Contacts of the strand formed by residues 286 - 291 (chain A) in PDB entry 6S1M
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 3.8 28.9 - - + -
87A LEU* 4.3 24.2 - - + -
94A LEU* 4.1 25.4 - - + -
131A THR* 4.3 9.9 - - + -
135A PHE* 4.6 9.9 - - + -
136A SER 3.1 4.3 + - - +
137A VAL* 3.3 30.6 - - + -
138A CYS 2.9 26.5 + - - +
275A LEU* 5.3 6.5 - - + -
276A ARG* 5.5 0.4 - - - +
284A CYS* 4.3 2.7 - - - +
285A GLN* 1.3 78.9 - - + +
287A GLU* 1.3 60.4 + - - +
288A ALA 4.1 0.7 - - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A CYS* 3.4 8.3 - - + +
140A HIS* 2.9 31.9 + - + -
275A LEU* 2.9 32.6 - - - +
276A ARG* 3.7 15.1 + - - +
278A LYS* 3.3 24.0 - - + +
280A LYS* 3.7 29.5 - - + +
281A ALA* 4.5 2.6 + - - +
282A THR* 3.4 29.8 + - - +
284A CYS* 5.3 2.6 - - + +
285A GLN 3.9 2.4 + - - -
286A LEU* 1.3 74.1 - - - +
288A ALA* 1.3 68.3 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.5 9.6 - - + -
137A VAL* 5.6 0.2 - - + -
138A CYS 3.1 11.6 + - - +
139A CYS* 4.0 4.9 - - + -
140A HIS* 3.3 29.0 + - - +
268A LEU* 3.8 28.7 - - + -
273A TYR* 4.5 12.6 - - + -
274A ALA 4.0 4.9 - - - -
275A LEU* 4.5 4.2 - - + +
278A LYS* 4.9 0.2 - - - +
286A LEU* 4.1 1.0 - - - +
287A GLU* 1.3 77.1 - - - +
289A ASP* 1.3 64.8 + - - +
290A VAL* 4.0 4.9 - - + -
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Residues in contact with ASP 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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140A HIS* 3.5 9.8 - - - +
142A HIS* 2.4 39.5 + - - -
272A LYS 4.9 0.9 - - - +
273A TYR* 4.5 0.9 - - - -
274A ALA* 3.3 30.8 + - - +
277A LEU* 3.3 38.6 - - + +
278A LYS* 3.7 24.4 + - + +
288A ALA* 1.3 78.8 - - - +
290A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 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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139A CYS* 3.8 12.3 - - - -
140A HIS 2.8 18.0 + - - +
141A ILE* 3.4 3.6 - - + -
142A HIS* 3.2 23.1 + - - -
268A LEU* 3.7 46.0 - - + -
272A LYS* 4.3 10.8 - - + +
273A TYR* 3.7 13.2 - - + -
289A ASP* 1.3 84.5 - - - +
291A LEU* 1.3 73.7 + - - +
294A ASP* 3.5 21.3 - - + +
295A VAL* 4.6 4.5 - - + -
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Residues in contact with LEU 291 (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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110A PRO* 5.9 5.4 - - + -
141A ILE* 4.5 1.3 - - - -
142A HIS* 3.7 25.4 - - + +
143A GLY* 4.9 4.3 - - - -
272A LYS 5.1 0.4 + - - -
290A VAL* 1.3 84.4 - - - +
292A TRP* 1.3 64.8 + - + +
293A SER* 3.0 16.9 + - - +
294A ASP* 3.2 34.5 + - - +
295A VAL* 4.4 3.3 + - - +
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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