Contacts of the strand formed by residues 287 - 292 (chain B) in PDB entry 2POD
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 ALA 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU* 4.9 0.4 - - - +
266B VAL* 3.8 14.8 - - + +
268B ALA* 4.9 0.9 - - + -
281B LEU* 3.9 38.1 + - + +
282B LEU* 5.7 1.6 - - + -
284B THR* 4.3 2.4 + - - -
285B ASN 5.0 1.6 - - - -
286B ALA* 1.3 81.3 + - - +
288B GLY* 1.3 59.3 + - - +
289B ILE 4.4 9.6 - - - +
290B VAL* 5.0 0.4 - - + -
315B LEU* 3.4 28.8 - - + +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B PRO* 4.0 17.5 - - - -
266B VAL 2.8 11.5 + - - +
286B ALA 3.8 1.8 + - - -
287B ALA* 1.3 73.9 - - - +
289B ILE* 1.3 66.3 + - - +
290B VAL 4.2 0.2 - - - -
315B LEU* 3.5 16.1 - - - +
316B PRO* 3.3 22.0 - - - +
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Residues in contact with ILE 289 (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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241B PHE* 4.7 4.3 - - + +
242B TRP* 3.8 40.6 - - + -
265B PRO* 3.8 22.0 - - + -
266B VAL 3.0 8.2 + - - +
267B CYS* 3.4 17.1 - - + -
268B ALA 3.1 27.0 + - - +
287B ALA* 4.4 3.1 - - - +
288B GLY* 1.3 81.7 - - - +
290B VAL* 1.3 65.6 + - - +
291B MSE 3.4 0.2 + - - -
316B PRO* 3.5 25.4 - - + +
318B ALA* 4.0 26.9 - - + +
342B LEU* 4.1 9.6 - - + -
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Residues in contact with VAL 290 (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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268B ALA 3.4 3.1 - - - -
278B PHE* 3.7 28.9 - - + -
281B LEU* 4.6 10.3 - - + -
282B LEU* 4.1 12.1 - - + -
287B ALA* 5.0 1.1 - - + -
288B GLY 4.3 0.2 + - - -
289B ILE* 1.3 70.7 - - - +
291B MSE 1.3 61.3 + - - +
292B LEU* 5.0 1.1 - - + -
306B ILE* 4.0 11.2 - - + -
310B ALA* 3.8 19.3 - - + -
315B LEU* 4.0 22.4 - - + -
316B PRO 2.9 13.2 + - - +
317B VAL* 3.2 24.8 - - + +
318B ALA 3.1 21.9 + - - -
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Residues in contact with MSE 291 (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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118B TYR* 4.6 4.0 - - - -
174B LYS* 4.4 3.1 - - - -
242B TRP* 4.9 0.4 - - - -
244B GLU* 3.3 45.8 - - + +
245B ASP* 4.3 1.3 - - - +
267B CYS* 3.6 19.7 - - - -
268B ALA 2.6 15.0 + - - +
269B SER* 3.1 22.8 + - - +
270B GLU* 3.4 40.6 - - + +
278B PHE* 3.2 17.8 - - - -
289B ILE 3.4 0.8 + - - -
290B VAL* 1.3 72.3 - - - +
292B LEU* 1.3 60.3 + - - +
318B ALA* 2.9 24.9 - - + +
319B PRO 5.5 0.2 - - - -
320B HIS* 4.4 17.3 - - - -
345B GLU* 4.4 4.0 - - - +
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Residues in contact with LEU 292 (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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269B SER 4.4 3.4 + - - -
270B GLU* 4.5 1.5 - - - +
278B PHE* 3.7 29.2 - - + -
290B VAL* 5.0 0.2 - - + -
291B MSE 1.3 80.3 - - - +
293B ASP* 1.3 56.4 + - - +
294B ILE* 4.1 1.6 + - + +
297B CYS* 3.6 25.1 - - + -
303B ALA* 3.9 31.9 - - + +
306B ILE* 3.7 24.7 - - + -
317B VAL* 3.9 31.2 - - + -
318B ALA 3.7 0.8 + - - -
319B PRO* 3.4 7.0 - - + +
320B HIS* 2.6 34.9 + - - -
334B LEU* 4.5 5.2 - - + -
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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