Contacts of the strand formed by residues 273 - 284 (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 ASP 273 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 2.7 22.9 + - - -
2C SER* 5.7 0.9 - - - -
3C ASN* 3.6 19.1 - - - +
6C ALA* 3.7 9.7 - - + +
10C TYR* 2.5 33.6 + - + +
51C VAL* 3.0 34.1 + - + +
52C THR* 5.2 0.2 - - + -
266C VAL* 4.5 0.9 - - - +
267C VAL 3.2 5.6 - - - +
268C THR* 2.6 34.3 + - - +
272C ASN* 1.3 70.6 - - - +
274C TYR* 1.3 71.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.6 8.1 - - + -
87B VAL* 3.7 35.4 - - + -
106B ILE* 3.6 25.7 - - + +
2C SER* 5.8 4.9 - - - -
3C ASN* 4.1 19.5 - - + +
6C ALA* 4.2 3.8 - - - -
266C VAL* 3.4 4.3 - - - +
267C VAL* 2.8 45.4 + - + +
269C ILE* 4.1 22.1 + - + -
272C ASN* 3.5 40.5 + - + +
273C ASP* 1.3 77.4 - - - +
275C THR* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.2 12.1 - - + -
56B THR* 4.2 2.7 - - - -
58B SER* 3.4 10.2 + - - -
60B LEU* 5.5 0.5 - - - +
87B VAL* 5.9 0.5 - - - +
3C ASN* 4.3 3.8 + - - +
5C GLU* 2.9 44.2 + - - +
6C ALA* 3.7 23.4 + - + -
9C VAL* 4.0 16.5 - - + +
10C TYR* 4.4 5.8 - - + -
265C GLY 3.3 9.0 - - - -
266C VAL* 4.2 17.7 - - + -
274C TYR* 1.3 82.7 - - - +
276C PHE* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 5.0 0.5 - - - +
56B THR* 3.0 12.4 + - - -
58B SER* 3.7 10.3 - - - +
60B LEU* 3.9 26.2 - - + +
5C GLU* 4.1 0.4 - - - -
244C MET* 3.7 33.9 - - + -
246C CYS* 3.7 12.6 - - + -
262C LEU* 4.0 6.1 - - + -
263C LYS 4.0 11.0 - - - -
264C ASP* 3.4 5.2 - - - -
265C GLY* 2.8 65.5 + - - +
266C VAL 3.9 2.0 - - - -
267C VAL* 4.4 6.7 - - + -
275C THR* 1.3 77.1 - - - +
277C GLN* 1.3 59.3 + - - +
278C LYS* 3.6 29.4 - - - +
279C ALA* 3.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 4.2 0.3 - - - +
53B LYS 4.0 12.6 + - - +
56B THR* 3.1 34.4 + - + +
57B GLN* 3.8 15.2 - - - +
58B SER 2.7 16.1 + - - +
59B LYS* 4.3 11.0 - - + -
263C LYS* 3.0 25.3 - - - +
264C ASP* 3.0 30.9 + - - +
276C PHE* 1.3 73.2 - - - +
278C LYS* 1.3 74.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER 3.6 1.6 + - - -
59B LYS* 3.0 39.3 - - + +
60B LEU 3.0 23.1 + - - -
249C ASP* 4.2 17.2 + - - -
262C LEU 3.4 9.4 + - - +
263C LYS* 4.8 10.9 - - - +
276C PHE* 3.6 7.2 - - - -
277C GLN* 1.3 94.9 + - + +
279C ALA* 1.3 62.1 + - - +
280C GLN* 5.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.0 21.8 - - + +
244C MET* 4.8 1.3 - - + -
260C CYS 3.4 0.7 - - - +
262C LEU* 2.9 47.2 + - + -
276C PHE* 3.3 31.9 - - + -
278C LYS* 1.3 73.5 - - - +
280C GLN* 1.3 72.0 + - - +
281C VAL* 4.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU 3.0 7.2 + - - +
61B THR* 3.1 21.4 - - + +
62B VAL 2.6 34.5 + - - +
259C LYS* 5.9 1.9 - - - +
260C CYS 3.5 10.1 + - - +
261C SER* 3.7 21.3 - - - +
262C LEU 4.6 1.4 + - - +
278C LYS* 5.3 9.9 - - + +
279C ALA* 1.3 86.9 + - - +
281C VAL* 1.3 59.4 + - - +
282C GLU* 5.3 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.2 25.8 - - + +
78B PHE* 6.1 1.8 - - + -
80B VAL* 4.5 4.7 - - + -
113B ILE* 4.0 21.5 - - + -
258C TRP* 4.3 0.9 - - + -
259C LYS* 3.2 7.3 - - - +
260C CYS* 2.8 51.0 + - + +
262C LEU* 3.3 32.3 - - + -
279C ALA* 5.1 0.2 - - + -
280C GLN* 1.3 77.5 + - - +
282C GLU* 1.3 71.4 + - - +
283C ALA* 4.0 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL 2.8 13.3 + - - +
63B LYS* 3.3 38.2 + - + +
64B GLY 3.2 19.4 + - - +
258C TRP 3.4 7.4 - - - +
259C LYS* 3.2 33.4 + - + +
280C GLN* 5.3 8.7 - - + +
281C VAL* 1.3 81.4 - - - +
283C ALA* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 2.9 14.8 - - - +
65B ASN 4.1 0.4 - - - -
66B LEU* 3.4 31.0 - - + +
80B VAL* 4.3 15.7 - - + -
256C ALA 3.9 0.2 - - - +
257C ARG* 5.0 0.2 - - - -
258C TRP* 2.9 37.3 + - + +
281C VAL* 4.0 7.9 - - + +
282C GLU* 1.3 76.6 - - - +
284C GLU* 1.3 61.4 + - - +
285C TRP 3.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 3.2 9.3 + - - +
65B ASN* 3.7 18.0 + - - +
66B LEU 3.2 13.7 + - - -
256C ALA* 3.3 15.2 - - - +
257C ARG* 4.3 19.9 + - + +
283C ALA* 1.3 71.6 - - - +
285C TRP* 1.3 53.6 + - - +
286C VAL* 2.7 49.1 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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