Contacts of the strand formed by residues 145 - 151 (chain D) in PDB entry 3RMD
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 ARG 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D TYR* 3.3 6.0 - - - -
140D ASP 3.1 26.5 + - - -
143D ASP* 2.9 27.1 + - + +
144D ASP* 1.3 113.5 + - - +
146D PHE* 1.3 59.8 + - - +
147D TYR* 3.2 30.9 - - + +
184D ASP 4.4 4.9 + - - -
185D LYS* 2.8 42.5 + - - +
186D ILE 4.7 0.2 - - - -
187D ILE* 3.8 23.3 - - + -
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR* 4.2 13.7 - - + -
138D HIS 4.0 0.2 - - - -
139D TYR* 3.5 41.3 - + + +
144D ASP* 5.5 0.2 - - - -
145D ARG* 1.3 68.6 - - - +
147D TYR* 1.3 65.7 + - - +
148D VAL* 3.2 4.9 + - + +
182D ILE* 3.3 37.2 - - + -
185D LYS* 3.2 24.1 + - + -
186D ILE* 3.4 22.3 - - + +
187D ILE 3.1 19.3 + - - -
325D ILE* 4.7 4.5 - - + -
328D VAL* 4.3 7.9 - - + -
329D TYR* 3.5 35.2 - + + -
332D LEU* 3.7 15.0 - - + -
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR* 3.3 1.7 - - - -
138D HIS 2.8 44.4 + - - +
140D ASP* 4.6 4.3 - - + -
143D ASP* 2.7 32.5 + - + +
145D ARG* 3.2 38.0 - - + +
146D PHE* 1.3 69.9 - - - +
148D VAL* 1.3 59.3 + - - +
149D PHE* 3.5 12.8 - + + -
187D ILE* 4.0 21.1 - - + +
189D MET* 3.4 28.3 - - + -
204D PHE* 3.5 32.3 - + + -
208D LYS* 3.2 12.8 - - - -
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE 3.4 6.3 - - - +
137D THR* 3.3 26.7 - - + +
146D PHE* 3.2 14.6 + - + +
147D TYR* 1.3 71.2 - - - +
149D PHE* 1.3 69.1 + - - +
150D ASP* 3.8 1.5 + - + +
186D ILE* 4.9 5.4 - - + -
187D ILE 3.5 5.9 + - - +
188D TYR* 4.2 18.6 - - + -
189D MET* 3.0 33.1 + - - +
321D ILE* 3.8 28.5 - - + -
324D ASN* 5.2 0.7 - - - +
325D ILE* 3.6 23.8 - - + -
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ALA* 3.6 3.8 + - - -
136D ILE* 2.8 48.0 + - + +
138D HIS* 4.9 0.4 - - + -
147D TYR* 3.5 21.1 - + + -
148D VAL* 1.3 75.6 - - - +
150D ASP* 1.3 60.5 + - - +
151D LEU 4.1 0.2 + - - -
189D MET* 3.4 33.7 - - + -
191D PHE* 4.0 15.7 - + - -
197D LEU* 3.1 34.5 - - + +
200D GLU* 4.1 7.2 - - + -
201D TYR* 3.6 38.4 - + + -
204D PHE* 3.6 29.2 - + + -
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASP 4.5 0.7 - - - +
135D ALA* 4.8 4.0 - - - +
148D VAL* 3.8 2.8 + - + -
149D PHE* 1.3 74.4 - - - +
151D LEU* 1.3 88.8 + - - +
152D LEU* 3.9 3.8 + - - +
162D TRP* 4.2 0.2 - - - +
188D TYR* 3.2 40.2 + - + +
189D MET 3.2 6.1 + - - -
190D PRO* 4.3 2.9 - - + -
191D PHE* 2.7 37.4 + - - +
197D LEU* 4.1 1.3 - - - +
317D HIS* 3.4 13.7 + - - -
321D ILE* 2.8 40.2 - - + +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE 4.5 3.4 - - - +
134D ASP* 3.8 31.4 + - + +
149D PHE 4.1 0.2 + - - -
150D ASP* 1.3 90.2 + - - +
152D LEU* 1.3 57.4 + - - +
153D ASN* 2.7 34.5 - - + +
159D VAL* 4.3 1.0 - - - +
191D PHE* 3.6 4.7 - - + +
192D ASP 3.2 23.3 - - - +
193D ASN 3.0 29.8 - - - +
194D GLU* 4.1 13.9 - - + +
197D LEU* 3.3 27.4 - - + -
313D ARG* 2.8 22.5 + - - -
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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