Contacts of the strand formed by residues 295 - 301 (chain D) in PDB entry 4RZR
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 ILE 295 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ILE* 6.2 1.8 - - + -
287D VAL* 4.0 23.3 - - + -
288D ALA 3.4 1.8 - - - -
289D VAL* 3.5 31.2 - - + -
293D LEU 4.6 5.6 - - - +
294D ASP* 1.3 89.9 + - - +
296D VAL* 1.3 66.4 + - - +
297D SER* 5.3 3.1 - - - +
8F C 4.4 11.5 + - + +
9F C 4.4 20.4 + - + +
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 3.6 1.2 - - - +
288D ALA* 2.7 47.4 + - + +
290D THR* 4.0 20.6 - - + -
294D ASP* 4.6 5.6 - - - +
295D ILE* 1.3 79.9 - - - +
297D SER* 1.3 64.5 + - - +
298D ARG* 3.6 24.2 - - - +
322D ILE* 4.2 19.4 - - + +
326D ASP* 3.9 25.1 - - + +
328D ARG* 4.2 6.3 - - - +
8F C 3.7 10.3 - - - +
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Residues in contact with SER 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D HIS* 4.8 11.4 + - - -
286D VAL 3.3 13.7 - - - -
287D VAL* 4.2 15.0 - - - -
295D ILE* 5.4 2.9 - - - -
296D VAL* 1.3 78.0 - - - +
298D ARG* 1.3 85.1 + - - +
322D ILE* 4.4 0.9 - - - -
7F A 3.7 18.6 + - - +
8F C 2.9 23.9 + - - -
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Residues in contact with ARG 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D HIS* 4.2 3.4 - - - -
286D VAL* 2.8 29.4 + - - +
296D VAL* 3.6 18.6 - - - +
297D SER* 1.3 90.4 + - - +
299D GLY* 1.3 59.7 + - - +
318D LEU* 3.6 34.3 - - + +
321D LYS* 3.8 20.1 - - + +
322D ILE* 3.5 21.2 - - + +
325D GLU* 2.6 43.4 + - - +
326D ASP* 6.0 1.2 - - - +
7F A 3.2 30.9 + - - +
8F C 3.5 21.4 + - - -
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Residues in contact with GLY 299 (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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284D ILE 3.0 14.1 - - - -
285D HIS* 3.5 16.7 + - - -
298D ARG* 1.3 74.8 - - - +
300D ARG* 1.3 62.3 + - - +
318D LEU* 3.9 11.6 - - - +
6F T 4.6 6.9 + - - +
7F A 2.8 21.2 + - - -
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Residues in contact with ARG 300 (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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282D LYS 4.0 0.3 - - - +
283D ALA* 3.3 2.1 - - - -
284D ILE* 2.8 38.6 + - + +
285D HIS* 4.9 2.7 - - - -
299D GLY* 1.3 75.0 - - - +
301D THR* 1.3 74.6 + - - +
302D PHE* 3.4 40.4 - - + -
303D PRO* 5.8 2.8 - - - +
304D HIS* 6.0 0.2 - - - -
314D GLU* 3.3 37.8 + - + +
317D LYS* 5.4 3.6 - - - +
318D LEU* 4.8 3.4 - - + -
6F T 3.9 6.3 - - - +
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Residues in contact with THR 301 (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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282D LYS* 3.3 13.5 - - + +
283D ALA* 3.6 6.3 - - - +
285D HIS* 5.6 2.1 + - - -
300D ARG* 1.3 87.9 + - - +
302D PHE* 1.3 75.0 + - - +
303D PRO* 4.5 1.9 - - - +
339D LYS* 2.6 42.3 + - + +
5F A 4.0 4.7 + - - -
6F T 3.2 19.1 + - - -
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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
------------------------------------------------------------
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