Contacts of the strand formed by residues 258 - 263 (chain D) in PDB entry 6S6A
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 LYS 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D ILE* 5.0 0.2 - - - -
256D ILE* 3.2 7.6 + - - +
257D GLU* 1.3 80.3 - - + +
259D ALA* 1.3 68.2 + - - +
260D PHE* 3.9 23.1 - - + -
272D THR* 3.7 11.3 + - - +
273D ASP* 3.0 25.1 + - - +
275D SER* 2.7 43.9 + - - +
276D PRO 3.1 18.4 + - - +
277D VAL* 3.7 15.0 - - - +
278D ASP 5.3 0.4 - - - +
281D SER* 5.1 3.4 - - - +
340D ILE* 2.9 51.9 + - + +
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D LEU* 4.3 6.2 - - + +
251D ILE* 3.6 21.1 - - + -
258D LYS* 1.3 78.1 - - - +
260D PHE* 1.3 63.3 + - - +
272D THR* 3.6 2.4 + - - -
273D ASP* 3.2 35.0 + - - +
337D LEU* 4.6 8.1 - - + -
338D VAL 3.2 6.7 - - - -
339D CYS* 3.3 29.2 - - - -
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Residues in contact with PHE 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D LEU* 5.2 0.2 - - - -
258D LYS* 3.9 22.4 - - + -
259D ALA* 1.3 72.4 - - - +
261D LEU* 1.3 58.6 - - - +
262D PHE* 3.5 24.6 + + + -
269D TYR* 4.1 17.7 - + + -
271D ALA 4.2 3.4 - - - -
272D THR* 3.5 22.0 - - - -
277D VAL* 4.0 17.9 - - + -
278D ASP 4.5 2.5 - - - -
281D SER* 4.0 9.0 - - - -
282D TYR* 3.9 29.2 - + + -
285D CYS* 3.5 34.8 - - + -
337D LEU* 3.5 9.7 - - - +
338D VAL 2.9 34.0 + - - +
340D ILE* 4.2 11.9 - - + -
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D LEU* 4.4 16.8 - - + -
247D LEU* 4.3 9.4 - - + +
260D PHE* 1.3 71.4 - - - +
262D PHE* 1.3 57.0 + - - +
269D TYR* 3.6 1.8 - - - -
270D ILE* 2.7 50.3 + - + +
271D ALA* 3.3 36.9 + - + +
331D VAL* 4.4 19.7 - - + -
335D LEU* 4.7 21.1 - - + -
336D ALA 3.8 9.6 - - - +
337D LEU* 4.4 11.4 - - + -
359D PHE* 4.9 1.8 - - + -
363D ILE* 4.5 19.5 - - + -
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Residues in contact with PHE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D PHE* 3.5 25.8 - - + -
261D LEU* 1.3 72.2 - - - +
263D ASP* 1.3 61.8 + - - +
264D VAL 4.1 0.4 - - - +
267D LYS 3.3 32.3 - - - -
268D ILE 3.6 7.0 - - - -
269D TYR* 4.2 2.2 - - + +
270D ILE* 5.0 1.3 - - - -
282D TYR* 3.3 24.9 - + - -
285D CYS* 3.3 27.1 - - + -
286D CYS* 3.6 8.3 - - - -
289D ILE* 3.4 21.1 - - + -
335D LEU* 3.1 33.9 - - - +
336D ALA* 2.8 18.8 + - + +
338D VAL* 3.3 35.4 - - + -
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Residues in contact with ASP 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D SER 4.9 1.0 - - - +
108D SER* 2.6 40.2 + - - +
109D PHE* 3.4 12.3 - - + +
110D VAL* 4.8 5.0 - - + +
262D PHE* 1.3 74.6 - - - +
264D VAL* 1.3 59.0 + - - +
265D VAL* 4.6 1.8 + - - +
266D SER* 2.6 37.7 + - - +
267D LYS* 2.7 35.2 + - - -
268D ILE* 3.0 14.5 + - + +
270D ILE* 5.0 6.5 - - + +
289D ILE* 5.3 0.2 - - - +
334D PHE* 3.5 12.3 - - - +
335D LEU* 4.4 5.2 - - + -
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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