Contacts of the strand formed by residues 335 - 342 (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 LEU 335 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 4.5 31.4 - - + -
261D LEU* 4.7 20.0 - - + -
262D PHE 3.1 23.6 - - - +
263D ASP* 4.4 3.8 - - - -
264D VAL* 4.3 0.2 - - - -
270D ILE* 4.5 14.4 - - + -
310D TYR* 2.7 20.7 + - - -
331D VAL* 3.0 24.8 + - + -
332D THR* 3.1 29.3 + - + +
334D PHE* 1.3 85.8 - - + +
336D ALA* 1.3 54.9 - - - +
363D ILE* 4.8 16.4 - - + -
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Residues in contact with ALA 336 (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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261D LEU* 3.7 3.3 - - - +
262D PHE* 2.8 42.6 + - + +
264D VAL* 3.9 15.7 - - + +
289D ILE* 5.5 3.6 - - + -
310D TYR* 3.6 15.9 - - + +
328D LEU* 4.5 20.2 - - + -
329D LYS 3.6 9.2 - - - +
331D VAL* 4.2 4.0 - - - -
335D LEU* 1.3 74.1 - - - +
337D LEU* 1.3 59.2 + - - +
338D VAL* 5.0 1.8 - - + -
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Residues in contact with LEU 337 (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* 3.4 32.5 - - + -
250D PHE* 3.7 22.4 - - + -
259D ALA* 4.6 3.6 - - + -
260D PHE 3.5 14.8 - - - +
261D LEU* 4.4 7.6 - - + -
327D TYR 3.6 1.4 - - - +
328D LEU* 3.2 5.4 - - - +
329D LYS* 2.9 37.8 + - + +
331D VAL* 3.9 12.5 - - + +
336D ALA* 1.3 73.0 - - - +
338D VAL* 1.3 62.0 + - - +
339D CYS* 3.3 26.9 - - - -
356D PHE* 4.3 16.4 - - + -
359D PHE* 4.2 10.8 - - + -
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Residues in contact with VAL 338 (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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259D ALA* 3.2 1.9 - - - -
260D PHE* 2.9 40.5 + - - -
262D PHE* 3.3 35.9 - - + -
285D CYS* 3.8 24.9 - - + -
288D MET* 4.0 24.7 - - + -
289D ILE* 4.1 8.3 - - + -
326D LEU* 5.2 2.0 - - + -
327D TYR 3.2 10.3 - - - +
328D LEU* 4.0 18.6 - - + -
336D ALA* 4.9 1.8 - - + +
337D LEU* 1.3 75.8 - - - +
339D CYS* 1.3 65.2 + - - +
340D ILE* 4.4 0.5 + - - +
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Residues in contact with CYS 339 (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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250D PHE* 4.3 9.0 - - - -
256D ILE* 3.8 13.7 - - + -
258D LYS 3.4 3.8 - - - -
259D ALA* 3.3 24.2 - - - -
325D VAL 3.6 1.0 - - - +
326D LEU* 3.2 5.0 - - - +
327D TYR* 2.6 52.3 + - + +
337D LEU* 3.3 30.1 - - - -
338D VAL* 1.3 74.0 - - - +
340D ILE* 1.3 62.4 + - - +
341D LEU* 3.7 18.8 - - + -
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Residues in contact with ILE 340 (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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256D ILE 3.8 0.3 - - - -
257D GLU* 3.1 26.9 + - + +
258D LYS* 2.9 34.3 + - + +
260D PHE* 4.2 12.3 - - + -
281D SER* 2.9 32.3 - - - +
284D LEU* 6.1 2.2 - - + -
285D CYS* 4.4 15.3 - - - -
324D THR* 3.7 17.7 - - + -
325D VAL 3.4 2.0 - - - -
326D LEU* 3.4 29.4 - - + -
338D VAL 5.1 0.4 - - - +
339D CYS* 1.3 73.5 - - - +
341D LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 341 (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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255D GLY 3.4 17.5 - - - +
256D ILE* 3.9 17.9 - - + -
257D GLU* 4.3 10.5 - - - +
324D THR* 3.4 9.6 - - - +
325D VAL* 2.6 46.1 + - + +
327D TYR* 4.4 11.9 - - + -
339D CYS* 3.7 28.5 - - + +
340D ILE* 1.3 77.3 - - - +
342D ARG* 1.3 57.5 + - - +
345D SER 4.2 2.2 - - - -
346D PHE* 3.6 44.2 - - + +
352D ILE* 4.1 14.6 - - + -
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Residues in contact with ARG 342 (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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255D GLY 4.7 0.2 + - - -
257D GLU* 2.5 45.1 + - - +
322D ASN* 3.4 11.3 + - - -
323D THR* 3.4 21.3 + - - +
324D THR* 3.2 32.2 + - - +
325D VAL* 4.5 2.5 - - - -
341D LEU* 1.3 76.1 - - - +
343D GLU* 1.3 55.9 + - - +
344D GLU* 2.7 26.0 + - + +
345D SER* 2.9 27.5 + - - +
346D PHE* 3.1 12.8 + - - +
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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