Contacts of the strand formed by residues 190 - 197 (chain A) in PDB entry 1RM1
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 PHE 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TYR* 4.5 0.3 - - - -
186A GLU 3.3 5.8 + - - +
187A PRO* 3.3 17.9 - - - +
189A LEU* 1.3 81.9 - - + +
191A PRO* 1.3 68.3 - - + +
192A GLY* 3.2 43.6 + - - +
194A ILE* 5.2 8.3 - - + -
205A LEU* 4.7 7.2 - - + -
207A PHE* 3.6 27.4 - + - -
10D T 3.5 16.4 - - - -
11D A 3.3 72.2 - + - +
26E T 4.0 3.8 - + - -
27E A 3.5 25.6 - + - -
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Residues in contact with PRO 191 (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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172A LEU* 3.7 8.5 - - - +
185A TYR* 3.3 20.4 + - - -
187A PRO* 3.9 15.0 - - + +
189A LEU 4.5 1.8 - - - +
190A PHE* 1.3 96.5 - - + +
192A GLY* 1.3 57.0 + - - +
207A PHE* 4.5 2.5 - - - -
208A VAL* 5.0 3.6 - - - +
27E A 3.3 46.4 - - + +
28E T 3.6 42.2 - - - +
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Residues in contact with GLY 192 (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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184A SER 4.5 1.9 - - - +
185A TYR* 3.8 6.2 - - - -
190A PHE* 3.2 31.2 - - - +
191A PRO* 1.3 80.6 - - - +
193A LEU* 1.3 63.1 + - - -
194A ILE* 3.8 5.0 + - - +
205A LEU* 5.5 0.7 - - - -
206A ILE 3.4 10.5 - - - -
207A PHE* 3.6 21.7 - - - -
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Residues in contact with LEU 193 (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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172A LEU* 3.4 38.8 - - + +
175A LEU* 4.3 11.0 - - + -
176A ALA* 3.7 25.4 - - + +
183A SER* 3.3 26.2 - - - -
184A SER 3.9 1.6 - - - +
185A TYR* 3.9 21.9 - - + -
192A GLY* 1.3 72.5 - - - -
194A ILE* 1.3 65.3 + - - +
195A TYR* 3.8 4.0 - - + +
204A LEU 3.4 1.2 - - - +
205A LEU* 3.3 4.9 - - - -
206A ILE* 2.7 61.3 + - + +
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Residues in contact with ILE 194 (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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182A PHE 3.3 3.1 - - - +
183A SER* 3.1 3.5 - - - -
184A SER* 3.0 52.6 + - - +
190A PHE* 5.2 4.9 - - + -
192A GLY 4.4 7.6 - - - +
193A LEU* 1.3 74.9 - - - +
195A TYR* 1.3 59.9 + - - +
196A ARG* 4.1 20.7 - - + +
203A VAL* 4.0 23.3 - - + -
204A LEU 3.5 3.6 - - - +
205A LEU* 4.0 14.1 - - + -
11D A 3.2 35.0 - - - +
12D T 3.6 16.4 - - - +
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Residues in contact with TYR 195 (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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175A LEU* 4.4 10.8 - - + -
179A HIS* 3.8 29.3 - + + -
182A PHE* 3.4 37.5 - + + -
183A SER* 4.0 15.3 - - - -
193A LEU* 3.6 2.8 + - + -
194A ILE* 1.3 73.4 - - - +
196A ARG* 1.3 60.2 + - - +
197A MET* 3.5 39.4 + - + -
202A ILE 3.7 0.2 - - - +
203A VAL* 3.5 2.5 - - - -
204A LEU* 2.8 44.1 + - + +
206A ILE* 3.8 20.0 - - + -
230A ILE* 3.8 30.1 - - + +
233A VAL* 5.6 1.7 - - + +
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Residues in contact with ARG 196 (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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182A PHE* 2.7 39.1 + - - +
184A SER* 5.3 3.2 + - - -
194A ILE* 4.1 16.4 - - + +
195A TYR* 1.3 73.7 - - - +
197A MET* 1.3 65.4 + - - +
198A VAL* 3.7 2.1 + - - +
202A ILE 4.2 2.7 - - - -
203A VAL* 3.6 20.1 - - + +
12D T 3.4 32.7 + - - -
13D A 2.6 30.9 + - - -
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Residues in contact with MET 197 (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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182A PHE* 5.3 0.4 - - - -
195A TYR* 3.5 17.9 + - + -
196A ARG* 1.3 74.7 - - - +
198A VAL* 1.3 63.3 + - - +
199A LYS 4.0 7.9 - - - +
200A PRO* 3.2 28.0 - - - +
201A LYS* 3.4 17.3 + - - +
202A ILE 3.0 20.7 + - - +
204A LEU* 3.7 17.9 - - + -
226A ALA* 3.5 41.7 - - - +
229A ALA* 4.0 17.7 - - + -
230A ILE* 3.9 22.9 - - + +
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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