Contacts of the strand formed by residues 113 - 124 (chain A) in PDB entry 1XO8
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 ASP 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.1 17.8 - - - +
111A ASP* 3.0 11.0 + - - +
112A TRP* 1.3 111.6 - - + +
114A ILE* 1.3 60.1 + - - +
141A GLU* 3.4 29.6 - - - +
142A ILE* 3.2 29.3 - - - +
143A LYS* 3.7 2.9 + - - +
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Residues in contact with ILE 114 (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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66A SER* 3.1 24.7 - - - +
67A ALA* 3.7 20.4 - - + +
104A LEU* 4.4 6.7 - - + +
105A ALA* 4.6 7.0 - - + -
108A VAL* 3.3 34.1 - - + -
109A GLY 3.9 3.8 - - - +
112A TRP 3.1 22.4 - - - +
113A ASP* 1.3 75.2 - - - +
115A ASP* 1.3 71.2 - - - +
116A TYR* 3.7 13.4 - - + +
141A GLU* 3.2 3.7 - - - -
142A ILE 3.1 28.0 + - - +
144A LEU* 3.4 29.6 - - + -
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 2.8 39.6 + - - +
67A ALA* 5.4 2.9 - - - +
114A ILE* 1.3 75.5 - - - +
116A TYR* 1.3 76.0 + - - +
117A GLU* 4.0 1.4 + - - +
139A LYS* 2.7 43.2 + - - +
140A GLY* 3.5 13.8 + - - -
141A GLU* 3.0 34.9 - - + +
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Residues in contact with TYR 116 (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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29A VAL* 6.3 2.2 - - + -
31A LEU* 5.4 12.7 - - + +
64A PHE* 4.8 11.5 - + + -
65A HIS 3.2 4.5 - - - +
66A SER* 3.3 25.1 + - - -
71A ILE* 3.7 27.4 - - + -
96A VAL* 6.5 0.2 - - + -
101A LEU* 3.4 26.8 - - + +
104A LEU* 4.1 1.6 - - - +
114A ILE* 3.7 17.2 - - + +
115A ASP* 1.3 79.0 + - - +
117A GLU* 1.3 60.7 + - - +
138A SER 3.2 3.8 - - - +
139A LYS* 2.8 2.8 - - - -
140A GLY 2.7 37.3 + - - +
142A ILE* 3.3 37.2 - - + -
143A LYS 5.5 0.9 - - - -
144A LEU* 4.5 2.8 - - - -
145A PRO* 3.7 14.2 - - - +
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Residues in contact with GLU 117 (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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63A THR 3.7 0.9 - - - +
64A PHE* 3.1 9.2 - - - -
65A HIS* 2.6 77.0 + - + +
66A SER 4.8 1.5 + - - +
115A ASP* 4.0 1.5 + - - +
116A TYR* 1.3 74.2 - - - +
118A LEU* 1.3 66.6 + - - +
119A GLN* 4.0 21.9 + - - +
137A SER* 4.6 4.2 - - - -
138A SER 3.5 2.2 - - - -
139A LYS* 3.2 44.0 - - + +
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Residues in contact with LEU 118 (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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25A SER 4.8 4.0 - - - +
26A VAL* 4.0 15.9 - - + -
29A VAL* 5.1 4.9 - - + -
43A ALA* 5.8 2.5 - - + -
45A VAL* 5.9 2.9 - - + -
62A PHE* 3.5 23.1 - - + -
63A THR 3.8 1.6 - - - +
64A PHE* 3.2 45.5 - - + -
92A ILE* 6.4 1.3 - - + -
117A GLU* 1.3 75.1 - - - +
119A GLN* 1.3 75.6 + - - +
120A ILE* 3.7 27.1 - - + -
137A SER* 2.8 32.6 - - - -
138A SER* 2.8 23.8 + - - +
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Residues in contact with GLN 119 (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 SER 3.3 4.2 - - - +
63A THR* 2.7 57.1 + - - +
65A HIS* 4.7 4.7 - - + +
117A GLU* 4.0 18.4 + - - +
118A LEU* 1.3 74.0 + - - +
120A ILE* 1.3 57.9 + - - +
121A GLY 3.9 0.6 + - - -
135A PRO* 5.3 12.3 - - + +
136A ILE 3.8 3.1 + - - +
137A SER* 2.8 34.1 + - - -
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Residues in contact with ILE 120 (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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25A SER* 4.5 5.2 - - - +
26A VAL* 3.5 20.4 - - + -
45A VAL* 5.9 0.4 - - + -
60A ILE* 3.6 22.0 - - + -
61A SER 3.1 36.6 - - - +
62A PHE* 3.6 14.8 - - + -
92A ILE* 5.4 1.6 - - + -
118A LEU* 3.7 17.3 - - + -
119A GLN* 1.3 73.0 - - - +
121A GLY* 1.3 59.0 + - - +
122A LEU* 3.4 19.6 - - + +
135A PRO* 3.3 3.8 - - - +
136A ILE* 2.8 64.1 + - + +
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Residues in contact with GLY 121 (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 GLU 3.1 16.5 - - - +
61A SER* 2.6 34.4 + - - -
119A GLN 3.9 1.0 + - - -
120A ILE* 1.3 70.9 - - - +
122A LEU* 1.3 62.8 + - - +
123A THR* 3.4 2.5 + - - -
133A THR* 4.7 10.8 - - - -
134A ILE 4.0 3.4 - - - -
135A PRO* 4.0 10.1 - - - +
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Residues in contact with LEU 122 (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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23A GLU* 2.9 30.5 - - + +
24A GLY* 3.3 21.5 - - - +
25A SER* 3.2 20.6 - - - +
59A GLU 4.0 2.7 - - - +
60A ILE* 5.2 1.3 - - + -
120A ILE* 3.4 43.1 - - + +
121A GLY* 1.3 68.7 - - - +
123A THR* 1.3 62.4 + - - +
124A ILE* 3.9 13.4 + - + +
132A PHE 2.9 12.8 - - - +
133A THR* 3.9 0.4 - - - -
134A ILE* 2.7 45.3 + - + +
136A ILE* 3.9 7.9 - - + -
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Residues in contact with THR 123 (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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58A CYS* 3.2 2.3 - - - +
59A GLU* 2.5 75.1 + - + +
61A SER* 5.9 0.2 - - - -
121A GLY 3.4 1.2 + - - -
122A LEU* 1.3 73.3 - - - +
124A ILE* 1.3 65.8 + - - +
131A GLU* 4.7 22.9 - - + +
132A PHE 3.0 8.1 - - - +
133A THR* 2.7 30.8 + - - +
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Residues in contact with ILE 124 (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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19A ILE* 4.1 9.4 - - + -
23A GLU* 5.4 2.5 - - + -
25A SER* 5.5 0.9 - - - +
47A VAL* 4.4 14.6 - - + -
48A THR 4.8 6.3 - - - +
49A ASN* 4.9 1.3 - - - -
50A PRO* 3.9 22.4 - - + -
55A ILE* 3.7 15.5 - - + -
57A ILE 3.9 2.9 - - - -
58A CYS* 3.2 26.2 - - + -
59A GLU 5.7 0.2 - - - +
122A LEU* 4.8 14.1 - - + +
123A THR* 1.3 80.6 - - - +
125A ASP* 1.3 59.9 + - - +
126A LEU* 3.2 33.6 + - + +
131A GLU* 3.1 21.0 - - - -
132A PHE 3.1 12.3 + - - +
134A ILE* 6.2 1.6 - - + -
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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