Contacts of the strand formed by residues 301 - 306 (chain B) in PDB entry 2W8B
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 ASN 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B TRP* 3.7 7.8 - - - -
296B PHE* 2.8 49.1 + - + +
298B ASP* 2.8 30.5 + - - +
300B GLN* 1.3 85.2 - - - +
302B LEU* 1.3 59.9 + - - +
316B LYS* 4.0 21.3 - - - +
317B VAL 3.4 4.8 - - - +
318B ASN* 3.3 34.4 + - - +
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Residues in contact with LEU 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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259B ALA* 4.0 19.5 - - + -
270B LEU* 4.0 25.8 - - + -
272B VAL* 4.6 4.5 - - + -
283B VAL* 4.8 5.2 - - + -
293B PRO* 4.2 8.1 - - + -
294B THR 3.3 14.8 - - - +
295B TRP* 3.4 41.7 - - + +
296B PHE* 3.6 5.4 - - - -
301B ASN* 1.3 74.3 - - - +
303B ALA* 1.3 65.9 + - - +
304B PHE* 4.2 1.2 - - - -
316B LYS* 3.1 4.5 - - - +
317B VAL* 2.8 41.3 + - + +
319B ILE* 3.9 25.4 - - + -
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Residues in contact with ALA 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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293B PRO* 3.3 1.0 - - - +
294B THR* 2.8 51.5 + - + +
296B PHE* 3.4 18.2 - - + -
302B LEU* 1.3 73.4 - - - +
304B PHE* 1.3 65.4 + - - +
314B VAL* 4.1 13.9 - - + -
315B TYR 3.0 11.2 - - - +
316B LYS* 4.2 0.2 - - - +
327B ILE* 4.6 6.1 - - + -
337B ALA* 5.0 0.2 - - + -
339B VAL* 4.0 8.5 - - + -
346B MET* 4.8 2.0 - - - -
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Residues in contact with PHE 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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270B LEU* 3.6 23.6 - - + -
284B THR* 4.3 7.0 - - + -
290B ASN* 3.3 32.8 - - + -
291B THR 3.4 9.2 - - - +
292B GLU 3.7 8.1 - - - -
293B PRO* 4.0 8.3 - - + -
294B THR* 5.4 0.2 - - - -
302B LEU 4.2 5.8 - - - -
303B ALA* 1.3 79.6 - - - +
305B THR* 1.3 78.8 + - - +
306B SER* 3.9 9.2 - - - -
308B GLN* 6.1 0.4 - - - -
314B VAL* 3.2 9.4 - - - +
315B TYR* 2.9 53.7 + + + -
316B LYS 4.1 0.4 - - - -
317B VAL* 3.7 25.6 - - + -
324B PRO* 3.7 29.2 - - + -
336B ASP 5.8 0.2 - - - -
337B ALA* 6.0 2.0 - - - -
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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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289B ASN 3.7 0.7 - - - +
290B ASN* 3.2 5.4 - - - -
291B THR* 2.9 38.8 + - - +
292B GLU* 2.4 32.8 + - - +
304B PHE* 1.3 75.1 - - - +
306B SER* 1.3 62.5 + - - +
312B PRO* 3.6 19.7 - - + -
313B GLN 3.6 6.7 - - - +
314B VAL* 4.6 1.3 - - - +
335B GLN* 3.4 25.2 - - + -
336B ASP 2.9 15.6 + - - -
337B ALA 4.6 0.2 + - - -
117C TYR* 4.2 14.4 - - + -
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Residues in contact with SER 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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288B SER* 3.6 1.0 + - - -
289B ASN 3.3 5.9 + - - -
290B ASN* 2.8 25.6 + - - -
304B PHE* 3.8 7.7 + - - -
305B THR* 1.3 75.5 - - - +
307B ASP* 1.3 61.9 + - - +
308B GLN* 3.0 27.3 + - - +
309B ALA 5.0 0.5 + - - -
311B ARG 4.2 0.7 - - - +
312B PRO* 3.3 2.8 - - - +
313B GLN 3.0 31.6 + - - +
315B TYR* 3.7 25.1 - - - -
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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
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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