Contacts of the strand formed by residues 303 - 310 (chain O) in PDB entry 2X1W
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 GLY 303 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263O PRO* 3.9 5.4 - - - -
301O ASP 3.7 0.8 + - - -
302O GLN* 1.3 77.2 - - - +
304O LEU* 1.3 62.0 + - - -
305O TYR* 3.5 8.2 - - - -
321O PHE* 3.5 24.3 - - - -
322O VAL 2.8 35.5 + - - -
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Residues in contact with LEU 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261O GLU* 3.7 6.9 - - - +
262O TYR* 3.7 1.6 - - - -
263O PRO* 3.6 18.4 - - - +
303O GLY* 1.3 71.5 - - - -
305O TYR* 1.3 60.8 + - - +
306O THR* 4.0 16.3 + - - +
319O SER* 3.7 24.9 - - - +
320O THR* 3.8 15.7 - - - +
321O PHE* 4.0 17.0 - - + +
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Residues in contact with TYR 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228O LEU* 4.1 2.9 - - - +
242O LEU* 4.0 13.8 - - + +
244O LEU* 3.9 22.9 - - + -
260O TRP* 4.6 4.9 - + + -
261O GLU 3.4 3.6 - - - +
262O TYR* 3.5 23.8 - + + -
263O PRO* 3.8 12.8 - - + -
270O LYS* 3.6 10.1 + - + -
292O LEU* 3.6 27.6 - - + -
294O ILE* 3.5 19.2 - - + +
301O ASP* 2.6 33.4 + - - +
303O GLY 3.5 12.1 - - - -
304O LEU* 1.3 75.0 - - - +
306O THR* 1.3 60.7 + - - +
319O SER* 3.1 4.6 - - - -
320O THR* 3.0 36.2 + - + +
322O VAL* 3.6 22.2 - - + -
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Residues in contact with THR 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259O ASN 3.9 0.6 - - - +
260O TRP* 3.2 11.2 - - - -
261O GLU* 2.9 57.8 + - + +
304O LEU* 4.0 14.1 + - - +
305O TYR* 1.3 73.8 - - - +
307O CYS* 1.3 70.0 + - - +
308O ALA* 4.6 2.7 - - + +
317O LYS* 4.2 26.2 - - + +
318O ASN 3.4 12.6 - - - +
319O SER* 3.3 15.5 - - - -
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Residues in contact with CYS 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O VAL* 3.9 2.8 - - + +
228O LEU* 3.9 8.3 - - + +
246O CYS* 2.0 53.2 - - + -
258O PHE* 3.6 21.8 - - - -
259O ASN 4.0 2.0 - - - -
260O TRP* 3.9 23.3 - - + -
305O TYR 4.3 0.2 + - - -
306O THR* 1.3 72.8 - - - +
308O ALA* 1.3 63.2 + - - +
317O LYS* 3.1 5.1 - - - -
318O ASN 2.9 33.2 + - - +
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Residues in contact with ALA 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257O ASP 3.7 1.0 - - - +
258O PHE* 3.4 5.9 - - - -
259O ASN* 2.8 53.8 + - + +
306O THR* 4.1 2.9 - - + -
307O CYS* 1.3 75.6 - - - +
309O ALA* 1.3 60.7 + - - +
310O SER* 5.7 0.7 - - - -
315O THR* 4.2 13.9 - - + -
316O LYS 3.6 3.8 - - - -
317O LYS* 3.7 17.7 - - + -
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Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O ILE* 3.2 12.0 - - + +
226O VAL* 3.8 24.5 - - + -
248O ALA* 3.9 13.0 - - + -
256O ILE* 3.9 18.8 - - + -
257O ASP 3.7 4.0 - - - -
258O PHE* 4.0 9.0 - - + -
307O CYS 4.2 0.8 + - - -
308O ALA* 1.3 72.9 - - - +
310O SER* 1.3 60.6 + - - +
315O THR* 3.4 1.9 - - - -
316O LYS 2.8 32.1 + - - -
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Residues in contact with SER 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C PRO* 4.3 0.9 - - - +
256O ILE* 3.3 6.7 - - - +
257O ASP* 2.8 50.1 + - - +
259O ASN* 5.1 7.4 - - - -
308O ALA* 4.1 0.6 - - - -
309O ALA* 1.3 73.6 - - - +
311O SER* 1.3 62.1 + - - +
312O GLY* 3.2 15.1 + - - -
314O MET 3.6 4.6 + - - -
315O THR* 3.3 21.0 + - - -
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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