Contacts of the helix formed by residues 55 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D TYR* 4.9 9.6 - - + -
54D PHE* 1.3 75.3 - - - +
56D GLN* 1.3 73.2 + - - +
57D TYR* 4.2 20.4 - - + +
58D GLU* 2.7 29.0 + - + +
59D TYR* 2.7 16.6 + - - +
107D GLU* 6.5 0.2 - - - -
114D ASP 4.6 7.0 - - - +
115D ILE* 4.5 4.9 - - - +
116D LEU* 4.5 2.0 - - - +
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE 4.2 0.8 + - - -
55D LYS* 1.3 72.8 - - - +
57D TYR* 1.3 64.0 + - + +
59D TYR* 3.2 6.8 + - - +
60D LEU* 3.2 25.4 + - + +
88D LEU 4.0 1.8 + - - -
89D LEU* 3.0 38.2 - - - +
91D ARG* 6.0 0.2 - - - -
111D ASP* 3.5 30.5 - - + +
112D THR* 2.9 23.0 + - - +
113D ALA* 2.8 48.7 + - - +
114D ASP 4.9 2.2 + - - -
115D ILE* 4.9 0.4 - - - +
116D LEU* 3.8 16.4 - - - +
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Residues in contact with TYR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LYS* 3.0 18.9 + - + +
56D GLN* 1.3 77.0 - - + +
58D GLU* 1.3 87.7 + - + +
60D LEU* 2.8 17.0 + - - +
61D ASN* 2.8 41.2 + - - -
91D ARG* 3.5 13.7 - - - +
105D PHE* 3.6 25.4 - - + -
106D GLU* 3.0 29.2 - - - +
107D GLU* 3.7 34.5 + - + -
111D ASP* 4.6 2.0 - - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 2.6 37.0 + - - -
53D THR 4.3 1.0 - - - +
54D PHE* 3.5 27.6 - - + -
55D LYS* 2.7 32.9 + - + +
57D TYR* 1.3 97.0 + - + +
59D TYR* 1.3 62.3 + - - +
61D ASN* 3.5 6.8 + - - +
62D ASP* 3.2 20.3 + - - +
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Residues in contact with TYR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.8 38.5 - + + +
55D LYS 2.7 13.0 + - - +
56D GLN 3.4 8.7 - - - +
58D GLU* 1.3 72.3 - - - +
60D LEU* 1.3 72.2 + - + +
62D ASP* 3.2 8.8 + - + +
63D LEU* 3.1 40.3 + - + +
79D LEU 5.6 0.2 + - - -
80D PHE* 3.7 27.8 - + - -
89D LEU* 4.1 4.9 - - + -
116D LEU* 3.9 22.7 - - + -
118D VAL* 4.2 15.7 - - + -
123D TYR* 2.8 41.4 + + - -
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLN* 3.2 11.8 + - + +
57D TYR* 2.8 17.6 + - - +
59D TYR* 1.3 82.2 - - + +
61D ASN* 1.3 52.5 + - - +
63D LEU* 2.7 31.3 + - - +
64D PHE* 3.3 21.8 + - + -
80D PHE* 3.3 37.0 - - + -
89D LEU* 3.3 24.2 - - + +
90D SER* 4.9 1.6 - - - -
91D ARG* 3.7 41.3 - - + +
105D PHE* 3.7 14.6 - - + -
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D TYR* 2.8 30.1 + - - +
58D GLU* 3.8 6.7 - - - +
60D LEU* 1.3 72.3 - - - +
62D ASP* 1.3 60.4 + - - +
64D PHE 3.6 0.5 + - - -
65D MET* 3.0 35.5 + - - +
99D TRP* 3.2 16.2 + - - +
104D LEU* 3.7 27.7 - - + +
105D PHE* 2.9 53.8 + - - +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.7 31.3 - - + -
58D GLU 3.2 9.5 + - - +
59D TYR* 3.2 14.8 + - + +
60D LEU 3.1 0.6 - - - -
61D ASN* 1.3 78.0 - - - +
63D LEU* 1.3 61.2 + - - +
65D MET* 4.1 7.3 - - - +
66D LYS* 3.3 45.5 + - - +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 3.1 31.9 + - + +
60D LEU* 2.7 15.6 + - + +
62D ASP* 1.3 81.3 - - - +
64D PHE* 1.3 66.0 + - + +
65D MET 3.5 0.3 + - - -
66D LYS* 5.0 4.0 - - + +
67D ASN* 2.5 38.2 + - - +
79D LEU* 3.6 37.9 - - + +
80D PHE* 3.5 41.1 - - + -
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.3 16.6 + - + -
63D LEU* 1.3 93.9 - - + +
65D MET* 1.3 57.8 + - - +
67D ASN 3.1 24.6 - - - +
68D PRO* 3.7 3.3 - - - +
70D ILE 5.2 0.2 - - - +
76D ARG* 4.1 19.5 - - + -
77D TYR* 5.5 1.8 - + - -
79D LEU* 3.3 28.5 - - + -
80D PHE* 4.7 8.1 - + - -
96D THR* 4.0 26.5 - - + -
99D TRP* 3.2 56.1 - + + -
101D ILE* 5.5 0.2 - - - +
105D PHE* 3.4 32.1 - + - -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ASN* 3.0 28.6 + - - +
62D ASP* 4.1 7.2 - - - +
64D PHE* 1.3 75.7 - - - +
66D LYS* 1.3 58.5 + - + +
67D ASN 2.9 9.4 + - - -
68D PRO* 3.5 14.4 - - - +
99D TRP* 3.8 17.5 - - + -
101D ILE* 4.3 18.4 - - + +
104D LEU* 4.1 23.1 - - + -
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASP* 3.3 38.2 + - - +
63D LEU* 5.0 3.6 - - + +
64D PHE 3.5 0.2 - - - -
65D MET* 1.3 77.9 - - + +
67D ASN* 1.3 74.1 + - - +
68D PRO* 3.6 6.4 - - - +
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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