Contacts of the strand formed by residues 298 - 304 (chain B) in PDB entry 4R8U
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 GLN 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B LYS* 3.6 34.7 + - + +
291B LEU 3.1 13.0 - - - +
292B LYS* 3.3 36.7 + - + +
293B PHE* 4.6 2.5 - - - -
296B PHE 3.6 1.5 + - - +
297B GLN* 1.3 76.1 - - - +
299B THR* 1.3 62.1 + - - +
300B THR* 4.9 6.3 - - - +
332B LEU* 6.0 0.2 - - - +
49D G 4.1 11.4 + - - +
50D G 5.3 10.3 + - - +
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Residues in contact with THR 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 VAL 4.1 0.2 - - - +
290B LYS* 3.3 3.7 - - - +
291B LEU* 2.8 39.8 + - + +
293B PHE* 3.6 30.5 - - + -
298B GLN* 1.3 76.4 - - - +
300B THR* 1.3 61.2 - - - +
320B THR* 3.8 21.3 - - + +
324B ARG* 2.8 39.1 + - + -
49D G 2.9 22.2 + - - -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL 3.3 7.6 - - - +
290B LYS* 3.7 30.7 - - + -
298B GLN* 4.9 5.8 - - - +
299B THR* 1.3 78.2 + - - +
301B GLN* 1.3 61.1 + - - +
302B GLU* 4.7 14.4 + - - +
324B ARG* 3.0 16.3 + - - -
336B HIS* 6.5 1.1 - - + -
48D A 3.3 33.3 + - - +
49D G 3.0 11.8 + - - -
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY* 3.3 1.6 - - - -
289B VAL* 2.9 31.5 + - + +
300B THR* 1.3 74.1 - - - +
302B GLU* 1.3 65.2 + - - +
303B HIS* 5.7 2.5 + - - +
316B THR* 3.7 19.1 - - + +
319B LYS* 4.0 26.0 - - - +
320B THR* 3.0 37.2 + - + +
323B GLU* 4.5 6.4 + - - +
324B ARG* 3.4 24.6 + - - +
48D A 3.2 16.2 - - - +
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Residues in contact with GLU 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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286B ARG* 3.1 38.9 + - - +
287B GLN 3.1 19.8 + - - +
288B GLY* 3.6 6.7 - - - -
300B THR* 4.7 13.6 + - - +
301B GLN* 1.3 79.5 - - - +
303B HIS* 1.3 63.7 + - - +
336B HIS* 3.8 27.5 + - - -
338B THR* 3.8 5.0 + - - -
47D T 3.4 18.6 - - + +
48D A 2.6 32.7 + - + +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 3.4 5.7 - - - -
287B GLN* 3.1 33.3 + - - -
288B GLY* 5.7 0.2 - - - -
301B GLN* 5.7 2.4 + - - +
302B GLU* 1.3 76.9 - - - +
304B VAL* 1.3 79.6 + - - +
305B TRP* 3.3 17.1 + + + +
312B ASP* 2.8 35.0 + - - -
313B LEU* 6.4 0.2 - - + -
316B THR* 3.0 34.4 + - + +
47D T 3.3 18.6 - - - +
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Residues in contact with VAL 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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285B ALA 3.3 14.4 - - - +
286B ARG* 3.7 11.4 - - + +
303B HIS* 1.3 83.5 - - - +
305B TRP* 1.3 69.5 + - - +
306B PRO* 5.4 1.1 - - + -
46D C 4.0 35.4 - - - +
47D T 2.8 22.8 + - - +
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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