Contacts of the strand formed by residues 314 - 320 (chain B) in PDB entry 4TLG
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 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B VAL* 4.9 8.5 - - + -
307B PHE* 3.8 30.5 - - + -
309B SER* 4.2 19.3 - - - -
313B ASP* 1.3 78.6 - - - +
315B GLY* 1.3 71.7 + - - +
340B GLN 3.9 0.2 - - - +
341B ARG* 4.2 0.2 - - - -
342B TYR* 2.8 27.5 + - - +
344B ALA* 4.3 3.8 - - + -
365B PHE* 4.3 17.3 - - + -
366B ASP 3.4 26.0 - - - +
367B ASN* 4.0 19.7 - - + +
369B TYR* 3.3 7.9 - - - -
375B LYS* 4.6 10.5 - - + -
377B LEU* 4.4 9.4 - - + -
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Residues in contact with GLY 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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314B ILE* 1.3 76.9 - - - +
316B PHE* 1.3 59.0 + - - +
339B SER* 4.1 2.2 - - - -
340B GLN 3.2 13.2 - - - -
341B ARG* 4.1 3.1 - - - -
365B PHE* 3.3 6.4 - - - +
366B ASP* 2.7 55.3 + - - -
369B TYR* 3.4 9.0 + - - -
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Residues in contact with PHE 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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305B TRP* 3.6 43.1 - + - -
307B PHE* 3.8 23.8 - + + -
315B GLY* 1.3 73.9 - - - +
317B GLY* 1.3 63.6 + - - +
318B VAL* 3.9 9.0 - - + -
337B LEU* 4.0 13.3 - - + +
338B PRO 3.9 2.3 - - - +
339B SER* 3.3 6.6 + - - -
340B GLN 2.8 28.3 + - - +
342B TYR* 3.8 12.9 + + + -
363B LEU* 3.5 40.4 - - + -
364B ARG 3.5 5.2 - - - -
365B PHE* 3.7 27.8 - + + -
503B EDO 3.8 18.8 - - - -
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Residues in contact with GLY 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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316B PHE* 1.3 79.5 - - - +
318B VAL* 1.3 64.5 + - - +
319B PHE* 4.2 9.0 - - - -
337B LEU* 3.3 14.6 - - - -
338B PRO 4.3 0.4 - - - -
339B SER* 3.7 12.7 + - - -
363B LEU* 3.6 4.0 - - - -
364B ARG* 2.9 34.9 + - - +
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Residues in contact with VAL 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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303B LEU* 4.9 0.7 - - + -
305B TRP* 4.3 10.1 - - + -
316B PHE* 3.9 20.2 - - + -
317B GLY* 1.3 77.9 - - - +
319B PHE* 1.3 70.3 + - - +
335B GLU* 3.9 0.5 - - - -
336B VAL* 2.9 33.1 + - + -
337B LEU* 2.9 39.2 + - + +
353B LEU* 4.2 21.5 - - + -
361B TYR* 4.3 8.5 - - + -
362B VAL 3.2 9.0 - - - +
363B LEU* 4.1 17.9 - - + -
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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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317B GLY* 4.2 11.0 - - - -
318B VAL* 1.3 81.2 - - - +
320B LEU* 1.3 60.4 + - - +
321B LYS 4.3 0.4 - - - -
330B ALA* 4.0 28.7 - - + -
333B MET* 3.6 33.2 - - + -
334B THR 3.2 18.6 - - - +
335B GLU* 3.7 31.0 - - + -
336B VAL* 4.1 4.5 - - - -
337B LEU 5.3 0.4 - - - -
339B SER* 5.1 9.6 - - - -
361B TYR* 3.4 5.2 - - - +
362B VAL* 2.7 39.7 + - + +
364B ARG* 3.9 44.6 - - + -
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Residues in contact with LEU 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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319B PHE* 1.3 74.4 - - - +
321B LYS* 1.3 73.1 + - - +
333B MET* 3.5 5.0 - - - +
334B THR* 2.9 51.6 + - + +
336B VAL* 3.9 17.0 - - + +
357B GLN* 3.4 42.0 - - + +
358B ALA 5.1 0.2 - - - +
359B GLY* 4.1 7.0 - - - -
360B VAL 3.5 26.2 - - - +
361B TYR* 3.8 30.5 - - + +
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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