Contacts of the strand formed by residues 146 - 157 (chain A) in PDB entry 3HKS
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 GLU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.0 37.8 + - - -
38A PRO* 5.8 0.4 - - + +
65A PHE* 3.3 32.4 - - + +
66A THR* 5.4 1.4 - - - +
142A SER* 3.3 3.7 - - - -
143A SER 2.9 36.2 + - - +
144A MET* 4.4 3.8 - - + +
145A GLY* 1.3 79.0 - - - +
147A GLU* 1.3 68.0 + - - +
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Residues in contact with GLU 147 (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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65A PHE* 4.2 2.4 - - - -
90A TYR* 4.9 2.8 + - - -
111A LYS* 2.7 38.3 + - - -
113A ASP* 4.0 5.7 - - - +
114A LEU* 3.6 22.2 - - + +
140A VAL* 3.9 10.0 - - + +
141A MET 3.2 6.3 - - - +
142A SER* 3.6 21.9 - - - -
145A GLY 5.0 2.9 - - - -
146A GLU* 1.3 89.3 - - - +
148A GLN* 1.3 62.0 + - - +
163A EDO 3.9 15.7 + - - -
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Residues in contact with GLN 148 (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 ILE 4.7 5.2 - - - +
65A PHE* 3.7 50.0 + - + +
114A LEU* 5.4 0.2 - - - -
117A PRO* 6.0 0.9 - - + -
140A VAL* 3.5 3.3 - - - -
141A MET* 2.8 44.1 + - + +
147A GLU* 1.3 77.8 - - - +
149A ILE* 1.3 76.7 + - - +
150A CYS* 3.3 7.6 + - + +
163A EDO 3.5 9.0 - - - +
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Residues in contact with ILE 149 (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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101A VAL* 4.6 8.1 - - + -
103A LEU* 5.5 0.7 - - + -
114A LEU* 4.1 24.7 - - + -
115A LYS 3.4 26.2 - - - +
117A PRO* 3.8 34.1 - - + +
122A LEU* 3.8 11.6 - - + +
126A MET* 4.1 17.5 - - + -
138A VAL* 3.5 34.3 - - + -
139A SER 3.5 4.9 - - - +
140A VAL* 4.2 2.0 - - + +
148A GLN* 1.3 78.2 - - - +
150A CYS* 1.3 60.7 + - - +
151A ALA 4.2 8.3 - - - +
152A VAL* 4.3 4.0 - - + -
163A EDO 2.9 13.7 + - - +
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Residues in contact with CYS 150 (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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87A ARG* 3.4 30.7 + - - -
122A LEU* 4.0 14.2 - - - +
139A SER* 2.9 24.5 + - - -
140A VAL 4.3 0.9 - - - -
141A MET* 4.0 28.7 - - + -
148A GLN* 4.0 13.2 - - + +
149A ILE* 1.3 73.5 - - - +
151A ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 151 (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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87A ARG* 3.8 18.4 - - - +
122A LEU* 4.4 6.7 - - - +
137A VAL 4.6 0.2 - - - -
138A VAL* 3.6 2.9 - - - +
139A SER* 3.0 43.6 + - - +
149A ILE* 3.8 1.1 - - - +
150A CYS* 1.3 80.2 - - - +
152A VAL* 1.3 70.1 + - - +
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Residues in contact with VAL 152 (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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122A LEU* 3.8 25.9 - - + +
125A GLN* 3.3 45.8 + - + +
126A MET* 3.5 31.9 - - + +
136A ILE* 3.7 27.4 - - + -
137A VAL 3.5 4.9 - - - +
138A VAL* 4.8 3.4 - - + -
149A ILE* 4.3 2.9 - - + -
151A ALA* 1.3 83.2 - - - +
153A LYS* 1.3 66.9 + - - +
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Residues in contact with LYS 153 (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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89A ASP* 4.3 13.3 + - - -
125A GLN* 5.1 1.3 - - - -
136A ILE* 3.4 8.6 - - - +
137A VAL* 2.8 65.3 + - + +
139A SER* 5.7 2.5 - - - -
152A VAL* 1.3 76.3 - - - +
154A GLU* 1.3 62.1 + - - +
155A VAL* 4.1 18.0 - - + +
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Residues in contact with GLU 154 (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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132A GLU* 4.7 1.2 - - - +
134A LYS* 2.9 45.9 + - + +
135A ASP 3.3 6.5 - - - +
136A ILE* 3.6 20.6 - - + +
153A LYS* 1.3 76.4 - - - +
155A VAL* 1.3 64.5 + - - +
156A GLY* 4.5 8.9 + - - +
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Residues in contact with VAL 155 (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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135A ASP* 2.8 41.3 + - - +
137A VAL* 3.8 26.9 - - + -
153A LYS* 4.1 24.5 - - + +
154A GLU* 1.3 78.4 - - - +
156A GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 156 (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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134A LYS* 3.5 10.4 - - - +
135A ASP* 2.9 26.9 + - - +
154A GLU* 3.7 9.4 + - - +
155A VAL* 1.3 81.1 - - - +
157A GLY* 1.3 65.9 + - - -
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Residues in contact with GLY 157 (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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133A GLY 4.2 5.4 - - - -
134A LYS* 4.3 8.9 - - - +
135A ASP* 4.5 3.8 - - - +
156A GLY* 1.3 76.7 - - - +
158A GLY* 1.3 58.8 + - - -
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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