Contacts of the strand formed by residues 60 - 67 (chain A) 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 HIS 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.8 24.9 - - + -
55A ALA* 4.1 9.4 - - + +
56A LYS 3.0 22.3 + - - -
58A GLU* 2.9 29.8 + - - +
59A LEU* 1.3 76.6 - - - +
61A VAL* 1.3 60.7 + - - +
62A VAL* 5.4 1.5 - - + +
79A ALA 3.8 0.9 - - - +
80A SER* 3.4 4.3 - - - -
81A LEU* 2.8 40.0 + - + +
104A LEU* 4.4 0.6 - - + +
106A SER 3.2 6.3 - - - +
107A GLY* 3.9 1.4 - - - -
108A SER* 3.5 21.5 + - - -
109A GLY* 2.9 42.2 + - - -
111A VAL* 4.0 12.9 - - + +
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Residues in contact with VAL 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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59A LEU* 4.3 13.9 - - + -
60A HIS* 1.3 75.2 - - - +
62A VAL* 1.3 69.4 + - - +
77A ALA* 4.6 13.7 - - + -
79A ALA 3.4 8.5 - - - +
80A SER* 3.5 21.8 - - - +
104A LEU* 3.6 5.9 - - - +
105A LYS* 2.8 50.9 + - + +
106A SER* 2.9 29.8 + - - +
51E LEU 4.4 2.9 - - - +
52E GLY* 5.0 2.9 - - - -
53E ALA* 4.6 7.2 - - + +
112E TYR* 6.0 1.8 - - + -
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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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24A LEU* 4.0 18.8 - - + -
49A VAL* 4.0 13.5 - - + -
60A HIS* 5.4 1.6 - - + -
61A VAL* 1.3 77.7 - - - +
63A GLU* 1.3 68.0 + - - +
77A ALA* 3.7 3.1 - - - -
78A LEU* 2.8 37.0 + - + -
79A ALA 3.0 17.5 + - - +
81A LEU* 5.9 1.3 - - + -
102A LEU* 5.0 2.5 - - + -
103A ARG 3.3 9.0 - - - +
104A LEU* 4.4 7.4 - - + -
111A VAL* 3.7 33.0 - - + -
113A VAL* 4.4 12.8 - - + -
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Residues in contact with GLU 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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62A VAL* 1.3 75.8 - - - +
64A ALA* 1.3 64.6 + - - +
75A LYS* 3.6 30.0 - - - +
76A ILE 3.1 16.3 - - - +
77A ALA* 4.2 3.1 - - - -
78A LEU* 4.2 3.8 - - - +
101A ILE 3.7 0.2 - - - +
102A LEU* 3.4 4.2 - - - +
103A ARG* 2.8 79.7 + - + +
105A LYS* 3.6 37.1 + - + +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 1.3 78.2 - - - +
65A GLU* 1.3 59.3 + - - +
66A GLY 4.2 0.4 + - - -
74A ILE 3.8 1.0 - - - +
75A LYS* 3.4 2.2 - - - -
76A ILE* 2.8 42.8 + - + +
78A LEU* 4.0 28.2 - - + +
96A ILE* 4.4 6.7 - - + -
100A VAL* 4.0 17.3 - - + -
101A ILE 3.3 4.3 - - - -
102A LEU* 4.1 5.8 - - + -
19E LEU* 4.4 2.2 - - + +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ALA* 1.3 74.4 - - - +
66A GLY* 1.3 57.4 + - - +
73A THR* 3.4 29.8 - - + +
74A ILE 3.3 7.4 - - - +
75A LYS* 3.6 17.9 - - + +
99A PRO 4.3 0.2 - - - +
100A VAL* 3.4 7.1 - - - +
101A ILE* 2.8 57.3 + - + +
103A ARG* 2.8 43.7 + - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A GLU* 1.3 76.2 - - - +
67A ILE* 1.3 65.5 + - - -
73A THR* 4.2 5.4 - - - -
74A ILE* 2.8 36.7 + - - +
96A ILE* 6.2 0.4 - - - -
99A PRO 4.2 13.2 - - - -
100A VAL* 4.7 1.8 - - - -
19E LEU* 3.6 16.1 - - - +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLY* 1.3 73.0 - - - -
68A ASN* 1.3 73.2 + - - +
71A GLY* 3.7 31.4 - - - +
72A LYS 3.5 2.0 - - - -
73A THR* 4.0 19.5 - - - +
97A THR 5.9 2.1 + - - +
99A PRO* 4.9 16.7 + - + +
18E PHE* 3.8 19.0 - - + +
19E LEU* 3.1 24.0 + - - +
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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