Contacts of the strand formed by residues 124 - 132 (chain A) in PDB entry 4I9X
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR* 6.2 0.2 - - - -
69A VAL 3.0 14.6 - - - -
70A MSE 4.0 1.6 - - - -
71A THR* 3.3 4.5 - - - -
121A LEU* 2.6 38.1 + - - +
122A HIS 3.1 1.8 - - - -
123A LEU* 1.3 88.1 - - - +
125A GLN* 1.3 70.7 + - - -
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Residues in contact with GLN 125 (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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67A CYS 3.9 0.7 - - - +
68A THR* 3.6 2.9 - - - +
69A VAL* 2.9 41.0 + - + +
71A THR* 3.1 21.7 + - - +
72A HIS* 3.8 26.5 + - - -
77A VAL* 6.4 0.7 - - + -
97A ALA 4.0 7.8 - - - +
118A PHE* 3.5 36.1 - - + -
119A SER 3.2 9.4 - - - +
120A GLN* 2.7 38.7 + - - +
121A LEU* 4.6 0.4 - - - -
124A GLY* 1.3 88.6 - - - +
126A ILE* 1.3 62.5 + - - +
127A PHE* 4.4 2.1 - - + -
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Residues in contact with ILE 126 (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 PRO* 5.6 0.2 - - + -
67A CYS 3.2 19.5 - - - +
68A THR* 3.8 17.9 - - + +
118A PHE* 3.3 2.8 - - - -
119A SER* 2.7 47.0 + - - +
121A LEU* 3.7 32.3 - - + +
125A GLN* 1.3 74.9 - - - +
127A PHE* 1.3 68.3 + - - +
128A SER* 5.1 3.6 - - - -
64B THR* 6.0 0.2 - - + -
66B PRO* 3.8 13.9 - - + -
126B ILE* 4.2 35.4 - - + -
128B SER* 5.9 3.1 - - - -
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Residues in contact with PHE 127 (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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67A CYS* 2.9 59.9 + - + +
69A VAL* 3.8 34.5 - - + -
77A VAL* 3.5 40.6 - - + -
78A SER 3.6 22.2 - - - -
79A ILE* 3.9 15.9 - - + -
95A LEU* 4.0 11.0 - - + -
117A ASN 3.2 12.8 - - - +
118A PHE* 3.9 17.9 - + + -
125A GLN* 4.4 5.4 - - + -
126A ILE* 1.3 79.9 - - - +
128A SER* 1.3 63.0 + - - +
143A CYS* 4.6 0.7 - - + -
144A VAL 4.2 10.3 - - - -
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Residues in contact with SER 128 (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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64A THR* 3.5 18.5 - - - +
65A ILE 3.2 16.8 - - - -
66A PRO* 4.3 4.7 - - - -
79A ILE* 3.5 9.0 - - - +
95A LEU* 5.8 0.5 - - - +
116A TRP* 3.1 24.5 - - - +
117A ASN* 3.0 36.5 + - - +
126A ILE* 5.1 5.6 - - - -
127A PHE* 1.3 76.9 - - - +
129A LEU* 1.3 61.4 + - - +
130A THR* 4.9 0.9 + - - -
126B ILE* 5.7 3.1 - - - -
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Residues in contact with LEU 129 (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 VAL 3.9 0.7 - - - +
64A THR* 3.2 2.1 - - - -
65A ILE* 2.8 37.3 + - + +
79A ILE* 3.6 29.2 - - + -
93A LEU* 4.5 13.9 - - + -
107A LEU* 3.8 30.7 - - + -
111A LEU* 4.2 3.4 - - + -
114A ALA* 3.9 21.3 - - + -
115A THR 3.6 15.3 - - - +
116A TRP* 4.7 2.7 - - + -
128A SER* 1.3 76.6 - - - +
130A THR* 1.3 61.9 + - - +
131A PHE* 4.0 23.4 - - + -
141A TYR* 4.0 16.8 - - + -
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Residues in contact with THR 130 (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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62A GLN* 3.5 36.8 - - + +
63A VAL 3.4 3.6 - - - +
64A THR* 2.6 31.2 + - - +
113A TYR 4.7 0.5 - - - +
114A ALA* 3.3 8.0 - - - +
115A THR* 2.8 51.2 + - - +
117A ASN* 4.9 5.9 + - - -
128A SER* 4.9 1.7 + - - -
129A LEU* 1.3 71.9 + - - +
131A PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 131 (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 GLN* 3.4 3.3 - - - +
63A VAL* 2.9 53.1 + - + +
65A ILE* 3.8 28.0 - - + -
111A LEU* 3.8 25.8 - - + -
113A TYR 5.7 1.6 - - - -
114A ALA* 4.4 11.2 - - + +
129A LEU* 4.0 17.7 - - + -
130A THR* 1.3 80.1 - - - +
132A ASN* 1.3 77.0 + - - +
133A VAL* 4.4 7.6 - - + -
137A THR* 3.9 15.7 - - - -
141A TYR* 3.4 38.4 - + - -
159A ILE* 4.6 4.3 - - + -
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Residues in contact with ASN 132 (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 GLY* 4.5 11.5 - - - -
61A GLU 3.4 4.5 - - - +
62A GLN* 3.3 26.5 + - - +
111A LEU* 5.2 0.3 - - - +
131A PHE* 1.3 78.0 - - - +
133A VAL* 1.3 63.6 + - - +
134A SER* 3.6 2.1 + - - -
137A THR* 3.5 12.8 + - - +
303A NAG 1.5 66.8 + - - +
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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