Contacts of the strand formed by residues 120 - 132 (chain O) in PDB entry 5XS0
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 TYR 120 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26N PHE* 4.2 7.4 - + - -
85N ALA* 3.1 36.2 - - + +
86N HIS 3.2 37.0 - - - -
87N SER* 3.6 19.9 + - - -
112N ARG* 4.7 5.0 + - - -
114N GLN* 2.9 38.4 + - - +
112O ARG* 3.9 42.4 - - + +
113O VAL 3.0 13.7 - - - +
114O GLN* 4.3 2.5 - - - -
118O GLY 3.3 15.3 - - - +
119O SER* 1.3 76.9 + - - +
121O HIS* 1.3 79.3 + - - +
158O PHE* 4.6 1.1 - - - -
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Residues in contact with HIS 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N TYR 4.2 2.8 + - - -
84N TRP* 3.4 53.9 + + - -
85N ALA* 4.0 0.4 - - - -
86N HIS* 2.9 31.2 + - + -
112O ARG* 3.6 1.3 - - - -
113O VAL* 2.8 33.4 + - - +
120O TYR* 1.3 80.6 + - - +
122O GLU* 1.3 58.3 + - - +
154O ALA* 3.6 25.1 - - - +
157O SER* 3.5 23.2 + - - -
158O PHE* 3.3 46.2 - + + -
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Residues in contact with GLU 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N HIS* 2.8 32.5 + - - +
87N SER* 3.3 21.7 - - - -
88N ILE* 2.8 50.3 + - + +
147N VAL* 4.9 0.3 - - - +
89O THR* 3.2 33.0 + - - +
110O PHE* 4.1 8.2 - - - +
111O VAL 3.4 14.1 - - - +
112O ARG* 4.0 18.6 - - + +
121O HIS* 1.3 74.7 - - - +
123O ASP* 1.3 66.6 + - - +
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Residues in contact with ASP 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N HIS* 4.2 8.4 + - - +
88N ILE* 3.8 12.2 - - - +
147N VAL* 3.4 19.2 - - - +
148N THR* 5.5 1.6 + - - -
151N LEU* 5.5 3.5 - - - +
110O PHE* 3.6 4.2 - - - -
111O VAL* 3.1 30.8 + - - +
122O GLU* 1.3 76.7 - - - +
124O VAL* 1.3 72.0 + - - +
150O GLY 4.9 2.2 - - - -
153O ARG* 3.3 45.5 + - + +
154O ALA* 3.8 24.8 - - + +
157O SER* 4.5 4.3 + - - -
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Residues in contact with VAL 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N ILE* 3.8 1.8 - - + +
91N GLN* 3.9 5.4 - - - +
143N ARG* 4.2 26.5 - - + +
144N LYS* 4.4 11.5 - - + +
147N VAL* 3.6 27.1 - - + -
108O CYS* 5.0 2.9 - - + -
109O ALA 3.4 2.9 - - - +
110O PHE* 3.5 40.6 - - + -
123O ASP* 1.3 82.5 + - - +
125O GLY* 1.3 70.6 + - - +
126O TYR* 5.5 1.8 - - + -
150O GLY* 4.0 3.4 - - - -
153O ARG* 2.7 34.3 + - - +
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Residues in contact with GLY 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N LYS* 4.8 0.7 - - - -
108O CYS* 3.3 4.3 - - - -
109O ALA 2.7 34.6 + - - +
124O VAL* 1.3 81.6 - - - +
126O TYR* 1.3 60.0 + - - +
146O ALA* 3.5 9.2 - - - -
149O ASP* 3.6 4.9 - - - -
150O GLY* 3.4 28.1 - - - -
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Residues in contact with TYR 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N ALA 3.2 20.4 - - - -
139N LEU* 3.3 22.7 - - + +
140N GLU* 3.4 46.0 - - + +
143N ARG* 4.1 11.7 - - + -
144N LYS* 4.3 3.5 - - + +
94O ASP* 2.6 32.8 + - - -
95O PHE* 4.1 0.7 - - - -
106O GLY* 3.5 15.8 - - - -
107O VAL 3.2 20.9 - - - -
108O CYS* 3.6 14.4 - - + -
124O VAL* 5.5 1.1 - - + -
125O GLY* 1.3 71.9 - - - -
127O GLY* 1.3 73.9 + - - +
128O VAL* 3.7 13.9 - - + -
145O GLU* 3.5 7.4 - - - +
146O ALA* 3.3 15.1 + - - +
149O ASP* 3.3 15.4 + - - +
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Residues in contact with GLY 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O GLY* 3.6 5.0 - - - -
107O VAL 2.7 34.7 + - - -
126O TYR* 1.3 76.8 - - - +
128O VAL* 1.3 64.2 + - - +
142O ALA* 3.2 30.9 - - - +
145O GLU* 3.9 7.2 - - - -
146O ALA* 3.5 3.3 - - - +
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Residues in contact with VAL 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N ALA* 3.6 19.7 - - + +
137N LEU* 4.0 13.0 - - + -
140N GLU* 4.1 15.7 - - - +
105O VAL 3.6 2.9 - - - -
126O TYR* 3.7 20.4 - - + -
127O GLY* 1.3 79.0 - - - +
129O SER* 1.3 65.2 + - - +
130O GLU* 3.6 29.8 - - + +
141O LYS* 3.0 28.4 + - - +
142O ALA* 4.1 2.8 - - - +
145O GLU* 3.6 9.2 + - - +
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Residues in contact with SER 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O PHE 3.3 2.8 - - - +
104O TYR* 3.3 3.3 - - - -
105O VAL* 2.9 33.2 + - - +
128O VAL* 1.3 77.6 - - - +
130O GLU* 1.3 61.1 + - - +
132O LEU* 3.7 14.9 - - - +
138O SER* 3.2 49.4 + - - -
141O LYS* 3.9 13.0 - - - +
142O ALA* 4.5 1.8 - - - +
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Residues in contact with GLU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N SER* 2.7 36.0 + - - -
135N LYS 4.7 1.7 + - - -
136N ALA* 4.4 6.8 - - + +
137N LEU* 3.7 10.4 - - - +
95O PHE* 5.8 0.3 - - - -
103O PHE 3.7 2.5 - - - -
104O TYR* 3.5 28.0 - - + +
128O VAL* 3.6 17.6 - - + +
129O SER* 1.3 76.4 + - - +
131O GLY* 1.3 58.8 + - - +
132O LEU* 3.5 4.7 + - - +
2Y C 3.3 25.6 - - - +
3Y C 3.2 20.4 + - - +
6Y C 3.2 14.9 + - - +
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Residues in contact with GLY 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O LYS* 3.1 42.2 - - - +
103O PHE 3.1 8.5 + - - -
104O TYR* 4.1 5.8 - - - -
130O GLU* 1.3 72.3 - - - +
132O LEU* 1.3 65.4 + - - +
133O LYS 3.6 0.3 + - - -
3Y C 3.3 10.8 + - - -
5Y C 4.6 0.7 - - - -
6Y C 3.2 17.7 + - - -
7Y C 3.9 2.6 + - - -
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Residues in contact with LEU 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O PHE* 2.8 37.6 + - - +
129O SER* 3.7 17.7 - - - +
130O GLU 3.5 2.9 - - - +
131O GLY* 1.3 76.5 - - - +
133O LYS* 1.3 59.7 - - - +
134O SER 3.4 6.1 - - - +
137O LEU* 4.2 17.7 - - + +
138O SER* 3.3 27.1 - - - +
141O LYS* 4.8 11.4 - - + -
6Y C 4.1 30.5 - - + +
7Y C 3.7 33.9 - - + +
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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