Contacts of the strand formed by residues 289 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER 3.0 11.5 + - - +
245B GLN* 3.2 11.4 - - - +
246B LEU* 2.8 22.4 + - - -
280B PHE* 4.6 9.3 - - - -
281B ILE 3.2 14.6 - - - -
282B THR* 4.0 16.2 - - - -
287B GLY 4.2 6.6 + - - -
288B SER* 1.3 76.7 + - - +
290B LYS* 1.3 62.7 + - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLN* 4.2 24.0 - - - +
246B LEU* 2.8 30.8 + - + +
248B GLY 2.9 28.9 + - - +
250B HIS* 4.4 1.3 - - - -
279B TYR 3.7 1.0 - - - +
280B PHE* 3.4 4.1 - - - -
281B ILE* 3.0 41.6 + - + +
289B SER* 1.3 77.3 - - - +
291B CYS* 1.3 63.6 - - - +
292B VAL 3.5 19.6 + - - +
293B CYS* 3.6 28.0 - - - +
408B CIT 3.0 30.5 + - - +
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Residues in contact with CYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLN* 5.0 3.3 + - - -
269B PHE* 3.5 7.4 - - - -
279B TYR 3.4 0.9 - - - +
280B PHE* 3.3 56.2 - - + +
290B LYS* 1.3 76.0 - - - +
292B VAL* 1.3 71.1 + - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B HIS* 5.6 0.3 - - - -
269B PHE* 4.1 13.2 - - + -
278B ASN* 3.8 30.7 - - + +
279B TYR 3.7 1.8 - - - -
290B LYS* 3.7 16.5 - - - +
291B CYS* 1.3 89.8 - - + +
293B CYS* 1.3 59.4 + - - +
294B SER 3.9 1.4 + - - -
346B LEU* 3.5 34.1 - - + +
408B CIT 4.3 4.0 - - - +
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Residues in contact with CYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 5.3 0.4 - - - -
248B GLY 3.8 5.4 - - - -
249B LEU* 3.3 33.0 - - - -
250B HIS* 4.3 1.8 - - - -
255B LEU* 6.3 0.2 - - - -
266B LEU* 6.2 0.2 - - + -
277B LYS 3.7 0.3 - - - +
278B ASN* 3.5 2.2 - - - -
279B TYR* 2.7 42.7 + - + +
281B ILE* 3.7 24.0 - - + -
290B LYS* 3.6 27.4 - - + +
292B VAL* 1.3 71.6 - - - +
294B SER* 1.3 67.8 + - - +
295B VAL* 3.6 13.0 + - + +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B HIS* 2.7 51.1 + - - +
276B VAL* 3.9 15.0 - - - -
277B LYS 3.3 6.5 - - - -
278B ASN* 3.2 16.7 + - - -
292B VAL* 3.9 3.6 + - - +
293B CYS* 1.3 73.0 - - - +
295B VAL* 1.3 60.6 + - - +
343B TYR* 5.3 0.3 - - - -
344B PRO* 3.7 24.6 + - - +
346B LEU* 4.0 15.2 - - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU 4.0 14.4 - - - +
250B HIS 3.4 4.0 - - - +
252B LEU* 4.0 38.4 - - + +
255B LEU* 4.1 19.5 - - + -
266B LEU* 5.7 0.7 - - + -
275B THR 4.4 0.3 - - - +
276B VAL* 3.7 3.0 - - - +
277B LYS* 2.7 37.9 + - + +
279B TYR* 3.8 24.2 - - + -
293B CYS* 3.7 15.9 - - + +
294B SER* 1.3 80.3 - - - +
296B ILE* 1.3 65.8 + - - +
344B PRO* 5.5 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
------------------------------------------------------------
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