Contacts of the strand formed by residues 150 - 155 (chain B) in PDB entry 1HRN
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 VAL 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PHE* 3.5 12.0 - - - -
148B GLU* 3.1 18.2 + - + +
149B ASP* 1.3 79.4 - - - +
151B PHE* 1.3 58.7 + - - +
168B GLY* 2.5 32.9 + - - -
169B GLY* 3.7 24.2 - - - +
312B GLU* 3.4 33.9 - - + +
313B PHE 3.3 7.0 - - - +
314B ASP* 3.7 30.3 - - + +
315B ARG 4.5 0.2 - - - +
316B ARG* 5.6 0.9 - - + -
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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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33B THR* 3.7 13.0 - - + -
123B MET* 3.6 48.2 - - + -
137B PHE* 3.8 28.0 - + + -
150B VAL* 1.3 76.1 - - - +
152B SER* 1.3 58.7 + - - +
153B PHE* 3.6 20.4 - + - -
165B ILE* 4.7 2.0 - - + -
166B VAL 3.0 12.8 - - - +
167B LEU* 3.7 18.4 - - + -
190B TRP* 3.9 16.4 - + - -
312B GLU 3.6 0.2 - - - -
313B PHE* 2.7 70.8 + + + +
315B ARG* 4.7 2.9 - - + -
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Residues in contact with SER 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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151B PHE* 1.3 70.4 - - - +
153B PHE* 1.3 65.7 + - - +
164B GLN 3.6 0.7 - - - +
165B ILE* 3.0 10.0 - - - +
166B VAL* 2.7 35.1 + - - -
169B GLY 2.9 21.6 + - - -
170B SER* 3.3 8.1 - - - -
310B TYR* 3.3 28.3 - - - -
311B THR 3.3 4.7 - - - -
312B GLU* 3.3 23.6 - - - +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.8 1.3 - - + -
31B PHE* 3.5 32.5 - - + -
33B THR* 4.4 0.2 - - + -
123B MET* 4.5 4.7 - - + -
151B PHE* 3.6 29.6 - + - -
152B SER* 1.3 78.0 - - - +
154B TYR* 1.3 59.6 + - - +
155B TYR* 3.7 23.3 - + - -
164B GLN 3.5 1.6 - - - -
165B ILE* 3.6 34.5 - - + -
216B THR* 3.5 27.8 - - + -
306B ILE* 4.0 18.3 - - + +
310B TYR* 3.8 9.4 - - - -
311B THR* 2.8 33.9 + - - +
313B PHE* 3.6 17.7 - + + -
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Residues in contact with TYR 154 (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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153B PHE* 1.3 72.9 - - - +
155B TYR* 1.3 78.0 + - - +
156B ASN* 3.0 39.8 + - + -
161B LEU* 3.9 18.2 - - + +
163B GLY* 3.0 13.8 - - - -
164B GLN* 2.8 45.8 + - + +
174B HIS* 3.7 47.3 + + + +
306B ILE* 5.0 0.4 - - - -
310B TYR* 3.6 20.9 - + + +
325B ALA* 4.2 15.3 - - + -
326B ARG* 3.7 25.0 + - - -
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Residues in contact with TYR 155 (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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6B LEU* 3.5 25.2 - - + +
14B TYR* 3.4 51.2 + + + +
30B VAL* 5.4 0.5 - - - +
31B PHE 4.1 2.8 + - - -
153B PHE* 3.7 20.4 - + - -
154B TYR* 1.3 97.2 - - - +
156B ASN* 1.3 60.8 + - - +
157B ARG* 5.2 0.3 - - - +
162B GLY 4.0 0.7 - - - -
216B THR* 2.6 37.2 + - - -
303B ALA* 3.8 32.1 - - + -
306B ILE* 3.9 30.7 + - + +
307B ARG* 3.5 26.9 - - + +
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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