Contacts of the strand formed by residues 147 - 153 (chain B) in PDB entry 4HNE
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 ILE 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B PHE* 3.5 43.3 - - + -
140B VAL 3.4 13.5 - - - +
141B LYS* 3.9 23.6 - - - +
145B GLY 5.3 0.2 - - - +
146B ARG* 1.3 79.5 - - + +
148B ILE* 1.3 68.3 + - - +
149B ALA 4.1 3.4 - - - +
263B PHE* 3.6 43.4 - - + -
265B GLU* 5.1 3.1 - - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.7 40.9 - - + +
116B GLN* 4.8 3.4 - - + -
117B ALA* 4.4 13.9 - - + +
140B VAL* 2.9 12.5 + - + +
141B LYS* 3.8 27.8 - - - +
142B ASP* 3.7 31.6 - - - +
146B ARG* 4.0 5.8 - - + +
147B ILE* 1.3 79.3 - - - +
149B ALA* 1.3 70.7 + - + +
260B PHE* 5.1 0.4 - - + -
262B LEU* 4.1 11.4 - - - +
263B PHE* 3.4 20.1 + - - -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B TYR 3.6 1.0 - - - +
139B PHE* 3.6 5.5 - - - -
140B VAL* 2.9 35.3 + - + +
147B ILE* 4.1 2.6 - - - +
148B ILE* 1.3 82.4 - - + +
150B VAL* 1.3 66.9 + - - +
260B PHE* 3.4 40.4 - - + -
261B GLN 3.1 13.9 - - - +
263B PHE* 3.5 7.0 - - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 5.0 3.8 - - + -
137B SER* 4.9 4.9 - - - -
138B TYR 3.4 12.1 - - - +
139B PHE* 4.0 20.2 - - + -
140B VAL* 4.6 0.2 - - - -
149B ALA* 1.3 77.8 - - - +
151B PHE* 1.3 61.2 + - - +
152B LYS* 4.0 26.6 + - + -
259B SER* 3.2 8.0 + - - +
260B PHE* 4.7 0.7 - - - -
261B GLN* 2.7 39.9 + - + +
263B PHE* 4.5 2.2 - - + -
500B ADP 3.7 45.8 - - + +
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.5 0.5 - - - +
137B SER* 3.4 4.0 - - - -
138B TYR* 2.9 40.2 + - + +
140B VAL* 3.6 21.6 - - + +
150B VAL* 1.3 72.3 - - - +
152B LYS* 1.3 59.5 + - - +
153B PRO* 3.5 30.7 - - + -
214B VAL* 3.4 38.8 - - + -
216B LEU* 3.9 12.3 - - + -
221B PHE* 3.4 37.9 - + + -
256B LYS* 3.6 11.7 - - + -
258B GLY* 3.6 22.7 - - - -
259B SER 3.2 13.0 - - - -
260B PHE* 3.9 17.3 - + + +
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.0 16.2 - - - +
137B SER* 4.2 9.6 - - - +
150B VAL* 4.2 17.0 - - + +
151B PHE* 1.3 79.3 - - - +
153B PRO* 1.3 68.2 - - - +
154B LYS 3.5 0.5 + - - -
157B GLU* 4.7 4.5 - - + +
190B TYR* 4.0 8.1 - - + +
193B GLU* 3.0 35.1 + - - +
258B GLY* 3.4 0.7 - - - -
259B SER* 2.9 42.9 + - - +
345B ILE 4.5 0.2 + - - -
346B ASP* 3.8 12.9 + - - -
500B ADP 3.5 36.2 + - - -
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Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.5 8.4 - - - +
138B TYR* 3.8 12.1 - - + -
151B PHE* 3.5 20.6 - - + +
152B LYS* 1.3 89.8 - - - +
154B LYS* 1.3 66.1 + - - +
155B ASN* 4.5 1.8 - - - +
156B GLU* 3.1 42.0 + - + +
157B GLU* 3.6 10.0 + - - +
221B PHE* 4.9 1.1 - - + -
256B LYS* 4.1 32.8 - - + -
257B VAL 3.6 6.7 - - - +
258B GLY* 3.7 3.4 - - - -
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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