Contacts of the strand formed by residues 312 - 317 (chain B) in PDB entry 5DTM
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 TYR 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 4.0 27.1 - - + -
146B GLN* 4.9 2.0 - - + -
147B MET* 3.3 39.7 - - + +
150B GLU* 2.5 34.6 + - - +
151B ILE* 4.0 6.6 - - + +
267B VAL* 3.6 18.8 - - + -
268B SER 3.5 13.0 - - - +
295B GLU* 3.6 4.7 - - - +
296B LEU* 2.8 67.2 + - + +
298B PRO* 5.5 0.7 - - + -
311B SER* 1.3 74.0 - - - +
313B TYR* 1.3 72.5 + - - +
314B LEU* 4.8 0.7 - - + -
401B 5F4 3.5 23.6 - + + -
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.4 23.5 - - + +
266B ILE 3.3 2.3 - - - +
267B VAL* 3.2 7.6 - - - +
268B SER* 2.8 41.7 + - - +
269B SER 3.5 21.1 - - - -
271B PRO* 3.6 39.7 - - + -
275B LEU* 4.1 18.4 - - + -
293B VAL* 4.6 2.0 - - + -
294B VAL 3.4 2.5 - - - +
295B GLU* 3.6 48.3 + - + -
311B SER* 4.4 8.8 - - - -
312B TYR* 1.3 81.4 - - - +
314B LEU* 1.3 60.8 + - - +
315B HIS* 3.5 20.4 + - + -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 3.7 30.3 - - + -
265B ARG* 4.0 27.8 - - + +
266B ILE 3.5 4.9 - - - +
267B VAL* 4.1 7.9 - - + +
292B ARG 3.7 1.6 - - - +
293B VAL* 3.4 2.4 - - - -
294B VAL* 2.9 51.2 + - + +
296B LEU* 3.6 23.8 - - + +
312B TYR* 4.2 3.0 - - + -
313B TYR* 1.3 72.4 - - - +
315B HIS* 1.3 70.0 + - - +
316B THR* 4.2 11.7 + - - +
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Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ARG* 3.2 7.3 - - - +
266B ILE* 2.8 57.0 + - + +
268B SER* 3.2 27.8 - - - -
271B PRO* 3.5 3.8 - - - +
272B PHE* 2.9 36.6 + + + -
291B MET* 3.6 37.0 - - + -
292B ARG 3.2 5.4 - - - -
293B VAL* 3.5 19.6 - - + +
313B TYR* 3.5 18.7 + - + -
314B LEU* 1.3 70.5 - - - +
316B THR* 1.3 65.9 + - - +
317B ILE 4.3 0.2 - - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLY* 4.2 15.9 - - - +
264B GLY 3.4 7.6 - - - +
265B ARG* 3.9 13.4 - - + +
291B MET* 3.2 3.6 - - - -
292B ARG* 2.8 70.5 + - - +
314B LEU* 4.2 13.5 + - - +
315B HIS* 1.3 75.6 + - - +
317B ILE* 1.3 75.9 + - - +
318B ASP* 3.2 2.8 + - - +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PHE 3.6 22.0 - - - +
260B MET* 3.9 14.8 - - + +
261B LYS 3.3 26.0 - - - +
262B GLU* 3.8 5.4 - - - +
263B GLY* 2.9 25.3 + - - -
264B GLY 2.8 21.6 + - - +
266B ILE* 4.2 8.5 - - + -
290B ILE* 3.5 16.6 - - + +
291B MET* 3.7 28.9 - - + -
292B ARG* 5.1 0.3 + - - -
316B THR* 1.3 70.7 - - - +
318B ASP* 1.3 63.8 + - - +
319B ARG* 3.5 32.1 - - + +
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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