Contacts of the strand formed by residues 243 - 254 (chain C) 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 LEU 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ARG* 4.2 29.4 - - + +
111B LEU* 4.2 0.2 - - - -
112B ARG* 3.3 45.1 - - + +
114B VAL* 4.1 14.4 - - + -
237C ASP* 6.1 0.9 - - + -
241C GLU* 3.4 25.1 + - - +
242C ASN* 1.3 75.4 - - - +
244C MET* 1.3 62.1 + - - +
245C LEU* 3.7 27.7 + - + +
266C VAL 4.0 0.7 - - - +
267C VAL* 3.3 5.9 - - - -
268C THR* 3.0 32.6 + - - -
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Residues in contact with MET 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.8 24.5 - - + -
62B VAL* 4.2 12.3 - - + -
85B VAL* 5.7 1.6 - - + -
111B LEU* 4.4 6.7 - - + -
112B ARG 2.7 14.6 + - - +
113B ILE* 3.4 32.0 - - + -
114B VAL* 2.8 29.3 + - - +
243C LEU* 1.3 73.8 - - - +
245C LEU* 1.3 67.3 + - - +
246C CYS* 4.0 5.6 - - - -
262C LEU* 4.2 11.2 - - - -
266C VAL 3.5 4.9 - - - +
267C VAL* 3.9 19.7 - - + -
276C PHE* 3.7 40.4 - - + -
279C ALA* 4.8 0.2 - - + -
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.3 41.3 - - + +
10B TYR* 3.7 11.8 - - + -
12B ARG* 3.6 14.1 - - - +
13B SER* 3.3 39.3 - - - +
114B VAL* 3.4 17.0 - - + -
243C LEU* 3.7 32.1 - - + +
244C MET* 1.3 75.7 - - - +
246C CYS* 1.3 63.0 + - - +
265C GLY* 3.3 0.7 - - - -
266C VAL* 3.0 34.5 + - + +
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Residues in contact with CYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.5 7.9 - - - +
10B TYR* 3.7 12.3 - - - -
113B ILE* 4.5 2.2 - - - -
114B VAL 3.1 5.5 + - - -
115B ALA* 3.0 12.6 - - - -
116B CYS 2.8 21.5 + - - -
244C MET* 4.0 11.2 - - - -
245C LEU* 1.3 77.9 - - - +
247C LEU* 1.3 80.2 + - - +
262C LEU* 3.7 21.5 - - - -
263C LYS 3.5 4.7 - - - +
265C GLY* 3.3 19.1 - - - -
276C PHE* 3.7 13.0 - - + -
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.9 28.0 - - + -
9B LEU* 5.1 0.7 - - + -
10B TYR* 3.8 14.6 - - + +
49B ALA* 6.4 2.0 - - + -
53B LYS* 5.7 4.3 - - - +
115B ALA* 4.0 1.6 - - - -
116B CYS* 3.1 13.2 - - + +
117B ASN 4.2 1.1 - - - +
118B SER* 4.1 19.7 - - - +
246C CYS* 1.3 85.0 - - - +
248C TYR* 1.3 60.9 + - - +
262C LEU* 3.3 12.8 - - - +
263C LYS* 3.1 42.3 + - + +
264C ASP* 4.0 27.1 + - + +
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Residues in contact with TYR 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.7 10.7 - - - -
74B ASP* 3.3 35.3 + - - -
76B TRP* 3.4 34.3 + + + -
78B PHE* 6.4 0.2 - - + -
115B ALA* 3.6 19.1 - - + -
116B CYS 2.8 25.5 + - - -
117B ASN* 3.3 35.7 + - - -
118B SER* 3.3 22.1 + - - -
119B LYS* 5.4 3.6 - - - -
247C LEU* 1.3 75.7 - - - +
249C ASP* 1.3 70.1 + - - +
250C LYS* 4.4 2.9 - - - -
251C VAL* 4.6 12.8 - - + -
261C SER 3.6 4.5 - - - +
262C LEU* 3.9 15.7 - - + -
263C LYS* 5.3 0.4 - - - -
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Residues in contact with ASP 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 5.2 2.1 + - - -
118B SER* 3.6 13.5 + - - -
119B LYS* 5.6 3.1 + - - -
248C TYR* 1.3 79.4 - - - +
250C LYS* 1.3 65.3 + - + +
261C SER* 2.8 27.3 + - - +
262C LEU* 4.4 4.6 - - - +
263C LYS* 2.9 41.7 + - - +
278C LYS* 4.2 12.8 + - - -
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C TYR* 3.7 4.0 - - - -
249C ASP* 1.3 82.5 - - + +
251C VAL* 1.3 64.4 + - - +
252C THR* 3.3 24.9 - - + +
259C LYS 3.7 3.5 - - - +
261C SER* 2.8 46.2 + - - +
7D C 4.5 4.2 + - - -
8D G 3.1 26.7 + - - -
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TRP* 3.7 47.6 - - + +
78B PHE* 4.0 8.7 - - + -
248C TYR* 4.6 14.6 - - + -
250C LYS* 1.3 76.3 - - - +
252C THR* 1.3 73.8 + - - +
258C TRP* 3.7 33.0 - - + -
259C LYS 3.7 3.1 - - - -
260C CYS* 4.1 18.8 - - + -
262C LEU* 5.5 0.4 - - + -
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Residues in contact with THR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 3.3 36.3 - - + +
251C VAL* 1.3 84.4 - - - +
253C ARG* 1.3 61.5 + - - +
257C ARG 4.0 0.3 - - - +
258C TRP* 3.4 6.6 - - - +
259C LYS* 2.8 50.8 + - - +
7D C 5.5 2.4 + - - -
8D G 4.7 6.5 - - - +
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 5.4 0.9 - - - +
105A ARG* 3.5 26.9 - - - +
252C THR* 1.3 76.5 - - - +
254C THR* 1.3 65.7 + - - +
255C LYS* 2.9 40.3 + - - +
257C ARG 3.2 9.2 - - - +
258C TRP* 3.5 50.3 - - + +
22E T 5.6 2.6 + - - -
23E T 3.3 34.4 + - - -
24E T 5.0 5.1 + - - -
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Residues in contact with THR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ARG* 1.3 76.0 + - - +
255C LYS* 1.3 83.7 + - + +
257C ARG* 2.9 48.7 + - - +
7D C 5.7 0.9 + - - -
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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