Contacts of the strand formed by residues 303 - 310 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M PRO* 3.6 7.9 - - - -
301M ASP 3.4 2.6 + - - -
302M GLN* 1.3 75.9 - - - +
304M LEU* 1.3 63.4 + - - -
305M TYR* 3.5 7.8 - - - -
321M PHE* 3.4 21.0 - - - -
322M VAL 2.9 32.8 + - - -
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Residues in contact with LEU 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M GLU* 3.7 2.8 - - - +
262M TYR* 3.7 6.9 - - - -
263M PRO* 3.6 16.5 - - - +
303M GLY* 1.3 72.1 - - - -
305M TYR* 1.3 59.4 + - - +
306M THR* 4.0 17.7 + - - +
319M SER* 3.7 23.8 - - - +
320M THR* 3.7 21.3 - - - +
321M PHE* 3.8 13.4 - - + +
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Residues in contact with TYR 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228M LEU* 4.0 3.6 - - - +
242M LEU* 4.0 13.9 - - + +
244M LEU* 3.8 22.4 - - + -
260M TRP* 4.7 3.6 - + + -
261M GLU 3.4 3.8 - - - +
262M TYR* 3.6 19.5 - + + -
263M PRO* 3.8 13.0 - - + +
270M LYS* 4.0 3.3 + - + -
292M LEU* 3.4 31.2 - - + -
294M ILE* 3.4 15.1 - - + +
301M ASP* 2.8 45.2 + - - +
303M GLY 3.5 11.7 - - - -
304M LEU* 1.3 74.0 - - - +
306M THR* 1.3 61.4 + - - +
307M CYS 4.2 0.2 - - - -
319M SER* 3.1 23.6 - - - -
320M THR* 3.0 15.1 + - + +
322M VAL* 3.7 22.0 - - + -
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Residues in contact with THR 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259M ASN 3.7 0.7 - - - +
260M TRP* 3.1 11.6 - - - -
261M GLU* 2.8 63.8 + - + +
304M LEU* 4.0 15.3 + - - +
305M TYR* 1.3 75.6 - - - +
307M CYS* 1.3 62.7 + - - +
308M ALA* 4.8 1.8 - - + +
317M LYS* 4.2 30.1 - - + +
318M ASN 3.5 13.2 - - - +
319M SER* 3.7 10.8 - - - -
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Residues in contact with CYS 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M VAL* 3.9 2.2 - - + +
228M LEU* 4.0 7.8 - - + +
246M CYS* 2.0 54.3 - - + -
258M PHE* 3.7 18.2 - - - -
259M ASN 3.8 2.2 - - - -
260M TRP* 3.9 23.9 - - + -
305M TYR 4.2 0.4 + - - -
306M THR* 1.3 73.6 - - - +
308M ALA* 1.3 64.3 + - - +
317M LYS* 3.0 5.1 - - - +
318M ASN 2.9 35.5 + - - +
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Residues in contact with ALA 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257M ASP 3.6 0.3 - - - +
258M PHE* 3.2 9.4 - - - -
259M ASN* 2.8 47.7 + - + +
306M THR* 4.1 2.4 - - + -
307M CYS* 1.3 77.9 - - - +
309M ALA* 1.3 60.0 + - - +
310M SER* 4.2 1.8 - - - +
315M THR* 4.2 11.4 - - + -
316M LYS 3.6 4.7 - - - +
317M LYS* 3.6 22.9 - - + -
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Residues in contact with ALA 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M ILE* 3.3 8.3 - - + +
226M VAL* 3.6 25.3 - - + +
248M ALA* 3.9 18.2 - - + -
256M ILE* 4.0 15.7 - - + -
257M ASP 3.6 3.4 - - - -
258M PHE* 4.1 6.3 - - + -
308M ALA* 1.3 74.3 - - - +
310M SER* 1.3 62.9 + - - +
315M THR* 3.2 5.1 - - - -
316M LYS 2.9 31.2 + - - -
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Residues in contact with SER 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 4.2 1.7 - - - +
191A PRO* 5.8 6.7 - - - -
255M GLY 3.4 1.2 - - - +
256M ILE* 3.3 7.2 - - - -
257M ASP* 2.8 51.8 + - - +
259M ASN* 4.9 7.8 + - - -
308M ALA* 5.2 1.7 - - - +
309M ALA* 1.3 74.8 + - - +
311M SER* 1.3 61.1 + - - +
312M GLY* 3.5 4.5 - - - -
314M MET 3.4 3.6 - - - -
315M THR* 2.8 25.6 + - - +
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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