Contacts of the strand formed by residues 277 - 283 (chain A) in PDB entry 6W01
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 LYS 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ASP* 2.9 27.4 + - - -
270A ILE 2.9 28.1 + - - -
272A MET* 2.9 26.5 + - - +
273A ASP* 5.2 0.4 - - - +
274A SER* 3.7 26.6 + - - +
275A THR 4.2 0.6 - - - +
276A VAL* 1.3 75.8 - - - +
278A ASN* 1.3 64.8 + - - +
279A TYR* 3.6 32.5 - - + +
293A CYS 3.7 1.0 - - - +
294A SER* 3.3 2.6 - - - -
295A VAL* 2.7 42.5 + - + +
346A LEU* 4.7 0.7 - - - -
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU 4.1 1.0 - - - +
268A ASP* 4.4 5.4 - - - +
269A PHE* 3.8 34.8 + - + -
270A ILE* 5.0 8.2 + - + +
277A LYS* 1.3 75.9 + - - +
279A TYR* 1.3 67.7 + - - +
292A VAL* 3.8 18.4 - - + +
293A CYS 3.6 2.5 - - - -
294A SER* 3.3 28.1 + - - -
346A LEU* 3.5 40.6 - - + +
405A PEG 3.6 15.1 + - - -
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Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU* 6.2 0.2 - - + -
255A LEU* 5.5 0.2 - - + -
266A LEU* 3.9 49.6 - - + -
267A GLU 3.3 5.2 - - - +
268A ASP* 3.8 39.2 + - + -
269A PHE* 3.9 1.6 - - - -
277A LYS* 3.6 37.2 - - + +
278A ASN* 1.3 78.9 - - - +
280A PHE* 1.3 59.2 + - - +
281A ILE* 3.6 1.1 + - + -
290A LYS 3.8 0.3 - - - +
291A CYS 3.5 4.9 - - - +
293A CYS* 2.8 42.8 + - + +
295A VAL* 3.8 33.4 - - + -
409A EDO 3.8 25.1 + - - -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 3.6 3.8 - - - +
267A GLU* 2.8 59.6 + - + +
269A PHE* 3.8 10.4 - + + -
279A TYR* 1.3 69.4 - - - +
281A ILE* 1.3 66.0 + - - +
282A THR* 4.3 14.4 + - - -
289A SER* 4.8 8.1 - - - -
290A LYS 3.5 8.5 - - - -
291A CYS* 3.3 48.0 + - + +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PHE* 5.4 1.1 - - + -
246A LEU* 3.8 22.4 - - + -
249A LEU* 3.5 31.2 - - + -
255A LEU* 4.9 1.8 - - + -
264A PHE* 4.0 18.8 - - + -
265A GLU 3.2 11.9 - - - +
266A LEU* 3.8 23.3 - - + -
279A TYR 3.6 0.6 + - - +
280A PHE* 1.3 73.8 - - - +
282A THR* 1.3 67.1 + - - +
283A ASP 4.2 0.4 - - - +
289A SER* 3.2 5.0 - - - -
290A LYS* 2.9 44.2 + - + +
293A CYS* 3.8 25.1 - - + -
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 3.3 2.4 - - - +
265A GLU* 2.9 44.5 + - + +
280A PHE* 4.1 13.6 + - - -
281A ILE* 1.3 76.6 + - - +
283A ASP* 1.3 70.4 + - - +
284A ALA* 3.5 3.6 + - - +
287A GLY* 5.1 6.5 - - - +
288A SER 3.8 3.4 - - - +
289A SER* 4.0 13.4 - - - -
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PHE* 3.5 20.4 - - + -
246A LEU* 4.4 3.4 - - + +
258A ARG* 2.8 41.0 + - - -
262A SER* 4.5 1.0 + - - -
263A PRO 4.1 4.3 - - - +
264A PHE* 3.8 15.1 - - + +
281A ILE 4.2 0.6 - - - -
282A THR* 1.3 74.8 - - - +
284A ALA* 1.3 59.0 + - - +
285A GLN 3.6 2.4 + - - -
286A THR* 2.7 34.5 + - - +
287A GLY* 2.8 30.8 + - - -
288A SER 2.8 20.0 + - - +
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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