Contacts of the strand formed by residues 386 - 395 (chain F) in PDB entry 4LQL
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 GLY 386 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384F ALA 4.3 0.2 + - - -
385F GLU* 1.3 73.7 - - - +
387F LYS* 1.3 65.5 + - - -
408F ASP* 3.8 12.4 - - - +
409F CYS* 2.7 37.5 + - - -
410F LYS* 4.3 3.5 - - - +
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Residues in contact with LYS 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F GLY* 1.3 74.2 - - - -
388F GLY* 1.3 57.9 + - - +
407F VAL 4.2 6.1 - - - +
408F ASP* 5.3 6.7 - - - +
409F CYS* 5.3 1.6 - - - -
452F LEU* 3.4 21.3 - - - +
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Residues in contact with GLY 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F LYS* 1.3 76.9 - - - +
389F TYR* 1.3 63.9 + - - -
406F PRO* 5.1 0.4 - - - -
407F VAL* 3.1 33.0 + - - +
409F CYS* 5.1 7.2 - - - -
450F LEU* 6.4 0.7 - - - -
451F THR 3.6 15.0 - - - -
452F LEU* 4.4 4.3 - - - -
453F ALA 5.9 0.4 - - - -
454F LEU 4.8 4.9 - - - -
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Residues in contact with TYR 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F GLY* 1.3 76.5 - - - -
390F ASP* 1.3 73.1 + - - +
391F ILE* 4.6 4.5 - - + -
404F GLY 5.3 3.1 - - - +
405F TYR 3.2 20.2 - - - +
406F PRO* 4.0 12.6 - - + -
407F VAL* 4.2 2.2 - - - -
450F LEU* 4.1 3.5 - - - +
451F THR* 3.6 25.4 + - - +
454F LEU 4.5 12.4 + - - +
455F SER* 5.0 10.8 - - - -
456F GLU* 5.2 8.7 - - + +
459F LEU* 5.1 11.4 - - + -
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Residues in contact with ASP 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F TYR* 1.3 77.1 - - - +
391F ILE* 1.3 55.9 + - - +
404F GLY* 3.1 1.5 - - - -
405F TYR* 2.6 47.3 + - - -
407F VAL* 4.1 8.5 - - + +
426F TRP* 4.4 17.7 - - + -
439F TRP* 3.9 11.9 - - - -
448F THR* 3.0 28.0 - - + +
449F VAL 3.0 16.8 - - - +
450F LEU* 4.2 9.0 - - + -
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Residues in contact with ILE 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F LEU* 4.2 6.9 - - + +
389F TYR* 4.6 5.7 - - + -
390F ASP* 1.3 72.2 - - - +
392F THR* 1.3 63.1 + - - +
402F PHE* 4.7 11.0 - - + -
403F ILE 3.5 8.5 - - - +
404F GLY* 3.7 7.0 - - - -
439F TRP* 4.6 0.4 - - - -
448F THR* 3.1 5.3 + - - -
449F VAL* 2.6 48.6 + - + +
459F LEU* 5.2 14.6 - - + -
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Residues in contact with THR 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F MET* 5.5 1.2 - - - +
314F LEU* 4.3 7.4 - - - -
391F ILE* 1.3 75.1 - - - +
393F LEU* 1.3 70.3 + - - +
394F SER* 4.1 6.2 + - - -
402F PHE* 3.5 11.2 - - - -
403F ILE* 2.7 36.7 + - - +
439F TRP* 3.8 21.3 - - - -
444F GLY* 5.8 0.2 - - - -
445F GLY* 4.7 10.6 + - - -
447F HIS 2.9 23.0 + - - -
448F THR 5.3 0.2 - - - -
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F VAL 5.0 4.7 - - - +
198F ALA* 6.0 1.8 - - + -
202F LEU* 4.7 20.4 - - + -
310F LYS* 3.9 41.8 + - + +
311F MET* 6.0 1.0 - - - +
314F LEU* 4.1 22.3 - - + +
392F THR* 1.3 83.4 + - - +
394F SER* 1.3 62.4 + - - +
400F TYR* 4.3 34.1 - - + -
401F LYS 3.7 12.1 - - - +
402F PHE* 4.4 15.3 - - + -
468F VAL* 5.2 8.5 - - + -
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Residues in contact with SER 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D TYR* 6.0 5.4 - - - -
190F VAL* 5.6 4.0 - - - -
392F THR* 4.8 6.1 + - - -
393F LEU* 1.3 75.0 - - - +
395F TYR* 1.3 60.5 + - - +
396F PHE* 3.7 17.2 + - - -
400F TYR* 3.4 6.9 - - - -
401F LYS* 3.0 37.9 + - - +
403F ILE* 4.3 10.4 - - - +
443F GLY* 4.7 1.0 - - - -
444F GLY* 3.9 25.1 + - - -
445F GLY 4.9 0.5 + - - -
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Residues in contact with TYR 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP* 3.9 14.1 - - - -
139D ARG* 3.0 21.6 + - - +
190F VAL 5.7 1.0 + - - -
192F GLU 4.1 7.2 + - - +
193F GLY* 3.7 24.2 - - - -
194F ASP* 3.9 9.2 - - + -
197F ALA* 6.1 0.9 - - + -
394F SER* 1.3 69.9 - - - +
396F PHE* 1.3 60.5 + - - +
397F ASP* 3.4 5.3 + - - -
399F GLY* 5.3 2.9 - - - -
400F TYR* 3.2 37.6 - + + +
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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