Contacts of the strand formed by residues 73 - 81 (chain I) in PDB entry 1XE0
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 73 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I GLU* 3.4 40.2 - - + +
66I GLY* 3.4 13.7 - - - +
67I ILE* 3.9 12.3 - - - +
71I GLY 4.2 0.4 + - - -
72I LYS* 1.3 75.2 - - - +
74I ILE* 1.4 64.1 + - - +
75I LYS* 5.7 1.1 - - + -
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Residues in contact with ILE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU* 3.5 30.8 - - + +
20H PHE* 4.1 5.6 - - - -
21H GLY* 4.1 6.3 - - - +
64I ALA 3.8 0.9 - - - +
65I GLU* 3.2 5.0 - - - +
66I GLY 2.9 41.0 + - - +
68I ASN* 3.8 30.7 - - + +
72I LYS* 3.5 1.5 + - + -
73I THR* 1.4 78.8 - - - +
75I LYS* 1.3 67.5 + - - +
76I ILE* 3.7 23.3 - - + -
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Residues in contact with LYS 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLY* 5.5 1.7 - - - -
63I GLU* 3.8 31.4 - - - +
64I ALA 3.4 4.7 - - - +
65I GLU* 3.8 31.9 - - + +
73I THR* 5.7 0.9 - - + -
74I ILE* 1.3 78.0 - - - +
76I ILE* 1.3 65.3 + - - +
103I ARG* 4.0 2.5 - - - +
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Residues in contact with ILE 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU* 3.9 23.6 - - + -
20H PHE 3.5 38.1 - - - +
21H GLY* 3.6 11.4 - - - +
112H TYR* 6.1 0.7 - - - -
113H VAL 5.2 0.4 - - - +
114H SER* 4.0 8.7 - - - -
115H GLY 4.3 0.2 - - - +
63I GLU* 3.2 4.8 - - - +
64I ALA* 2.9 40.7 + - + +
74I ILE* 3.7 18.4 - - + -
75I LYS* 1.3 81.1 - - - +
77I ALA* 1.3 59.2 + - - +
78I LEU* 3.6 8.5 + - + -
94I PHE* 3.8 26.9 - - + -
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Residues in contact with ALA 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H THR* 3.8 2.9 + - - -
50H SER* 3.8 12.1 + - - +
112H TYR* 3.6 42.8 - - + +
113H VAL 5.7 0.6 + - - -
114H SER* 3.4 20.1 + - - -
61I VAL* 4.4 18.4 - - + -
62I VAL 3.8 5.4 - - - -
63I GLU* 4.1 4.9 + - - -
76I ILE* 1.3 71.2 - - - +
78I LEU* 1.3 60.9 + - - +
79I ALA 4.8 0.2 - - - +
105I LYS* 4.8 6.0 - - - +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H THR* 2.8 33.3 + - - +
50H SER* 4.6 1.3 + - - -
88H THR* 4.4 0.7 - - - +
114H SER* 4.3 0.4 - - - +
46I LEU* 3.7 26.9 - - + -
49I VAL* 5.5 3.4 - - + -
62I VAL* 2.9 26.9 + - + +
64I ALA* 4.1 31.6 - - + +
76I ILE* 4.2 7.4 - - + -
77I ALA* 1.3 72.6 - - - +
79I ALA* 1.3 67.2 + - + +
91I LEU* 4.2 12.2 - - + +
94I PHE* 3.5 38.1 - - + -
96I ILE* 4.9 0.9 - - + -
102I LEU* 4.2 9.2 - - + -
113I VAL* 6.0 1.3 - - + -
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H SER* 4.3 5.2 - - - -
88H THR* 4.0 15.0 - - + -
49I VAL* 4.5 20.4 - - + -
60I HIS 3.8 0.7 - - - +
61I VAL* 3.4 6.0 - - - +
62I VAL* 3.0 29.4 + - + +
77I ALA 3.6 1.0 - - - -
78I LEU* 1.3 83.6 - - + +
80I SER* 1.3 62.2 + - - +
81I LEU* 4.2 9.3 - - + +
89I VAL* 4.3 19.7 - - + -
91I LEU* 4.9 0.9 - - + -
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Residues in contact with SER 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H SER* 3.7 8.5 + - - -
51H LEU 2.6 30.2 + - - -
87H PRO* 3.5 17.3 - - - +
88H THR* 2.8 29.5 + - - -
59I LEU* 3.8 17.0 - - - -
60I HIS 3.2 6.5 - - - -
61I VAL* 3.5 13.7 - - - +
79I ALA* 1.3 72.5 - - - +
81I LEU* 1.3 65.3 + - - +
86I GLN* 4.2 0.9 - - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H PRO* 4.8 1.1 - - - -
49I VAL* 3.5 44.6 - - + +
50I SER* 3.8 4.5 - - - +
51I LEU* 3.8 21.8 - - + -
58I GLU 3.6 0.9 - - - +
59I LEU* 3.4 6.6 - - - +
60I HIS* 2.7 37.5 + - + +
62I VAL* 6.0 1.3 - - + -
79I ALA* 4.3 5.6 - - + +
80I SER* 1.3 79.3 - - - +
82I LYS* 1.3 60.7 + - - +
86I GLN* 3.3 14.6 - - + +
87I PRO 3.6 13.9 - - - +
89I VAL* 3.0 39.5 - - + +
111I VAL* 4.7 1.3 - - + -
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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