Contacts of the strand formed by residues 315 - 320 (chain B) in PDB entry 1UNN
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 MET 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LYS* 3.5 34.5 - - + -
283B LEU 3.8 0.5 - - - +
284B TYR* 3.5 2.3 - - - +
285B VAL* 2.7 46.1 + - + +
310B TYR* 4.6 0.9 - - - +
313B ALA 4.2 2.2 - - - +
314B GLU* 1.3 79.1 - - - +
316B GLU* 1.3 64.0 + - - +
317B ILE* 3.5 38.1 - - + -
340B LEU* 3.8 22.2 - - + -
342B ASP* 3.6 35.2 - - - +
343B SER* 5.6 1.1 - - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 3.3 28.9 + - + -
283B LEU 3.1 11.2 - - - +
284B TYR* 3.4 43.8 + - + -
315B MET* 1.3 79.3 - - - +
317B ILE* 1.3 65.1 + - - +
343B SER* 3.0 25.5 - - - -
366B LEU* 3.6 19.6 - - + +
340C ASP* 4.8 0.2 - - - +
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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
----------------------------------------------------------
283B LEU* 2.7 55.8 + - + +
285B VAL* 5.6 2.5 - - + -
315B MET* 3.5 18.2 - - + -
316B GLU* 1.3 76.2 - - - +
318B GLY* 1.3 61.3 + - - +
319B PHE* 3.5 21.5 - - + -
340B LEU* 4.0 9.9 - - + -
342B ASP 3.4 22.2 - - - +
343B SER* 3.6 8.3 - - - +
345B SER 3.6 8.3 - - - +
347B VAL* 3.5 29.6 - - + -
363B PRO* 3.6 16.6 - - + -
366B LEU* 3.9 9.2 - - - -
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Residues in contact with GLY 318 (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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281B VAL 3.3 10.5 - - - -
317B ILE* 1.3 76.7 - - - +
319B PHE* 1.4 59.8 - - - -
343B SER 4.9 0.4 + - - -
363B PRO* 2.9 14.7 - - - +
364B MET* 2.8 31.6 + - - -
366B LEU* 3.5 9.4 - - - +
343C MET* 3.8 19.7 - - - -
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Residues in contact with PHE 319 (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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280B GLY* 3.4 1.0 - - - -
281B VAL* 2.8 35.3 + - + +
283B LEU* 3.9 28.7 - - + -
317B ILE* 3.5 33.0 - - + -
318B GLY* 1.4 78.1 - - - -
320B ASN* 1.3 63.7 + - - +
321B VAL 3.3 0.7 + - - -
324B VAL* 3.6 25.1 - - + -
338B MET* 5.1 2.7 - - + -
347B VAL* 3.3 38.6 - - + -
361B VAL* 3.4 44.0 - - + -
362B MET 3.7 6.3 - - - -
363B PRO* 3.5 11.9 - - + -
364B MET* 3.7 10.9 - - - +
343C MET* 4.9 0.2 - - - +
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Residues in contact with ASN 320 (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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277B LYS 5.7 0.8 + - - -
278B PHE 4.0 9.3 + - - -
279B ARG* 3.4 19.5 - - - +
319B PHE* 1.3 74.7 - - - +
321B VAL* 1.3 63.7 + - - +
322B SER* 2.8 26.7 + - - -
323B TYR* 3.0 58.9 + - + +
324B VAL* 3.3 11.3 + - - +
364B MET* 3.4 12.9 - - - +
346C GLN* 3.7 12.2 - - - +
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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