Contacts of the strand formed by residues 303 - 310 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263N PRO* 3.6 8.5 - - - -
301N ASP 3.4 2.2 + - - -
302N GLN* 1.3 74.8 - - - +
304N LEU* 1.3 64.2 + - - -
305N TYR* 3.5 6.9 - - - -
321N PHE* 3.4 21.2 - - - -
322N VAL 2.9 33.1 + - - -
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Residues in contact with LEU 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N GLU 3.7 2.8 - - - +
262N TYR* 3.7 6.4 - - - -
263N PRO* 3.6 17.4 - - - +
303N GLY* 1.3 71.8 - - - -
305N TYR* 1.3 60.2 + - - +
306N THR* 4.1 17.5 + - - +
319N SER* 3.7 23.8 - - - +
320N THR* 3.7 21.1 - - - +
321N PHE* 3.8 14.5 - - + +
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Residues in contact with TYR 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228N LEU* 4.0 3.8 - - - +
242N LEU* 4.0 14.1 - - + +
244N LEU* 3.8 22.2 - - + -
260N TRP* 4.7 3.6 - + + -
261N GLU 3.4 3.6 - - - -
262N TYR* 3.6 19.3 - + + -
263N PRO* 3.8 12.7 - - + +
270N LYS* 4.0 3.3 + - - -
292N LEU* 3.5 31.6 - - + -
294N ILE* 3.4 23.3 - - + +
301N ASP* 2.8 36.8 + - - +
303N GLY 3.5 12.1 - - - -
304N LEU* 1.3 74.2 - - - +
306N THR* 1.3 62.4 + - - +
319N SER* 3.1 24.0 - - - -
320N THR* 3.1 15.1 + - + +
322N VAL* 3.7 22.4 - - + -
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Residues in contact with THR 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259N ASN 3.8 0.9 - - - +
260N TRP* 3.1 12.1 - - - -
261N GLU* 2.8 62.0 + - + +
304N LEU* 4.1 14.6 + - - +
305N TYR* 1.3 75.5 - - - +
307N CYS* 1.3 63.7 + - - +
308N ALA* 4.8 1.6 - - + +
317N LYS* 4.2 29.8 - - + +
318N ASN 3.5 11.4 - - - +
319N SER* 3.7 12.3 - - - -
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Residues in contact with CYS 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N VAL* 3.9 2.1 - - + +
228N LEU* 4.1 7.1 - - + +
246N CYS* 2.0 54.5 - - + -
258N PHE* 3.7 18.6 - - - -
259N ASN 3.8 3.1 - - - -
260N TRP* 3.8 24.1 - - + -
305N TYR 4.2 0.8 + - - -
306N THR* 1.3 72.5 - - - +
308N ALA* 1.3 64.4 + - - +
317N LYS* 3.0 4.9 - - - +
318N ASN 2.9 37.5 + - - +
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Residues in contact with ALA 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N ASP 3.7 0.3 - - - +
258N PHE* 3.3 8.7 - - - -
259N ASN* 2.9 45.5 + - + +
306N THR* 4.1 2.4 - - + -
307N CYS* 1.3 78.2 - - - +
309N ALA* 1.3 60.2 + - - +
310N SER* 4.2 1.6 - - - +
315N THR* 4.2 12.3 - - + -
316N LYS 3.6 4.0 - - - -
317N LYS* 3.6 23.6 - - + -
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Residues in contact with ALA 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223N ILE* 3.3 8.4 - - + +
226N VAL* 3.7 25.1 - - + +
248N ALA* 4.0 17.9 - - + -
256N ILE* 4.0 15.9 - - + -
257N ASP 3.6 3.8 - - - -
258N PHE* 4.1 6.7 - - + -
308N ALA* 1.3 74.4 - - - +
310N SER* 1.3 61.9 + - - +
315N THR* 3.2 5.9 - - - -
316N LYS 2.9 30.1 + - - -
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Residues in contact with SER 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO* 3.7 4.6 - - - +
255N GLY 3.5 0.7 - - - +
256N ILE* 3.3 8.0 - - - +
257N ASP* 2.8 51.1 + - - -
259N ASN* 4.9 7.7 + - - -
308N ALA* 5.3 2.1 - - - +
309N ALA* 1.3 74.2 - - - +
311N SER* 1.3 60.4 + - - +
312N GLY* 3.5 4.9 - - - -
314N MET 3.4 3.8 - - - -
315N THR* 2.8 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