Contacts of the strand formed by residues 301 - 306 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F TRP* 3.7 8.1 - - - -
296F PHE* 2.9 44.8 + - + -
298F ASP* 2.8 30.2 + - - +
300F GLN* 1.3 87.3 - - - +
302F LEU* 1.3 63.6 + - - +
316F LYS* 4.2 19.1 - - - +
317F VAL 3.4 3.3 - - - +
318F ASN* 3.1 34.1 + - - +
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Residues in contact with LEU 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F ALA* 4.0 20.2 - - + -
270F LEU* 4.1 21.1 - - + -
272F VAL* 4.4 4.9 - - + -
283F VAL* 4.6 6.7 - - + -
293F PRO* 4.3 8.3 - - + -
294F THR 3.3 11.4 - - - +
295F TRP* 3.4 44.9 - - + +
296F PHE* 3.9 4.3 - - - -
301F ASN* 1.3 74.8 - - - +
303F ALA* 1.3 65.7 + - - +
304F PHE* 3.9 3.8 - - + -
316F LYS* 3.2 3.6 - - - +
317F VAL* 2.9 39.5 + - + +
319F ILE* 3.8 25.1 - - + -
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Residues in contact with ALA 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F PRO* 3.3 1.0 - - - +
294F THR* 2.9 51.0 + - + +
296F PHE* 3.6 10.6 - - + -
302F LEU* 1.3 73.5 - - - +
304F PHE* 1.3 65.7 + - - +
314F VAL* 3.9 14.8 - - + -
315F TYR 3.0 10.1 - - - +
316F LYS* 4.2 0.2 - - - +
327F ILE* 4.5 8.3 - - + -
337F ALA* 4.9 0.4 - - + -
339F VAL* 3.9 13.9 - - + -
346F MET* 4.7 2.7 - - - -
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Residues in contact with PHE 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F LEU* 3.6 22.9 - - + -
284F THR* 4.4 4.9 - - + -
290F ASN* 3.3 32.1 - - + -
291F THR 3.4 9.6 - - - +
292F GLU 3.6 8.1 - - - -
293F PRO* 3.9 9.4 - - + -
302F LEU 3.9 6.3 - - - -
303F ALA* 1.3 80.9 - - - +
305F THR* 1.3 72.6 + - - +
306F SER* 3.9 8.3 - - - -
314F VAL* 3.3 9.6 - - - +
315F TYR* 2.7 53.9 + + + -
316F LYS 4.0 0.4 - - - -
317F VAL* 3.5 26.5 - - + -
324F PRO* 3.5 29.6 - - + -
337F ALA* 5.8 2.7 - - - -
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Residues in contact with THR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F ASN 3.6 0.5 - - - +
290F ASN* 3.2 4.7 - - - -
291F THR* 2.8 42.1 + - - +
292F GLU* 2.5 30.6 + - - +
304F PHE* 1.3 75.7 - - - +
306F SER* 1.3 63.4 + - - +
312F PRO* 4.0 16.6 - - + -
313F GLN 3.6 5.6 - - - +
314F VAL* 4.8 0.7 - - - +
335F GLN* 3.7 20.3 - - + +
336F ASP 3.0 16.3 + - - -
337F ALA 4.8 0.2 + - - -
117G TYR* 4.0 18.6 - - + -
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Residues in contact with SER 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F SER* 3.8 1.6 + - - -
289F ASN 3.1 6.3 + - - -
290F ASN* 2.9 26.1 + - - -
304F PHE* 3.8 6.6 + - - -
305F THR* 1.3 74.0 - - - +
307F ASP* 1.3 58.6 + - - +
308F GLN* 2.8 28.0 + - - +
309F ALA 5.0 0.3 + - - -
311F ARG 4.3 0.5 - - - +
312F PRO* 3.4 3.0 - - - +
313F GLN 3.0 32.4 + - - +
315F TYR* 3.7 25.4 - - - -
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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