Contacts of the helix formed by residues 50 - 61 (chain A) in PDB entry 1XVI
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 THR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A SER 5.3 1.1 - - - +
49A LYS* 1.3 78.4 - - - +
51A SER* 1.3 58.3 + - - +
52A ALA 3.8 0.5 + - - -
53A GLU* 3.3 16.2 + - - +
54A MET* 2.9 28.2 + - - +
70A ALA* 4.1 0.4 - - - -
71A GLU* 3.7 10.8 - - + -
139A LEU 2.7 21.5 + - - -
140A THR 3.5 14.8 - - - +
142A LEU 3.0 23.5 + - - +
143A HIS* 3.5 32.1 - - + +
148A THR* 5.2 0.2 - - - +
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Residues in contact with SER 51 (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 THR* 1.3 74.8 - - - +
52A ALA* 1.3 57.2 + - - +
54A MET* 3.8 1.4 - - - +
55A LEU* 2.9 37.9 + - - +
68A LEU* 5.4 2.5 - - - +
70A ALA* 3.8 11.2 - - - +
71A GLU* 3.4 13.6 + - - -
75A VAL* 3.9 23.0 - - - +
77A GLN* 4.8 0.5 + - - +
90A ARG* 3.5 28.9 + - - -
142A LEU 4.8 0.2 + - - -
144A GLU* 4.2 13.2 - - - -
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Residues in contact with ALA 52 (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 THR* 3.3 1.2 + - - -
51A SER* 1.3 78.1 + - - +
53A GLU* 1.3 62.7 + - - +
55A LEU* 3.5 7.7 + - - +
56A TYR* 3.2 22.0 + - - +
139A LEU* 4.0 31.5 - - + +
142A LEU* 4.0 30.4 + - + -
144A GLU* 5.8 0.4 - - - +
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Residues in contact with GLU 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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49A LYS* 3.5 34.7 + - + +
50A THR* 3.3 33.8 + - - +
52A ALA* 1.3 77.3 - - - +
54A MET* 1.3 56.6 + - - +
56A TYR* 3.0 8.3 + - - +
57A LEU* 2.9 36.7 + - + +
132A LEU* 4.0 11.4 - - - +
136A GLN* 4.9 10.7 - - - +
139A LEU* 4.0 17.1 - - + +
140A THR* 2.5 38.0 + - - +
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Residues in contact with MET 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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15A ASP* 4.5 9.4 - - - +
45A LEU* 3.5 44.6 - - + +
46A CYS 4.4 0.7 - - - +
47A SER* 3.2 32.8 - - - -
49A LYS* 3.8 29.6 - - + +
50A THR 2.9 21.3 + - - +
51A SER 4.0 2.7 - - - +
53A GLU* 1.3 72.8 - - - +
55A LEU* 1.3 60.9 + - - +
57A LEU* 4.0 9.5 - - + +
58A GLN* 2.8 31.4 + - - +
68A LEU* 3.7 20.3 - - + +
69A ILE 4.4 3.4 - - - +
70A ALA* 4.4 6.5 - - + -
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Residues in contact with LEU 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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51A SER* 2.9 27.6 + - - +
52A ALA* 4.0 7.0 - - - +
53A GLU 3.3 0.2 - - - -
54A MET* 1.3 74.6 - - - +
56A TYR* 1.3 63.2 + - - +
58A GLN* 3.7 20.2 - - - +
59A LYS* 3.2 25.3 + - - +
64A GLN* 6.0 1.9 - - + +
68A LEU* 3.9 14.1 - - + -
77A GLN* 4.0 23.3 - - + +
90A ARG* 3.6 27.6 - - - +
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Residues in contact with TYR 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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24A TYR 5.1 5.8 - - - -
25A ASP* 2.2 33.8 + - - -
52A ALA 3.2 12.8 + - - +
53A GLU 3.0 10.7 + - - +
55A LEU* 1.3 77.3 - - - +
57A LEU* 1.3 74.7 + - + +
59A LYS* 3.2 27.7 + - - +
60A THR* 3.1 41.6 + - + +
136A GLN* 5.0 13.7 - - + +
139A LEU* 3.9 25.6 - - + -
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Residues in contact with LEU 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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15A ASP* 5.3 0.7 - - - +
19A LEU* 4.3 14.8 - - + -
24A TYR 5.9 1.1 - - - +
27A GLN* 4.4 19.7 - - - +
45A LEU* 5.4 2.0 - - + -
49A LYS* 3.5 38.6 - - + +
53A GLU* 2.9 31.3 + - + +
54A MET* 3.4 12.1 + - + +
56A TYR* 1.3 80.5 - - + +
58A GLN* 1.3 63.3 + - - +
60A THR* 2.9 20.3 + - + +
61A LEU* 3.0 25.8 + - + +
136A GLN* 3.8 21.8 - - - +
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Residues in contact with GLN 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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43A VAL 5.5 1.0 + - - -
45A LEU* 3.8 19.5 - - + +
54A MET 2.8 22.2 + - - +
55A LEU* 3.7 17.0 - - - +
57A LEU* 1.3 73.3 - - - +
59A LYS* 1.3 58.6 + - - +
61A LEU* 3.3 2.1 + - - -
62A GLY 3.3 4.2 + - - -
63A LEU* 2.8 61.8 + - + +
64A GLN* 3.7 13.5 - - - +
65A GLY 4.0 2.4 + - - -
66A LEU* 2.7 33.2 + - - +
67A PRO 3.6 7.1 + - - -
68A LEU* 3.4 25.6 - - + +
77A GLN* 5.2 0.5 - - - +
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Residues in contact with LYS 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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55A LEU 3.2 16.0 + - - +
56A TYR* 3.6 37.2 + - - +
57A LEU 3.2 0.2 - - - -
58A GLN* 1.3 78.0 - - - +
60A THR* 1.3 66.2 + - - +
62A GLY* 3.3 13.0 + - - -
64A GLN* 4.1 44.3 - - + +
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Residues in contact with THR 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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24A TYR 4.8 1.1 - - - +
25A ASP* 3.9 34.0 - - + +
27A GLN* 3.4 28.8 + - - +
30A ALA* 3.3 18.5 - - - +
56A TYR* 3.1 39.4 + - + +
57A LEU* 2.9 19.8 + - + +
59A LYS* 1.3 81.4 - - - +
61A LEU* 1.3 57.9 + - - +
62A GLY 3.3 0.4 + - - -
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Residues in contact with LEU 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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18A LEU* 4.9 8.1 - - + +
19A LEU* 4.0 23.1 - - + -
27A GLN* 3.8 28.7 - - + +
29A ALA* 3.8 25.4 - - + -
30A ALA* 3.4 22.1 - - - +
33A LEU* 3.5 23.1 - - + +
45A LEU* 4.0 29.2 - - + -
57A LEU* 3.0 21.5 + - + +
58A GLN 3.8 4.9 - - - +
59A LYS 3.2 0.2 - - - -
60A THR* 1.3 80.7 - - - +
62A GLY* 1.3 59.8 + - - +
63A LEU* 3.4 11.4 - - + -
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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