Contacts of the strand formed by residues 108 - 117 (chain A) in PDB entry 1I4R
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASN 4.3 0.6 + - - -
61A TYR* 4.1 2.7 - - - +
63A LYS* 3.5 29.6 - - + +
90A TYR* 3.6 17.8 - - - -
93A CYS* 4.6 4.2 - - - -
95A PHE* 3.6 51.4 - - + -
100A ASN* 4.5 11.2 - - - -
106A GLY 4.1 12.1 + - - +
107A GLY* 1.3 78.6 - - - +
109A THR* 1.3 62.5 + - - +
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Residues in contact with THR 109 (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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33A VAL* 4.4 1.3 - - + -
61A TYR* 3.7 19.5 - - + -
63A LYS 3.1 6.5 + - - +
64A VAL* 3.5 28.4 - - + -
65A LYS 3.1 23.0 + - - -
88A ASN* 2.9 32.7 + - + +
89A TYR 3.2 11.5 + - - -
90A TYR* 3.5 16.4 - - - -
93A CYS* 3.5 8.7 - - - -
95A PHE* 3.8 3.3 - - - -
108A LYS* 1.3 76.8 - - - +
110A CYS* 1.3 61.4 + - - +
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Residues in contact with CYS 110 (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 VAL* 5.2 0.2 - - - -
65A LYS* 3.4 36.8 - - - +
67A GLU* 6.4 0.4 - - + -
88A ASN* 3.0 7.9 - - - -
89A TYR* 2.8 56.4 + - + +
93A CYS* 2.0 51.8 - - + -
95A PHE* 4.0 1.8 - - - -
109A THR* 1.3 78.1 + - - +
111A MET* 1.3 63.7 + - - +
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Residues in contact with MET 111 (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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33A VAL* 4.2 15.3 - - - -
64A VAL* 3.7 26.2 - - + -
65A LYS 3.0 6.2 + - - +
66A THR* 3.2 18.9 - - - +
67A GLU* 3.0 23.6 + - - +
84A VAL* 3.7 27.1 - - + -
85A TYR 4.1 2.2 - - - -
86A GLY* 3.7 24.9 - - - +
87A SER 3.6 19.1 - - - +
88A ASN* 4.3 3.6 - - + -
89A TYR* 3.9 6.6 + - - -
110A CYS* 1.3 76.7 - - - +
112A TYR* 1.3 74.5 + - - +
113A GLY 3.4 23.3 - - - +
114A GLY* 4.1 0.9 - - - -
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Residues in contact with TYR 112 (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 THR* 3.3 1.6 - - - -
67A GLU* 3.3 50.4 + - + +
87A SER 4.8 1.8 + - - -
89A TYR* 3.7 18.4 - + - -
111A MET* 1.3 80.7 - - - +
113A GLY* 1.3 70.3 + - - +
157A GLN* 2.9 22.3 + - - +
211A SER* 2.8 44.5 + - - -
214A LEU* 3.4 35.6 - - + +
215A MET* 3.5 37.9 - - + +
217A TYR* 4.0 4.3 - - + -
218A ASN* 3.9 18.6 - - + +
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Residues in contact with GLY 113 (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 THR* 2.8 20.7 + - - -
67A GLU 3.0 12.9 + - - -
68A LEU* 3.7 13.0 - - - -
111A MET* 3.4 7.4 - - - +
112A TYR* 1.3 71.6 - - - +
114A GLY* 1.3 64.1 + - - -
115A ILE* 3.3 7.4 + - - +
217A TYR 3.5 14.4 + - - -
218A ASN* 4.1 0.6 - - - +
220A ASN* 3.2 16.8 - - - -
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Residues in contact with GLY 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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83A ASP 3.8 0.7 - - - +
84A VAL* 3.4 6.0 - - - +
85A TYR* 2.9 45.4 + - - +
111A MET* 4.1 2.0 - - - -
112A TYR 3.3 2.2 + - - -
113A GLY* 1.3 72.5 - - - -
115A ILE* 1.3 59.3 + - - +
116A THR* 4.3 0.7 + - - -
155A THR* 3.8 17.2 - - - +
157A GLN* 3.4 13.6 - - - +
217A TYR 4.6 0.8 + - - -
220A ASN* 3.0 7.2 - - - +
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Residues in contact with ILE 115 (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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49A LEU* 4.1 9.2 - - + -
51A TYR* 4.2 10.3 - - + +
66A THR* 4.4 13.7 - - + -
68A LEU* 4.0 22.4 - - + -
77A TYR* 3.7 41.7 + - + -
82A VAL* 4.5 7.6 - - + -
83A ASP 3.6 4.3 - - - +
84A VAL* 4.1 22.7 - - + -
113A GLY 3.7 9.0 - - - +
114A GLY* 1.3 82.5 - - - +
116A THR* 1.3 71.2 + - - +
155A THR* 4.0 0.7 - - - +
220A ASN* 2.9 44.9 + - - +
222A THR* 4.8 0.3 - - - +
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Residues in contact with THR 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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77A TYR* 4.6 4.9 - - - +
82A VAL* 3.1 7.4 - - - +
83A ASP* 2.8 34.9 + - - +
114A GLY 5.2 0.7 + - - -
115A ILE* 1.3 80.6 - - - +
117A LYS* 1.3 62.0 + - - +
121A ASN* 4.1 13.6 + - - -
151A LYS* 3.5 26.5 - - + +
153A SER* 3.6 19.7 - - - +
154A VAL* 4.7 0.4 - - - -
155A THR* 3.9 13.7 - - + +
222A THR* 3.8 21.8 - - + -
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Residues in contact with LYS 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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76A LYS* 4.0 31.2 - - - +
77A TYR* 3.8 21.1 + - + +
80A GLU* 4.0 35.4 + - + +
81A VAL 3.8 6.3 - - - +
82A VAL* 4.2 2.2 - - - -
83A ASP* 4.6 0.7 - - - +
116A THR* 1.3 75.4 + - - +
118A HIS* 1.3 63.2 + - - +
119A GLU* 4.5 11.2 - - + +
121A ASN* 3.3 23.0 + - - +
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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