Contacts of the strand formed by residues 312 - 317 (chain B) in PDB entry 5TQW
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 ILE 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B CYS* 4.6 4.7 - - - -
267B LEU* 4.7 9.9 - - + -
268B ILE* 4.1 25.6 - - + -
310B LEU* 3.5 13.7 + - + +
311B LYS* 1.3 76.2 - - - +
313B VAL* 1.3 70.6 + - - +
314B HIS* 4.0 18.1 + - + +
325B SER* 3.4 31.2 - - - +
326B PHE 3.4 8.7 - - - +
327B LEU* 3.8 30.5 - - + +
328B LEU* 4.5 0.9 - - - +
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Residues in contact with VAL 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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312B ILE* 1.3 80.9 - - - +
314B HIS* 1.3 74.7 + - - +
315B ILE* 3.6 8.6 + - + +
324B ILE 3.7 0.3 - - - +
325B SER* 4.4 1.6 - - - -
326B PHE* 3.2 31.6 + - + +
328B LEU* 5.3 15.0 - - + +
337B LEU* 6.0 6.3 - - + -
383B MET* 5.7 2.0 - - - +
384B VAL* 3.7 22.2 - - + -
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 5.4 5.1 + - - -
265B CYS* 5.1 6.8 - - + +
312B ILE* 4.0 17.9 + - + +
313B VAL* 1.3 79.4 - - - +
315B ILE* 1.3 59.4 + - - +
323B ILE* 3.6 21.1 - - + -
324B ILE 3.6 3.1 - - - -
325B SER* 3.1 26.0 + - - +
383B MET* 3.3 28.2 - - + +
384B VAL 3.1 21.0 + - - -
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Residues in contact with ILE 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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313B VAL* 4.4 9.0 - - + +
314B HIS* 1.3 76.1 - - - +
316B LEU* 1.3 67.6 + - - +
317B ASN* 3.6 2.5 + - + +
322B LYS 3.6 1.6 - - - +
323B ILE* 3.3 0.8 - - - -
324B ILE* 2.7 45.9 + - + +
326B PHE* 3.7 34.3 - - + -
337B LEU* 5.4 6.7 - - + -
341B ILE* 4.4 18.4 - - + -
345B THR* 6.5 0.7 - - + -
354B LEU* 4.9 2.2 - - + -
383B MET* 3.6 2.2 - - - -
384B VAL* 3.3 39.9 - - + +
386B LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 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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315B ILE* 1.3 72.8 - - - +
317B ASN* 1.3 63.7 + - - +
318B MET* 3.2 30.9 + - - +
321B ALA* 3.8 9.0 - - - -
322B LYS 3.3 35.2 - - - +
323B ILE* 3.7 17.5 - - + +
383B MET* 3.0 21.2 - - + -
384B VAL 3.0 7.5 + - - +
385B TYR* 3.6 14.5 - - + -
386B LEU 3.2 21.8 + - - -
440B ASP* 5.3 1.1 - - - +
443B ARG* 4.6 13.7 - - + -
444B LEU* 3.8 15.9 - - + -
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Residues in contact with ASN 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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315B ILE* 3.6 5.0 + - + +
316B LEU* 1.3 71.0 - - - +
318B MET* 1.3 59.1 + - - +
319B THR* 2.5 40.3 + - - +
320B SER* 3.1 26.6 + - - +
321B ALA* 2.9 28.1 + - - -
322B LYS* 2.8 15.2 + - + +
324B ILE* 5.9 3.8 - - + +
345B THR* 4.8 17.4 + - + +
347B ILE* 4.8 4.2 - - - +
386B LEU* 3.4 35.5 - - + +
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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