Contacts of the helix formed by residues 55 - 66 (chain A) in PDB entry 1XHU
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 LYS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.3 35.4 + - - -
39A LYS* 5.1 4.2 - - - +
42A TYR* 3.5 36.5 - - + +
54A PHE* 1.3 73.6 - - - +
56A GLN* 1.3 68.4 + - - +
57A TYR* 3.2 23.3 - - + +
58A GLU* 2.5 43.5 + - + +
59A TYR* 2.8 5.0 + - - -
107A GLU* 4.1 21.8 - - - +
114A ASP 3.3 16.8 - - - +
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Residues in contact with GLN 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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54A PHE 4.0 2.2 + - - -
55A LYS* 1.3 73.4 - - - +
57A TYR* 1.3 65.1 + - + +
59A TYR* 3.0 10.7 + - - +
60A LEU* 2.9 28.8 + - + +
88A LEU 3.7 11.4 + - - +
89A LEU* 3.3 38.3 + - + +
90A SER 5.3 1.4 + - - -
91A ARG* 5.1 0.6 - - - +
111A ASP* 3.3 30.9 + - - +
112A THR 3.3 22.0 - - - +
113A ALA* 3.5 32.1 + - + +
114A ASP 4.4 4.8 + - - -
116A LEU* 4.4 14.6 - - - +
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Residues in contact with TYR 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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55A LYS* 2.7 28.0 + - + +
56A GLN* 1.3 75.2 - - + +
58A GLU* 1.3 96.0 + - + +
60A LEU* 2.8 22.0 + - - +
61A ASN* 2.9 20.0 + - - -
91A ARG* 3.3 15.3 - - - +
105A PHE* 3.0 30.5 - - + +
106A GLU* 3.2 26.9 - - + +
107A GLU* 4.0 34.7 + - + -
111A ASP* 4.7 1.7 + - - +
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Residues in contact with GLU 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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42A TYR* 2.8 29.6 + - - -
46A LYS* 3.4 17.4 - - - -
53A THR 4.1 0.3 - - - +
54A PHE* 3.9 15.2 - - + -
55A LYS* 2.5 36.4 + - + +
57A TYR* 1.3 98.3 + - + +
59A TYR* 1.3 60.3 + - - +
61A ASN* 3.5 8.4 + - - +
62A ASP* 3.3 21.9 + - - +
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Residues in contact with TYR 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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54A PHE* 3.7 35.4 - + + -
55A LYS 2.8 7.1 + - - +
56A GLN 3.0 11.9 - - - +
58A GLU* 1.3 74.4 - - - +
60A LEU* 1.3 81.2 + - + +
62A ASP* 2.9 16.4 + - + +
63A LEU* 2.9 43.9 + - + +
66A LYS* 6.2 1.6 - - - -
80A PHE* 4.8 4.9 - + - -
85A LEU* 5.0 1.0 - - - +
89A LEU* 3.8 18.1 - - + +
116A LEU* 3.1 32.1 - - + -
118A VAL* 4.5 10.5 - - + -
123A TYR* 3.4 34.8 + + - -
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Residues in contact with LEU 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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56A GLN* 2.9 20.2 + - + +
57A TYR* 2.8 17.5 + - - +
59A TYR* 1.3 81.5 - - + +
61A ASN* 1.3 64.0 + - - +
62A ASP 2.9 1.4 + - - -
63A LEU* 3.0 7.8 + - + +
64A PHE* 3.0 26.8 + - + +
80A PHE* 3.6 34.8 - - + -
89A LEU* 2.9 30.7 - - + +
90A SER* 4.8 0.9 - - - -
91A ARG* 3.8 32.1 - - + +
105A PHE* 3.9 18.8 - - + -
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Residues in contact with ASN 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 TYR* 2.9 24.2 + - - -
58A GLU* 3.7 8.8 - - - +
60A LEU* 1.3 76.3 - - - +
62A ASP* 1.3 58.9 - - - +
65A MET* 2.9 33.3 + - + +
99A TRP* 2.6 28.2 + - - +
104A LEU* 3.5 20.4 - - + +
105A PHE* 2.6 57.1 + - - +
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Residues in contact with ASP 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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54A PHE* 3.8 23.0 - - + -
58A GLU* 3.3 13.1 + - - +
59A TYR* 2.9 13.9 + - + +
61A ASN* 1.3 77.1 - - - +
63A LEU* 1.3 67.4 + - - +
64A PHE 3.0 1.3 - - - -
65A MET* 3.1 25.4 + - - +
66A LYS* 2.7 38.5 + - + +
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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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59A TYR* 2.9 37.7 + - + +
60A LEU* 3.4 11.0 - - + +
62A ASP* 1.3 77.2 - - - +
64A PHE* 1.3 69.3 + - + +
66A LYS* 3.8 16.7 + - - +
67A ASN* 2.7 36.0 + - - +
79A LEU* 3.4 30.1 - - + +
80A PHE* 3.4 42.6 - - + -
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Residues in contact with PHE 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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60A LEU* 3.0 15.9 + - + +
63A LEU* 1.3 93.3 - - + +
65A MET* 1.3 61.2 + - - +
66A LYS 3.1 1.3 - - - -
67A ASN 2.8 31.8 + - - +
68A PRO* 3.6 1.0 - - - +
76A ARG* 3.8 48.2 - - + +
77A TYR* 5.8 0.2 - + - -
79A LEU* 3.8 12.3 - - + -
80A PHE* 4.1 15.9 - + - -
96A THR* 4.0 16.8 - - + -
99A TRP* 3.3 50.8 - + + -
105A PHE* 3.6 26.5 - + - -
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Residues in contact with MET 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 ASN* 2.9 24.0 + - + +
62A ASP* 3.3 30.1 - - - +
64A PHE* 1.3 75.5 - - - +
66A LYS* 1.3 61.0 + - - +
67A ASN 3.1 1.3 + - - -
68A PRO* 3.3 18.6 - - - +
99A TRP* 3.1 14.0 - - + -
101A ILE* 4.1 27.1 - - + -
104A LEU* 5.3 5.2 - - - -
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Residues in contact with LYS 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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59A TYR* 6.2 1.6 - - - -
62A ASP* 2.7 28.5 + - + +
63A LEU* 3.9 18.4 - - - +
65A MET* 1.3 72.1 - - - +
67A ASN* 1.3 66.8 + - - +
68A PRO* 3.2 8.0 - - - +
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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