Contacts of the strand formed by residues 298 - 306 (chain B) in PDB entry 2A4X
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 GLU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B VAL* 4.9 0.2 - - - -
296B GLY 4.0 0.2 + - - -
297B TYR* 1.3 71.3 - - - +
299B GLY* 1.3 68.4 + - - +
300B HIS* 4.5 7.1 + - - +
315B VAL* 3.1 9.3 - - - +
316B LYS* 3.0 73.0 + - + +
317B ASP 5.4 0.9 - - - +
320B GLY* 5.8 1.2 - - - -
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B TYR* 3.2 32.8 + - - -
293B VAL* 3.8 13.8 - - - +
297B TYR 3.4 5.9 + - - -
298B GLU* 1.3 75.9 - - - +
300B HIS* 1.3 60.8 + - - +
314B ILE 4.2 0.2 - - - -
315B VAL* 4.3 1.3 - - - -
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 2.8 42.3 + - - -
63A GLU* 6.3 2.7 - - + -
289B TYR* 4.2 0.7 - - - -
298B GLU* 3.4 10.4 + - + -
299B GLY* 1.3 75.2 - - - +
301B LEU* 1.3 73.3 + - + +
314B ILE* 2.8 39.5 + - + +
315B VAL* 4.2 3.8 - - - -
316B LYS* 4.3 35.2 + - + -
322B VAL* 5.1 3.3 - - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR 3.0 31.9 - - - +
61A ASP* 4.5 7.0 - - - +
62A PRO* 5.8 2.0 - - + -
289B TYR* 3.3 7.3 - - - -
300B HIS* 1.3 97.0 - - + +
302B LYS* 1.3 66.5 + - - +
304B TRP* 3.9 22.0 - - + -
313B ALA* 3.6 0.3 - - - -
314B ILE* 3.0 51.9 + - + -
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B TYR* 3.4 17.4 + - + +
301B LEU* 1.3 76.1 - - - +
303B PRO* 1.3 83.9 - - + +
304B TRP* 3.2 15.6 - - - +
312B TYR 4.3 0.2 - - - -
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Residues in contact with PRO 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B VAL* 4.8 2.5 - - + -
286B ASP* 3.5 46.7 - - - +
289B TYR* 3.7 23.6 - - + -
301B LEU 3.8 0.2 - - - -
302B LYS* 1.3 96.0 - - + +
304B TRP* 1.3 60.2 + - - +
311B ARG* 3.8 15.1 + - - +
312B TYR 3.1 11.0 - - - +
313B ALA* 3.9 13.0 - - + -
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Residues in contact with TRP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.2 16.8 - + + +
301B LEU* 3.9 28.9 - - + -
302B LYS 3.2 17.7 - - - +
303B PRO* 1.3 77.0 - - - +
305B ASN* 1.3 74.0 + - - +
306B ALA* 3.3 18.9 + - + +
307B VAL 4.8 1.0 - - - +
308B TRP* 4.0 23.2 - + - -
311B ARG* 3.5 14.5 - - - +
312B TYR* 2.8 77.6 + + + -
313B ALA* 4.2 3.4 - - - -
314B ILE* 4.1 14.1 - - + -
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TRP* 1.3 79.4 - - - +
306B ALA* 1.3 64.6 + - - +
307B VAL* 3.6 3.3 + - - +
310B GLN 3.7 4.0 - - - -
311B ARG* 2.8 40.9 - - - +
329B LEU* 3.6 31.3 - - + +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TRP* 3.3 19.1 + - - +
305B ASN* 1.3 75.1 - - - +
307B VAL* 1.3 63.4 + - - +
308B TRP* 3.1 48.7 - - + +
309B GLY* 3.0 14.2 + - - -
310B GLN 2.8 20.2 + - - +
312B TYR* 4.0 5.4 - - + -
329B LEU* 4.3 3.5 - - - +
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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