Contacts of the strand formed by residues 302 - 307 (chain B) in PDB entry 6BM0
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 TRP 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ASP* 3.2 23.9 + - - -
131A GLY* 3.6 22.4 - - - -
132A PHE* 3.4 37.5 - + - -
296B LEU* 3.3 28.8 - - - +
297B ASN* 3.2 36.3 + - - +
299B ASN* 4.1 8.8 + - - -
300B GLY 3.4 1.9 + - - -
301B ASN* 1.3 93.7 - - + +
303B LEU* 1.3 60.2 + - - +
304B LEU 4.0 0.8 + - - -
314B LEU* 4.6 15.3 - - + -
315B PHE 3.4 7.9 - - - +
316B ASP* 4.5 6.6 - - - -
317B ILE* 4.6 1.8 - - - -
324B LEU* 3.9 22.4 - - + +
339B TRP* 4.2 9.8 - + + -
344B GLU* 5.2 0.7 - - - -
345B GLY* 4.1 10.5 - - - -
361B VAL* 3.7 29.4 - - + -
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Residues in contact with LEU 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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260B VAL* 3.7 14.6 - - + -
270B ILE* 4.6 3.1 - - + -
272B PHE* 3.7 29.2 - - + -
284B LEU* 4.1 7.6 - - + -
294B VAL* 3.6 28.7 - - + -
295B LYS 3.9 2.2 - - - +
296B LEU* 3.7 18.4 - - + -
302B TRP* 1.3 71.6 - - - +
304B LEU* 1.3 58.8 + - - +
305B THR* 3.9 9.0 - - - +
313B LYS 3.6 1.6 - - - +
314B LEU* 3.5 4.0 - - - -
315B PHE* 2.5 71.1 + - + +
317B ILE* 3.8 11.2 - - + +
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Residues in contact with LEU 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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293B GLU 4.1 0.3 - - - +
294B VAL* 3.4 4.7 - - - +
295B LYS 2.9 34.3 + - - +
302B TRP 4.0 1.0 + - - -
303B LEU* 1.3 71.9 - - - +
305B THR* 1.3 68.8 + - - +
312B CYS* 4.7 2.0 - - + -
313B LYS 3.4 22.9 - - - +
314B LEU* 3.7 15.5 - - + -
327B PHE* 4.5 2.0 - - + -
337B VAL* 3.6 29.9 - - + +
339B TRP* 3.5 41.3 - - + +
347B PHE* 3.6 38.4 - - + -
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Residues in contact with THR 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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270B ILE* 3.8 13.3 - - + +
287B HIS* 3.4 32.5 + - + +
291B VAL* 3.7 22.7 - - + -
293B GLU 3.6 2.9 - - - -
294B VAL* 4.1 4.7 - - + +
303B LEU* 3.9 9.2 - - - +
304B LEU* 1.3 80.5 + - - +
306B ALA* 1.3 62.5 + - - +
312B CYS* 3.3 8.5 - - - +
313B LYS 3.1 34.2 + - - -
315B PHE* 3.8 21.3 - - - -
337B VAL* 5.3 0.4 - - - -
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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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291B VAL* 3.5 2.7 - - - -
292B MET* 2.6 30.8 + - - -
293B GLU* 2.8 25.6 + - + +
305B THR* 1.3 75.6 - - - +
307B SER* 1.3 55.1 + - - +
311B LEU 4.0 4.5 - - - -
312B CYS* 4.1 6.1 - - - -
334B ALA 3.4 20.4 - - - +
337B VAL* 3.7 29.4 - - + +
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Residues in contact with SER 307 (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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287B HIS* 3.5 26.1 - - - +
289B ASN 2.4 32.1 + - - -
290B THR 3.1 11.0 + - - -
291B VAL* 3.6 5.5 + - - -
292B MET 3.9 0.7 - - - +
305B THR 4.5 0.2 + - - -
306B ALA* 1.3 75.0 - - - +
308B ARG* 1.3 65.8 + - - +
309B ASP* 3.2 21.4 + - - -
310B HIS 4.0 1.9 + - - -
311B LEU 3.4 12.7 + - - +
334B ALA 3.6 22.3 + - - +
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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