Contacts of the strand formed by residues 120 - 132 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26U PHE* 4.1 12.8 - + - -
85U ALA* 3.1 37.6 - - + +
86U HIS 3.3 30.7 - - - -
87U SER* 3.6 17.9 + - - -
112U ARG* 4.7 6.9 + - - -
114U GLN* 3.6 29.4 + - - +
112V ARG* 4.0 42.2 - - + +
113V VAL 3.0 12.8 - - - +
114V GLN* 4.3 4.7 - - + -
118V GLY 3.4 15.9 - - - +
119V SER* 1.3 76.0 + - - +
121V HIS* 1.3 75.4 + - - +
158V PHE* 4.8 1.8 - - - -
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Residues in contact with HIS 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81U TYR 4.3 1.8 + - - -
84U TRP* 3.5 55.9 + + - -
85U ALA* 3.9 1.6 - - - -
86U HIS* 2.8 30.5 + - + -
112V ARG* 4.3 1.3 - - - -
113V VAL* 2.7 39.8 + - - +
119V SER* 5.1 0.2 - - - -
120V TYR* 1.3 83.6 + - - +
122V GLU* 1.3 57.8 + - - +
154V ALA* 3.6 23.6 - - - +
157V SER* 3.8 19.7 + - - -
158V PHE* 3.3 44.2 - + + -
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Residues in contact with GLU 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U HIS* 3.0 21.5 + - - +
87U SER* 3.5 19.1 - - - -
88U ILE* 3.0 49.0 + - + +
89V THR* 3.0 38.1 + - - +
110V PHE* 3.9 7.3 - - - +
111V VAL 3.2 15.5 - - - +
112V ARG* 3.7 19.8 + - + -
121V HIS* 1.3 74.2 - - - +
123V ASP* 1.3 75.3 + - - +
154V ALA* 4.7 0.4 - - - -
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Residues in contact with ASP 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72U ILE* 5.9 0.7 - - - +
86U HIS* 3.5 8.8 + - - -
88U ILE* 3.7 7.1 - - - +
147U VAL* 3.2 22.6 - - - +
148U THR* 5.7 0.2 + - - -
151U LEU* 5.5 3.0 - - - +
110V PHE* 3.5 3.6 - - - +
111V VAL* 3.0 32.6 + - - +
122V GLU* 1.3 81.8 - - - +
124V VAL* 1.3 65.0 + - - +
150V GLY 4.6 1.7 - - - +
153V ARG* 2.8 53.0 + - + +
154V ALA* 3.9 3.5 - - - +
156V ARG* 5.9 0.3 - - - -
157V SER* 3.5 12.7 + - - -
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Residues in contact with VAL 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88U ILE* 3.5 6.1 - - + -
91U GLN* 4.2 13.7 - - - +
143U ARG* 4.4 13.5 - - + +
144U LYS* 4.1 8.3 - - + -
147U VAL* 3.4 31.1 - - + +
108V CYS* 4.3 13.5 - - + -
109V ALA 3.3 11.9 - - - +
110V PHE* 3.5 26.5 - - + -
123V ASP* 1.3 76.4 + - - +
125V GLY* 1.3 70.2 + - - +
126V TYR* 5.5 0.7 - - + -
150V GLY* 4.0 2.9 - - - -
153V ARG* 2.6 36.4 + - - +
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Residues in contact with GLY 125 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144U LYS* 4.5 1.1 - - - -
108V CYS* 3.3 4.0 - - - -
109V ALA 2.8 31.7 + - - +
124V VAL* 1.3 80.3 - - - +
126V TYR* 1.3 60.2 + - - +
146V ALA* 3.6 7.9 - - - -
149V ASP* 3.4 6.7 - - - -
150V GLY* 3.3 28.7 - - - -
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Residues in contact with TYR 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U ALA 3.4 16.2 - - - -
139U LEU* 3.3 25.4 - - + +
140U GLU* 3.6 45.4 - - + +
143U ARG* 4.1 11.4 - - + -
144U LYS* 4.0 2.6 - - + +
94V ASP* 2.7 36.2 + - - +
95V PHE* 3.8 1.0 - - - -
106V GLY* 3.6 12.9 - - - -
107V VAL 3.4 11.0 - - - -
108V CYS* 3.5 22.7 - - + -
124V VAL* 5.5 0.7 - - + -
125V GLY* 1.3 72.8 - - - -
127V GLY* 1.3 75.8 + - - +
128V VAL* 3.7 17.0 - - + +
145V GLU* 3.8 2.4 - - - +
146V ALA* 3.5 11.1 - - - -
149V ASP* 3.1 20.7 + - - +
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Residues in contact with GLY 127 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106V GLY* 3.4 4.7 - - - -
107V VAL 2.7 36.8 + - - -
126V TYR* 1.3 74.1 - - - +
128V VAL* 1.3 63.2 + - - +
142V ALA* 3.3 29.8 - - - +
145V GLU* 4.2 6.1 - - - -
146V ALA* 3.4 5.1 - - - +
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Residues in contact with VAL 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U ALA* 3.6 27.1 - - + +
137U LEU* 4.8 8.3 - - + -
140U GLU* 4.5 12.1 - - - +
105V VAL 3.4 4.5 - - - +
126V TYR* 3.7 19.3 - - + -
127V GLY* 1.3 80.2 - - - +
129V SER* 1.3 65.2 + - - +
130V GLU* 3.6 29.4 - - + +
141V LYS* 3.0 26.2 + - - +
142V ALA* 4.2 3.3 - - - +
145V GLU* 3.7 6.6 + - - +
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Residues in contact with SER 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103V PHE 3.3 3.3 - - - +
104V TYR* 3.3 3.1 - - - -
105V VAL* 2.8 37.7 + - - +
128V VAL* 1.3 76.8 - - - +
130V GLU* 1.3 60.0 + - - +
132V LEU* 3.7 14.6 - - - +
138V SER* 3.2 47.4 + - - -
141V LYS* 3.7 15.5 - - - +
142V ALA* 4.4 2.0 - - - -
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Residues in contact with GLU 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134U SER* 4.0 22.5 + - - -
135U LYS 5.7 0.2 + - - -
136U ALA* 4.8 4.9 + - + +
137U LEU* 4.7 5.9 - - - +
95V PHE* 6.1 0.2 - - - -
103V PHE 3.6 3.1 - - - -
104V TYR* 3.7 32.9 - - + +
105V VAL 5.3 0.4 - - - +
128V VAL* 3.6 25.0 - - + +
129V SER* 1.3 77.9 + - - +
131V GLY* 1.3 58.8 + - - +
132V LEU* 3.5 4.9 + - - +
141V LYS* 5.9 0.2 - - - +
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Residues in contact with GLY 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102V LYS* 3.3 39.0 - - - +
103V PHE 3.1 8.9 + - - -
104V TYR* 4.5 7.3 - - - -
130V GLU* 1.3 72.2 - - - +
132V LEU* 1.3 67.3 + - - +
133V LYS* 3.6 2.9 + - - +
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Residues in contact with LEU 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103V PHE* 2.7 37.1 + - - +
129V SER* 3.7 17.9 - - - +
130V GLU 3.5 4.2 - - - +
131V GLY* 1.3 76.9 - - - +
133V LYS* 1.3 61.4 + - - +
134V SER* 3.5 5.6 - - - +
137V LEU* 4.1 20.9 - - + +
138V SER* 3.2 29.6 - - - +
141V LYS* 4.7 12.1 - - + -
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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