61A GLU* 3.5 15.9 - - - +
62A VAL* 2.9 40.1 + - + +
132A TRP* 3.7 12.3 - - - -
137A GLY 4.7 8.3 + - - -
138A VAL* 4.2 16.0 - - - +
141A ASP* 3.9 22.6 + - - +
145A ASP* 2.6 44.5 + - - +
148A LEU* 5.6 4.0 - - + -
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Residues in contact with LEU 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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42A LEU* 4.0 23.6 - - + +
43A THR* 5.2 1.1 - - + -
55A ALA 2.8 12.7 + - - +
56A ILE* 2.7 31.6 + - + +
58A ARG* 1.3 70.9 - - - +
60A LYS* 1.3 63.0 + - - +
62A VAL* 3.2 9.9 + - + +
63A LEU* 2.9 43.3 + - + +
148A LEU* 4.4 34.8 - - + +
149A LEU* 5.2 2.2 - - + -
152A CYS* 3.8 31.9 - - - -
155A ARG* 6.3 2.2 - - - -
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Residues in contact with LYS 60 (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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39A VAL* 3.8 21.3 - - + -
43A THR* 4.2 13.4 - - + +
56A ILE 2.9 9.7 + - - +
57A ALA* 3.2 14.1 - - - +
59A LEU* 1.3 75.5 - - - +
61A GLU* 1.3 53.0 + - - +
63A LEU* 2.9 13.2 + - - +
64A GLU* 2.6 66.2 + - - +
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Residues in contact with GLU 61 (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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57A ALA 3.1 8.3 + - - +
58A ARG* 3.5 20.1 - - - +
60A LYS* 1.3 79.0 - - - +
62A VAL* 1.3 58.3 + - - +
64A GLU* 3.9 7.4 - - - +
65A TYR* 3.0 30.0 + - + +
132A TRP* 3.7 27.9 - - + -
135A LYS* 5.9 1.7 - - - -
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Residues in contact with VAL 62 (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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58A ARG* 2.9 31.6 + - + +
59A LEU* 3.5 12.1 - - + +
61A GLU* 1.3 74.1 - - - +
63A LEU* 1.3 61.1 + - - +
66A ASN* 2.9 49.4 + - - +
115A VAL* 6.1 0.4 - - + -
132A TRP* 3.9 7.9 - - + -
145A ASP* 3.5 50.9 - - + +
148A LEU* 5.5 2.2 - - + -
149A LEU* 3.8 25.2 - - + +
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Residues in contact with LEU 63 (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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35A PHE* 3.8 23.4 - - + -
38A ILE* 5.8 1.1 - - + -
39A VAL* 4.2 19.1 - - + -
42A LEU* 4.2 30.7 - - + -
43A THR* 5.1 1.8 - - + -
59A LEU* 2.9 43.7 + - + +
60A LYS* 3.4 8.5 - - - +
62A VAL* 1.3 78.0 - - - +
64A GLU* 1.3 66.5 + - - +
67A ALA* 3.1 21.9 + - - +
68A ILE 4.2 0.3 + - - -
108A LEU* 3.7 29.4 - - + -
149A LEU* 3.7 14.8 - - + -
152A CYS* 4.5 3.4 - - - -
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Residues in contact with GLU 64 (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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35A PHE* 4.4 19.9 - - + -
39A VAL* 4.3 7.3 - - + +
60A LYS* 2.6 57.9 + - + +
61A GLU* 4.1 6.7 - - - +
63A LEU* 1.3 73.2 - - - +
65A TYR* 1.3 60.7 + - - +
68A ILE* 3.4 22.2 - - - +
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Residues in contact with TYR 65 (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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61A GLU* 3.0 19.7 + - + +
64A GLU* 1.3 76.1 - - - +
66A ASN* 1.3 75.5 + - - +
68A ILE 3.9 6.5 - - - +
127A ARG* 6.0 0.7 - - - -
129A GLN* 3.1 53.1 + - + +
130A ILE* 2.3 51.1 + - - +
131A CYS* 5.1 0.2 - - - -
132A TRP* 3.5 39.0 - + + -
135A LYS* 3.6 26.6 - - + +
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Residues in contact with ASN 66 (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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62A VAL* 2.9 35.1 + - - +
65A TYR* 1.3 86.0 - - - +
67A ALA* 1.3 60.2 + - - +
68A ILE 3.5 1.8 - - - -
111A ALA* 3.5 13.0 - - + +
115A VAL* 3.5 25.4 - - + +
127A ARG* 2.9 18.2 + - - +
132A TRP* 3.4 49.1 + - - +
149A LEU* 4.3 10.5 - - + -
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Residues in contact with ALA 67 (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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35A PHE* 4.3 6.1 - - + -
62A VAL 4.3 0.2 + - - -
63A LEU* 3.1 15.2 + - - +
66A ASN* 1.3 76.6 - - - +
68A ILE* 1.3 61.2 + - - +
72A TYR* 3.5 18.2 - - - -
104A TRP* 3.5 21.1 - - + -
107A GLU* 4.5 8.7 - - - +
108A LEU* 4.1 26.7 - - + -
111A ALA* 4.3 10.1 - - + -
127A ARG* 3.8 8.0 + - - +
149A LEU* 5.7 0.9 - - + -
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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