Contacts of the strand formed by residues 314 - 320 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A VAL* 4.8 9.0 - - + -
307A PHE* 3.8 32.1 - - + -
309A SER* 4.2 18.4 - - - +
313A ASP* 1.3 80.6 + - - +
315A GLY* 1.3 72.2 + - - +
316A PHE 4.1 0.2 + - - -
341A ARG* 4.3 0.7 - - - -
342A TYR* 2.9 27.5 + - - +
344A ALA* 4.2 4.3 - - + -
365A PHE* 4.2 17.7 - - + -
366A ASP 3.5 18.6 - - - +
367A ASN* 3.9 19.5 - - + +
369A TYR* 3.3 7.2 - - - -
375A LYS* 4.2 13.0 - - + -
377A LEU* 4.4 8.7 - - + -
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ILE* 1.3 77.7 - - - +
316A PHE* 1.3 61.3 + - - +
340A GLN 3.3 9.9 - - - -
341A ARG* 4.1 3.1 - - - -
365A PHE* 3.3 7.1 - - - +
366A ASP* 2.8 43.8 + - - -
369A TYR* 3.4 3.4 + - - -
510A EDO 3.7 17.7 - - - -
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TRP* 3.4 46.2 - + - -
307A PHE* 3.6 27.4 - + + -
315A GLY* 1.3 74.6 - - - +
317A GLY* 1.3 61.4 - - - +
318A VAL* 4.1 8.1 - - + -
337A LEU* 4.2 11.3 - - + +
338A PRO 3.9 2.3 - - - +
339A SER* 3.2 6.7 + - - -
340A GLN 2.9 27.2 + - - +
342A TYR* 3.7 11.7 + + + -
363A LEU* 3.7 38.4 - - + -
364A ARG 3.3 7.2 - - - -
365A PHE* 3.5 27.1 - + + -
504A EDO 3.8 19.3 - - - -
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE* 1.3 80.5 - - - +
318A VAL* 1.3 64.8 + - - +
319A PHE* 3.9 8.0 - - - -
337A LEU* 3.5 14.4 - - - -
338A PRO 4.3 1.1 - - - -
339A SER* 3.6 13.9 + - - -
363A LEU* 3.7 3.3 - - - -
364A ARG* 3.0 32.5 + - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU* 4.6 0.9 - - + -
305A TRP* 4.3 4.3 - - + -
316A PHE* 4.1 10.8 - - + -
317A GLY* 1.3 77.0 - - - +
319A PHE* 1.3 68.0 - - - +
335A GLU* 3.8 0.9 - - - -
336A VAL* 2.8 36.7 + - + -
337A LEU* 3.0 41.8 + - + +
353A LEU* 4.0 24.9 - - + -
361A TYR* 4.3 11.7 - - + -
362A VAL 3.4 8.7 - - - +
363A LEU* 4.0 23.8 - - + -
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLY* 3.9 20.6 - - - -
318A VAL* 1.3 80.3 - - - +
320A LEU* 1.3 60.4 + - - +
330A ALA* 3.9 33.0 - - + -
333A MET* 3.6 35.0 - - + -
334A THR 3.1 15.5 - - - +
335A GLU* 3.9 28.3 - - + -
336A VAL* 3.9 4.3 - - - -
339A SER* 4.5 14.8 - - - -
361A TYR* 3.4 5.4 - - - +
362A VAL* 2.8 34.5 + - - +
364A ARG* 4.0 35.0 - - + -
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PHE* 1.3 75.3 - - - +
321A LYS* 1.3 73.5 + - - +
333A MET* 3.4 4.3 - - - +
334A THR* 2.8 48.8 + - + +
336A VAL* 3.8 17.0 - - + -
357A GLN* 3.3 40.2 - - + +
359A GLY* 4.0 7.9 - - - -
360A VAL 3.5 26.2 - - - +
361A TYR* 3.8 28.5 - - + +
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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