Contacts of the strand formed by residues 284 - 290 (chain A) in PDB entry 4RA2
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 MET 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER 4.0 0.6 - - - +
28A SER* 3.2 2.4 - - - -
29A MET* 2.8 69.2 + - + +
31A GLY* 5.0 0.9 - - - -
36A MET* 4.1 0.3 - - - +
38A ASP* 3.5 0.7 - - - -
238A CYS* 3.7 2.9 - - - -
240A GLY* 3.7 21.8 - - - +
241A ILE* 3.9 12.8 - - + -
272A VAL* 3.6 29.5 - - + +
275A CYS* 3.7 20.4 - - - -
276A LEU* 3.8 22.2 - - + -
280A SER* 4.0 11.4 - - - +
282A ASP 3.7 15.3 - - - +
283A ASN* 1.3 79.6 - - - +
285A SER* 1.3 63.7 + - - +
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Residues in contact with SER 285 (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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27A SER 3.3 8.1 - - - -
28A SER* 3.6 12.1 - - - -
38A ASP* 2.7 38.2 + - - +
39A ALA 4.9 3.4 + - - -
40A HIS* 5.3 6.5 + - - -
58A VAL* 4.0 22.9 - - - -
237A ALA* 3.2 25.2 - - - +
238A CYS* 3.2 8.3 + - - -
241A ILE* 4.1 2.6 - - - +
272A VAL* 5.3 0.9 - - - -
284A MET* 1.3 75.0 + - - +
286A VAL* 1.3 59.6 + - - +
287A ILE* 6.4 0.2 - - - -
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Residues in contact with VAL 286 (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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26A LEU* 3.2 4.7 - - - +
27A SER* 3.0 31.7 + - - +
235A ILE* 3.9 20.6 - - + -
236A LEU 3.2 11.7 - - - +
237A ALA* 4.2 6.3 - - + -
241A ILE* 4.8 3.8 - - + -
268A CYS* 3.3 44.2 - - + +
271A VAL* 4.6 17.9 - - + -
272A VAL* 4.2 8.1 - - + -
285A SER* 1.3 76.0 - - - +
287A ILE* 1.3 69.4 + - - +
288A LEU* 5.5 2.2 - - + -
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Residues in contact with ILE 287 (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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24A TYR* 4.8 4.0 - - + -
25A GLY 3.6 9.9 - - - +
26A LEU* 4.0 17.3 - - + -
40A HIS* 4.3 9.4 - - + -
41A THR 3.7 14.8 - - - +
56A PHE* 4.0 14.6 - - + -
57A ALA 3.4 32.8 - - - +
58A VAL* 3.8 14.4 - - + -
234A ILE 3.7 1.0 - - - +
235A ILE* 3.5 5.2 - - - -
236A LEU* 2.8 39.1 + - + +
286A VAL* 1.3 83.5 - - - +
288A LEU* 1.3 61.8 + - - +
289A ILE* 3.8 25.0 + - + +
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Residues in contact with LEU 288 (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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24A TYR* 3.2 4.9 - - - +
25A GLY 2.8 33.3 + - - +
233A PHE* 3.8 31.6 - - + -
234A ILE 3.5 13.7 - - - +
235A ILE* 4.3 7.0 - - + +
254A VAL* 4.2 11.7 - - + -
258A LEU* 4.2 9.0 - - + -
264A LEU* 4.1 28.0 - - + +
267A VAL* 3.7 31.4 - - + -
268A CYS* 3.6 16.5 - - - -
286A VAL* 5.5 2.0 - - + -
287A ILE* 1.3 73.2 - - - +
289A ILE* 1.3 62.9 + - - +
290A CYS* 4.1 5.1 + - - -
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Residues in contact with ILE 289 (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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22A LEU* 4.3 19.5 - - + -
23A ARG 3.5 7.6 - - - +
24A TYR* 4.1 0.9 - - + -
56A PHE* 3.8 55.0 - - + -
132A VAL* 4.4 3.1 - - + -
134A ILE* 4.3 8.7 - - + -
233A PHE* 3.2 4.3 - - - +
234A ILE* 2.9 66.1 + - + +
236A LEU* 4.3 6.1 - - + -
287A ILE* 3.8 20.9 - - + +
288A LEU* 1.3 75.6 - - - +
290A CYS* 1.3 67.2 + - - +
291A PHE* 4.0 4.1 + - + -
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Residues in contact with CYS 290 (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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21A GLY 4.2 0.2 - - - +
22A LEU* 3.6 8.1 - - - +
23A ARG* 2.7 45.8 + - + +
232A GLN 3.7 2.9 - - - -
233A PHE* 4.0 7.0 - - - -
258A LEU* 4.0 19.1 - - - -
264A LEU* 3.9 31.2 - - + -
288A LEU* 4.1 6.7 - - - -
289A ILE* 1.3 76.7 - - - +
291A PHE* 1.3 64.6 + - - +
294A ALA* 3.8 23.3 - - + -
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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