Contacts of the strand formed by residues 120 - 130 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26O PHE* 4.3 12.1 - + - -
85O ALA* 3.1 37.6 - - + +
86O HIS 3.2 39.2 + - - -
87O SER* 3.5 18.3 + - - -
112O ARG* 4.6 8.0 + - - -
114O GLN* 3.3 29.3 + - - +
112P ARG* 3.7 45.3 - - + +
113P VAL 3.0 13.0 - - - +
114P GLN* 4.3 2.9 - - + -
118P GLY 3.4 14.4 - - - +
119P SER* 1.3 77.3 + - - +
121P HIS* 1.3 76.1 + - - +
158P PHE* 5.0 1.1 - - - -
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Residues in contact with HIS 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O TYR 4.2 4.3 - - - -
84O TRP* 3.3 52.0 + + - -
86O HIS* 3.2 33.0 - + + +
112P ARG* 3.5 1.7 - - - -
113P VAL* 2.8 36.4 + - - +
119P SER* 4.4 0.9 - - - -
120P TYR* 1.3 78.4 + - - +
122P GLU* 1.3 56.7 + - - +
154P ALA* 3.6 26.3 - - - +
157P SER* 3.4 24.2 - - - -
158P PHE* 3.2 43.9 - + + -
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Residues in contact with GLU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 3.1 30.3 + - - +
87O SER* 3.4 20.7 - - - -
88O ILE* 2.8 50.5 + - + +
147O VAL* 4.8 0.2 - - - +
89P THR* 2.9 36.5 + - - +
110P PHE* 4.0 8.8 - - - +
111P VAL 3.2 15.0 - - - +
112P ARG* 3.8 17.6 - - + +
121P HIS* 1.3 75.6 - - - +
123P ASP* 1.3 66.9 + - - +
154P ALA* 4.9 0.2 - - - -
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Residues in contact with ASP 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 4.4 9.0 - - + -
88O ILE* 3.7 11.3 - - - +
147O VAL* 3.6 17.4 - - - +
148O THR* 5.1 2.6 + - - -
151O LEU* 5.7 1.7 - - - +
110P PHE* 3.6 4.3 - - - -
111P VAL* 3.0 31.1 + - - +
122P GLU* 1.3 74.5 - - - +
124P VAL* 1.3 72.7 + - - +
150P GLY 4.7 1.8 - - - -
153P ARG* 3.1 46.1 + - + +
154P ALA* 3.7 25.9 - - - +
157P SER* 4.6 3.6 + - - -
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Residues in contact with VAL 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ILE* 3.8 1.8 - - + +
91O GLN* 3.9 5.4 - - - +
143O ARG* 4.2 21.5 - - + +
144O LYS* 4.4 12.4 - - + -
147O VAL* 3.6 27.4 - - + -
108P CYS* 4.9 6.5 - - + -
109P ALA 3.4 4.0 - - - +
110P PHE* 3.4 38.8 - - + -
123P ASP* 1.3 83.2 + - - +
125P GLY* 1.3 74.0 + - - +
126P TYR* 5.4 1.6 - - + -
150P GLY* 3.9 3.1 - - - -
153P ARG* 2.7 33.3 + - - +
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Residues in contact with GLY 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O LYS* 4.8 0.4 - - - -
108P CYS* 3.3 4.7 - - - -
109P ALA 2.7 31.8 + - - +
124P VAL* 1.3 82.3 - - - +
126P TYR* 1.3 61.4 + - - +
146P ALA 3.5 7.9 - - - -
149P ASP* 3.5 5.8 - - - -
150P GLY* 3.2 28.1 - - - -
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Residues in contact with TYR 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ALA* 3.6 15.9 - - - -
139O LEU* 3.3 22.5 - - + +
140O GLU* 3.6 44.9 - - + +
143O ARG* 4.1 12.6 - - + -
144O LYS* 4.2 4.5 - - + +
94P ASP* 2.7 34.3 + - - +
95P PHE* 3.9 1.9 - - - -
106P GLY* 3.9 15.6 - - - -
107P VAL 3.4 13.9 - - - -
108P CYS* 3.7 19.3 - - + -
124P VAL* 5.4 1.3 - - + -
125P GLY* 1.3 72.6 - - - -
127P GLY* 1.3 64.6 + - - +
128P VAL* 3.7 22.9 - - + -
145P GLU* 3.6 10.9 - - - +
146P ALA* 3.4 11.2 - - - -
149P ASP* 3.1 16.2 + - - +
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Residues in contact with GLY 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P GLY* 3.6 1.0 - - - -
107P VAL 2.7 36.6 + - - -
126P TYR* 1.3 76.3 - - - +
128P VAL* 1.3 65.3 + - - +
142P ALA* 3.2 29.1 - - - +
145P GLU* 3.8 7.2 - - - -
146P ALA* 3.5 6.0 - - - +
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Residues in contact with VAL 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ALA* 3.9 29.6 - - + -
137O LEU* 5.7 4.9 - - + -
140O GLU* 4.8 9.2 - - - +
105P VAL 3.5 7.2 - - - +
126P TYR* 3.7 21.3 - - + -
127P GLY* 1.3 79.8 - - - +
129P SER* 1.3 69.8 + - - +
130P GLU* 4.5 14.8 - - + +
141P LYS* 3.0 28.9 + - - +
142P ALA* 4.0 2.8 - - - +
145P GLU* 3.4 11.6 + - - +
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Residues in contact with SER 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P PHE 3.5 7.5 - - - +
105P VAL* 3.2 29.2 + - - +
128P VAL* 1.3 77.6 - - - +
130P GLU* 1.3 60.8 + - - +
132P LEU* 4.0 15.4 - - - +
138P SER* 3.2 45.7 + - - -
141P LYS* 3.6 20.1 - - - +
142P ALA* 4.2 2.2 - - - +
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Residues in contact with GLU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O SER* 4.8 9.0 + - - -
136O ALA* 5.7 1.9 - - - +
103P PHE 3.8 2.9 - - - -
104P TYR* 3.4 38.9 - - + +
128P VAL* 4.2 15.4 - - + +
129P SER* 1.3 74.9 + - - +
131P GLY* 1.3 63.4 + - - +
132P LEU* 3.5 5.3 + - - +
141P LYS* 5.4 0.8 - - - +
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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