Contacts of the strand formed by residues 257 - 268 (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 ARG 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C THR 4.0 0.2 - - - +
253C ARG* 3.2 2.3 - - - -
254C THR* 2.9 66.2 + - - +
255C LYS* 3.5 25.9 - - - +
256C ALA* 1.3 78.6 - - + +
258C TRP* 1.3 62.9 + - - +
259C LYS* 5.0 7.4 - - + +
283C ALA 4.1 2.7 - - - -
284C GLU* 4.3 21.7 + - + +
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Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 4.1 8.7 - - - -
105A ARG* 4.3 0.9 - - - -
66B LEU* 3.7 22.4 - - + +
69B TYR* 3.6 43.3 - + - -
76B TRP* 3.7 26.0 - + - -
78B PHE* 4.1 12.3 - + + -
251C VAL* 3.7 23.6 - - + -
252C THR 3.4 4.0 - - - -
253C ARG* 3.5 40.1 - - + +
256C ALA* 3.4 18.2 + - - +
257C ARG* 1.3 75.5 - - - +
259C LYS* 1.3 65.2 + - - +
260C CYS* 4.3 7.4 - - - -
281C VAL* 5.1 0.4 - - + -
282C GLU* 3.4 6.6 - - - +
283C ALA* 2.9 37.3 + - + +
285C TRP* 3.6 18.0 - - + +
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LYS* 3.7 2.6 - - - +
251C VAL* 3.7 2.9 - - - -
252C THR* 2.8 47.3 + - - +
257C ARG* 5.0 8.3 - - + +
258C TRP* 1.3 79.2 - - - +
260C CYS* 1.3 62.2 + - - +
261C SER 4.2 0.2 - - - -
280C GLN* 5.7 2.2 - - - +
281C VAL 3.2 5.4 - - - +
282C GLU* 3.2 33.4 + - + -
6D T 5.2 19.0 - - - +
7D C 5.5 4.0 - - - +
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Residues in contact with CYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.6 37.9 - - + -
250C LYS 3.8 2.7 - - - -
251C VAL* 4.1 13.2 - - + -
258C TRP* 5.0 6.7 - - - -
259C LYS* 1.3 80.5 - - - +
261C SER* 1.3 60.0 + - - +
262C LEU* 3.7 17.0 + - + -
279C ALA 3.4 6.1 - - - +
280C GLN* 3.5 5.4 + - - +
281C VAL* 2.8 59.0 + - + +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C TYR* 3.6 0.2 - - - -
249C ASP* 2.8 34.7 + - - +
250C LYS* 2.8 44.0 + - - +
259C LYS 4.1 0.4 + - - -
260C CYS* 1.3 69.2 - - - +
262C LEU* 1.3 68.2 + - - +
280C GLN* 3.7 21.8 - - - +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 5.6 3.8 - - + -
113B ILE* 4.5 7.6 - - + -
115B ALA* 4.8 4.3 - - + -
244C MET* 4.2 13.2 - - - -
246C CYS* 3.7 17.0 - - - -
247C LEU 3.3 16.4 - - - +
248C TYR* 3.9 13.9 - - + +
249C ASP* 4.4 4.8 - - - +
251C VAL* 5.5 1.6 - - + -
260C CYS* 3.9 16.6 - - + +
261C SER* 1.3 86.7 - - - +
263C LYS* 1.3 64.6 + - - +
276C PHE* 4.0 0.7 - - + -
278C LYS* 3.4 8.7 - - - +
279C ALA* 2.9 45.1 + - + +
280C GLN* 5.1 0.9 + - - -
281C VAL* 3.3 33.7 - - + -
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 6.2 0.7 - - - -
118B SER* 4.3 15.1 - - - -
246C CYS* 3.5 2.1 - - - +
247C LEU* 3.1 39.1 + - + +
249C ASP* 2.9 37.1 + - - +
262C LEU* 1.3 78.4 - - - +
264C ASP* 1.3 88.0 + - - +
265C GLY 3.2 3.6 + - - -
276C PHE* 4.0 2.2 - - - -
277C GLN 3.0 16.6 - - - +
278C LYS* 4.2 11.3 - - + +
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Residues in contact with ASP 264 (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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10B TYR* 2.6 30.2 + - - +
49B ALA* 4.7 3.3 - - - +
52B LEU* 3.6 24.5 - - + +
53B LYS* 3.6 41.2 - - + +
246C CYS* 3.8 0.9 - - - -
247C LEU* 4.0 18.3 + - + +
263C LYS* 1.3 88.5 - - - +
265C GLY* 1.3 55.5 + - - +
276C PHE 3.4 8.0 + - - -
277C GLN* 3.0 30.4 + - - +
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Residues in contact with GLY 265 (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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52B LEU* 3.7 9.7 - - - +
245C LEU 3.3 12.8 - - - -
246C CYS* 3.3 10.5 - - - -
263C LYS 3.2 2.0 + - - -
264C ASP* 1.3 76.4 - - - +
266C VAL* 1.3 59.7 + - - +
275C THR* 3.3 3.3 - - - -
276C PHE* 2.8 48.8 + - - +
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Residues in contact with VAL 266 (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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10B TYR* 4.0 22.2 - - + -
13B SER* 4.1 21.8 - - - -
14B THR 5.7 0.4 - - - +
15B ILE* 6.0 0.9 - - + -
48B VAL* 5.7 1.6 - - + -
52B LEU* 4.6 7.9 - - + -
10C TYR* 3.4 28.9 - - + +
243C LEU 4.0 0.7 - - - +
244C MET* 3.5 1.0 - - - +
245C LEU* 3.0 37.3 + - + +
265C GLY* 1.3 76.5 - - - +
267C VAL* 1.3 66.7 + - - +
268C THR* 5.7 0.9 - - - +
273C ASP* 4.5 4.5 - - - +
274C TYR 3.4 12.3 - - - +
275C THR* 4.2 11.7 - - + -
276C PHE* 3.9 1.3 - - - -
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.9 20.9 - - + -
111B LEU* 4.3 6.3 - - + -
243C LEU 3.3 19.5 - - - +
244C MET* 3.9 23.3 - - + -
266C VAL* 1.3 78.4 - - - +
268C THR* 1.3 65.9 + - - +
269C ILE* 3.5 25.1 - - + -
272C ASN 3.7 0.9 - - - +
273C ASP* 3.2 6.0 - - - +
274C TYR* 2.8 66.5 + - + +
276C PHE* 4.4 2.9 - - + -
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 5.8 0.2 - - - -
14B THR* 3.0 19.1 + - - +
51C VAL* 5.0 2.7 - - + -
239C PRO* 4.2 20.9 - - + +
241C GLU 4.2 11.0 - - - +
242C ASN* 3.1 25.5 - - - +
243C LEU* 3.0 14.7 + - - -
266C VAL* 5.7 0.5 - - - +
267C VAL* 1.3 72.0 - - - +
269C ILE* 1.3 63.4 + - - +
270C ASN 4.9 0.4 - - - +
271C ARG* 4.3 12.8 - - - +
272C ASN 3.3 7.6 - - - +
273C ASP* 2.6 22.0 + - - +
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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