Contacts of the strand formed by residues 302 - 307 (chain D) in PDB entry 6WNX
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 302 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D GLN 3.9 0.9 - - - +
298D TYR* 3.5 3.2 - - - -
299D ARG 2.9 35.9 + - - +
300D ASP* 3.5 0.6 - - + -
301D ARG* 1.3 78.2 - - + +
303D VAL* 1.3 66.7 + - - +
304D VAL* 3.9 16.8 - - + -
314D LEU* 4.2 12.8 - - + -
315D TRP 3.4 14.8 - - - +
323D LEU* 4.2 5.8 - - + -
338D PHE* 3.9 25.1 - - + -
357D LEU* 4.2 23.1 - - + -
361D LEU* 4.1 25.8 - - + -
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 4.4 9.9 - - + -
272D ILE* 4.3 9.0 - - + -
286D LEU* 4.6 7.2 - - + -
296D LEU* 3.7 33.2 - - + -
297D GLN 3.5 4.0 - - - +
298D TYR* 4.1 7.9 - - + -
302D LEU* 1.3 74.9 - - - +
304D VAL* 1.3 64.7 - - - +
314D LEU* 3.5 2.1 - - - -
315D TRP* 2.7 59.8 + - + +
317D ILE* 3.7 37.0 - - + -
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Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU* 3.2 5.2 - - - +
297D GLN 2.9 32.4 + - - +
302D LEU* 3.9 12.3 - - + -
303D VAL* 1.3 75.0 - - - +
305D SER* 1.3 63.2 + - - +
312D ILE* 4.0 10.1 - - + -
313D ARG 3.3 3.1 - - - -
314D LEU* 3.8 17.3 - - + -
336D ILE* 3.5 34.5 - - + +
338D PHE* 3.8 27.1 - - + -
343D ILE* 3.7 26.2 - - + -
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Residues in contact with SER 305 (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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272D ILE* 3.8 20.4 - - - -
289D HIS* 2.8 29.6 + - - -
293D ILE* 4.4 6.1 - - - -
295D CYS 3.5 10.8 - - - -
296D LEU* 4.2 4.7 - - - +
304D VAL* 1.3 75.3 - - - +
306D GLY* 1.3 58.2 + - - +
312D ILE* 3.1 7.8 - - - +
313D ARG 2.9 30.9 + - - -
315D TRP* 2.9 17.0 + - - -
336D ILE* 4.3 5.6 - - - -
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Residues in contact with GLY 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 4.6 0.2 - - - -
293D ILE* 3.6 4.6 - - - +
294D ALA 3.0 23.0 + - - -
295D CYS* 3.0 29.6 + - - +
305D SER* 1.3 73.4 - - - +
307D SER* 1.3 61.1 + - - -
311D THR 3.7 6.7 - - - -
312D ILE* 4.4 1.6 - - - -
333D VAL* 3.6 18.8 - - - +
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Residues in contact with SER 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 3.1 32.8 - - - -
291D ARG 3.0 12.5 + - - -
292D GLY 2.6 22.2 + - - -
293D ILE* 4.1 1.3 - - - +
294D ALA 5.0 0.9 - - - -
306D GLY* 1.3 72.8 - - - -
308D SER* 1.3 60.0 + - - +
309D ASP* 2.9 24.1 + - - -
310D ASN* 3.1 16.5 + - - -
311D THR 3.1 6.1 + - - -
332D LEU* 4.4 1.6 - - - -
333D VAL* 3.2 21.4 + - - +
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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
------------------------------------------------------------
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