Contacts of the strand formed by residues 148 - 155 (chain A) in PDB entry 1RMO
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 HIS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A CRO 3.1 22.0 + - + +
145A TYR* 3.7 11.0 - + - -
146A ASN* 3.1 33.8 + - + +
147A SER* 1.4 76.7 - - - +
149A ASN* 1.3 73.1 + - - +
150A VAL* 5.1 0.4 - - + -
165A PHE* 5.3 1.1 - - + -
166A LYS 3.4 24.2 - - - +
167A ILE* 3.4 27.1 - - + +
168A ARG* 3.1 41.8 + - - +
201A LEU 3.6 0.9 - - - +
202A SER* 3.6 0.3 + - - -
203A THR* 2.9 39.8 + - - +
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Residues in contact with ASN 149 (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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148A HIS* 1.3 83.3 + - - +
150A VAL* 1.3 61.3 + - - +
151A TYR* 3.5 37.2 + - + +
165A PHE* 3.4 16.8 - - - +
166A LYS 5.1 1.0 + - - +
200A TYR* 3.7 30.8 - - + -
201A LEU 3.3 2.7 - - - -
202A SER* 3.8 15.2 + - - +
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Residues in contact with VAL 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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66A CRO 3.6 36.1 - - + -
69A GLN* 3.8 17.9 - - - +
148A HIS* 4.8 1.1 - - + +
149A ASN* 1.3 75.0 - - - +
151A TYR* 1.3 58.8 + - - +
152A ILE* 3.8 5.5 + - + +
163A VAL* 3.3 29.8 - - + -
165A PHE* 3.6 19.1 - - + -
200A TYR* 3.0 6.9 - - - -
201A LEU* 2.8 47.9 + - + +
203A THR* 4.0 12.3 - - + -
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Residues in contact with TYR 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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149A ASN* 3.5 39.6 + - + +
150A VAL* 1.3 71.4 - - - +
152A ILE* 1.4 61.7 + - - +
153A MET* 5.3 3.3 - - + +
162A LYS 4.0 0.2 - - - +
163A VAL* 3.2 6.3 - - - +
164A ASN* 3.0 56.9 + - - +
165A PHE* 4.9 3.1 - - + -
199A HIS 3.7 4.5 - - - +
200A TYR* 3.7 29.8 - + + -
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Residues in contact with ILE 152 (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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74A TYR* 3.8 9.2 - - - +
84A PHE* 3.9 16.8 - - + -
150A VAL* 4.1 7.4 - - + +
151A TYR* 1.4 78.4 - - - +
153A MET* 1.4 70.0 - - - +
161A ILE* 3.9 21.5 - - + -
162A LYS 3.7 3.6 - - - +
163A VAL* 4.0 14.6 - - + -
196A PRO* 3.9 13.5 - - + -
197A ASP 4.4 0.4 - - - +
198A ASN* 3.4 7.1 - - - +
199A HIS* 2.9 66.0 + - + +
201A LEU* 3.9 22.7 - - + -
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Residues in contact with MET 153 (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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151A TYR* 5.3 4.0 - - + +
152A ILE* 1.4 82.6 - - - +
154A ALA* 1.3 66.2 + - - +
161A ILE* 3.3 5.4 - - - +
162A LYS* 2.9 69.6 + - + +
164A ASN* 5.7 4.7 - - - +
196A PRO* 4.7 1.1 - - - -
198A ASN* 3.9 26.2 - - - +
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Residues in contact with ALA 154 (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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153A MET* 1.3 85.6 - - - +
155A ASP* 1.3 59.3 + - - +
156A LYS* 3.7 22.1 + - - +
160A GLY 3.8 5.2 - - - +
162A LYS* 4.7 1.0 - - - +
195A LEU* 4.2 14.6 - - + -
196A PRO* 3.3 42.5 + - + +
198A ASN* 4.6 2.2 + - - -
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Residues in contact with ASP 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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153A MET 3.7 0.6 + - - -
154A ALA* 1.3 73.6 - - - +
156A LYS* 1.4 62.1 + - - +
157A GLN* 3.2 18.4 + - - +
158A LYS* 3.0 26.8 + - - +
159A ASN 3.1 2.8 + - - -
160A GLY* 2.8 42.0 + - - +
161A ILE 4.1 1.1 - - - +
162A LYS* 3.6 28.9 + - + +
184A GLN* 2.5 26.8 - - - +
195A LEU* 5.3 0.4 - - - -
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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