Contacts of the strand formed by residues 303 - 310 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263L PRO* 3.8 8.5 - - - -
301L ASP 3.8 1.4 + - - -
302L GLN* 1.3 76.6 - - - +
304L LEU* 1.3 61.8 + - - -
305L TYR* 3.6 5.2 - - - -
321L PHE* 3.4 25.2 - - - -
322L VAL 2.8 36.9 + - - -
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Residues in contact with LEU 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L GLU 3.7 2.6 - - - +
262L TYR 3.6 24.3 - - - +
263L PRO* 3.7 5.0 - - - +
303L GLY* 1.3 71.0 - - - -
305L TYR* 1.3 59.8 + - - +
306L THR* 4.0 15.9 - - - +
319L SER* 3.8 26.5 - - - +
320L THR* 3.9 15.0 - - - +
321L PHE* 4.0 17.2 - - + +
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Residues in contact with TYR 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L LEU* 4.1 2.8 - - - +
242L LEU* 4.0 13.5 - - + +
244L LEU* 3.9 22.9 - - + -
260L TRP* 4.5 4.5 - + + -
261L GLU 3.4 4.3 - - - +
262L TYR* 3.9 14.6 - + - -
263L PRO* 3.3 25.1 - - + +
270L LYS* 5.3 0.8 - - - -
292L LEU* 3.6 31.2 - - + -
294L ILE* 3.5 20.0 - - + +
301L ASP* 2.6 36.6 + - - +
303L GLY 3.6 10.5 - - - -
304L LEU* 1.3 74.7 - - - +
306L THR* 1.3 61.4 + - - +
318L ASN 4.1 0.2 - - - +
319L SER* 3.1 4.5 - - - -
320L THR 3.0 36.4 + - - +
322L VAL* 3.6 22.9 - - + -
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Residues in contact with THR 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L ASN 3.9 1.1 - - - +
260L TRP* 3.3 11.6 - - - -
261L GLU* 2.9 57.3 + - + +
304L LEU* 4.0 13.9 - - - +
305L TYR* 1.3 72.9 - - - +
307L CYS* 1.3 67.2 + - - +
308L ALA* 4.6 2.7 - - + +
317L LYS* 4.2 28.9 - - + +
318L ASN 3.4 11.2 - - - +
319L SER* 3.3 16.8 - - - -
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Residues in contact with CYS 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L VAL* 3.9 3.7 - - + +
228L LEU* 4.0 7.8 - - + +
246L CYS* 2.0 53.6 - - + -
258L PHE* 3.6 20.0 - - - -
259L ASN 3.9 2.0 - - - -
260L TRP* 3.9 24.7 - - + -
305L TYR 4.3 0.2 - - - -
306L THR* 1.3 73.6 - - - +
308L ALA* 1.3 63.4 + - - +
317L LYS* 3.1 4.4 - - - -
318L ASN 2.8 33.5 + - - +
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Residues in contact with ALA 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257L ASP 3.7 1.2 - - - +
258L PHE* 3.4 5.9 - - - -
259L ASN* 2.8 50.1 + - + +
306L THR* 4.1 2.9 - - + -
307L CYS* 1.3 76.0 - - - +
309L ALA* 1.3 60.4 + - - +
310L SER* 4.1 0.9 - - - -
315L THR* 4.3 13.7 - - + -
316L LYS 3.6 3.8 - - - -
317L LYS* 3.7 17.9 - - + -
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Residues in contact with ALA 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 3.2 12.3 - - + +
226L VAL* 3.8 23.6 - - + -
248L ALA* 3.9 13.9 - - + -
256L ILE* 3.8 18.4 - - + -
257L ASP 3.7 3.8 - - - -
258L PHE* 4.0 9.4 - - + -
307L CYS 4.2 0.6 + - - -
308L ALA* 1.3 73.6 - - - +
310L SER* 1.3 59.1 + - - +
315L THR* 3.4 1.5 - - - -
316L LYS 2.8 32.5 + - - -
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Residues in contact with SER 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D VAL* 3.6 9.8 - - - +
191D PRO* 5.7 0.5 - - - +
256L ILE* 3.3 6.5 - - - +
257L ASP* 2.7 45.7 + - - -
259L ASN* 5.1 7.4 - - - -
308L ALA 4.1 0.8 - - - -
309L ALA* 1.3 74.1 - - - +
311L SER* 1.3 60.7 + - - +
312L GLY* 3.2 14.1 + - - -
314L MET 3.6 5.1 + - - -
315L THR* 3.3 20.2 + - - -
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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