Contacts of the strand formed by residues 289 - 295 (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 SER 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER 3.1 9.7 + - - +
245A GLN* 3.3 10.6 - - - +
246A LEU* 2.8 22.1 + - - -
280A PHE* 4.8 8.5 - - - -
281A ILE 3.2 14.1 - - - -
282A THR* 4.0 16.2 - - - -
287A GLY 4.1 7.1 + - - -
288A SER* 1.3 75.5 + - - +
290A LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 4.1 24.7 - - + +
246A LEU* 2.8 29.2 + - + +
248A GLY 2.8 28.9 + - - +
250A HIS* 4.0 0.2 - - - -
279A TYR 3.8 1.0 - - - +
280A PHE* 3.5 4.6 - - - -
281A ILE* 2.9 41.7 + - + +
289A SER* 1.3 76.9 - - - +
291A CYS* 1.3 64.8 + - - +
292A VAL 3.7 17.9 - - - +
293A CYS* 3.6 27.6 - - - +
405A PEG 4.3 0.2 - - - -
412A CIT 2.9 31.3 + - - +
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Residues in contact with CYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 5.4 1.6 + - - -
269A PHE* 3.6 7.8 - - - -
279A TYR 3.5 0.5 - - - +
280A PHE* 3.3 55.5 - - + +
290A LYS* 1.3 74.8 - - - +
292A VAL* 1.3 70.1 - - + +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 4.2 13.2 - - + -
278A ASN* 3.8 33.4 - - + +
279A TYR 3.8 2.0 - - - -
290A LYS* 3.4 12.0 - - - +
291A CYS* 1.3 89.8 - - + +
293A CYS* 1.3 53.1 + - - +
405A PEG 2.7 48.1 + - - +
412A CIT 4.3 0.9 - - - +
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Residues in contact with CYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.1 0.2 - - - -
248A GLY 3.6 15.7 - - - -
249A LEU* 3.2 33.4 - - - -
250A HIS* 4.3 1.6 - - - -
255A LEU* 6.2 0.4 - - - -
266A LEU* 6.3 0.2 - - + -
278A ASN* 4.4 0.7 - - - -
279A TYR* 2.8 37.8 + - + +
281A ILE* 3.8 24.5 - - + -
290A LYS* 3.6 15.0 - - + +
292A VAL* 1.3 72.8 - - - +
294A SER* 1.3 67.6 + - - +
295A VAL* 3.6 13.4 + - + +
405A PEG 3.4 2.7 - - - -
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 4.1 0.2 - - - +
250A HIS* 2.8 39.6 + - - +
276A VAL* 4.0 6.1 - - - -
277A LYS 3.3 5.6 - - - -
278A ASN* 3.3 18.1 + - - -
292A VAL 3.9 0.8 - - - -
293A CYS* 1.3 71.6 - - - +
295A VAL* 1.3 60.9 + - - +
344A PRO* 2.8 40.7 + - - +
345A LYS* 5.0 1.1 - - - -
405A PEG 3.1 24.2 + - - -
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Residues in contact with VAL 295 (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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249A LEU 3.9 14.6 - - - +
250A HIS 3.4 3.6 - - - +
252A LEU* 4.0 34.1 - - + +
255A LEU* 4.0 23.6 - - + -
266A LEU* 5.8 0.7 - - + -
275A THR 4.5 0.3 - - - +
276A VAL* 3.8 2.9 - - - +
277A LYS* 2.7 39.7 + - + +
279A TYR* 3.8 24.2 - - + -
293A CYS* 3.6 15.9 - - - +
294A SER* 1.3 81.8 - - - +
296A ILE* 1.3 64.6 + - - +
344A PRO* 4.9 0.7 - - - -
409A EDO 6.1 0.2 - - - -
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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