Contacts of the helix formed by residues 385 - 399 (chain F) in PDB entry 4L18
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 ASN 385 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369F ASP* 6.3 0.2 - - - +
372F ALA* 3.3 11.7 - - - -
383F LYS 3.5 6.6 + - - +
384F MET* 1.3 79.8 - - - +
386F TYR* 1.3 58.7 + - - +
387F GLU* 2.9 28.2 + - - +
388F LYS* 2.9 36.8 + - - +
389F LEU* 2.9 23.4 + - - +
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Residues in contact with TYR 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F LEU* 4.1 23.6 - - + -
368F PRO* 3.7 37.5 - - + +
369F ASP* 4.7 7.8 + - - +
372F ALA* 3.3 9.0 - - - +
385F ASN* 1.3 71.7 - - - +
387F GLU* 1.3 63.9 + - - +
389F LEU* 4.1 12.6 - - + -
390F SER* 2.8 52.6 + - - -
410F TYR* 3.9 22.8 - + - -
412F TYR* 2.9 25.6 + + - -
302H A 4.8 17.3 - - + -
303H G 2.7 29.4 + - - -
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Residues in contact with GLU 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F ASN* 2.9 17.3 + - - +
386F TYR* 1.3 82.4 - - + +
388F LYS* 1.3 60.3 + - + +
390F SER* 2.9 18.6 + - - -
391F ARG* 3.7 7.8 + - - +
394F ARG* 4.4 4.5 + - - -
213G C 5.8 2.8 + - - -
302H A 5.4 8.5 - - - +
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Residues in contact with LYS 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F LYS* 2.8 33.8 + - - +
384F MET* 3.9 11.9 - - + +
385F ASN* 2.9 29.6 + - - +
387F GLU* 1.3 78.9 - - + +
389F LEU* 1.3 65.6 + - - +
390F SER 3.2 1.6 - - - -
391F ARG* 3.1 16.1 + - - +
392F GLY* 3.4 4.3 + - - -
210G A 4.6 5.8 + - + -
211G T 2.4 91.2 + - + +
212G C 5.0 6.9 + - + +
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Residues in contact with LEU 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F LEU* 3.8 16.8 - - + +
341F LEU* 5.1 2.7 - - + -
365F LEU* 4.8 6.1 - - + -
371F VAL* 3.9 27.8 - - + -
372F ALA* 4.0 18.2 - - + +
375F TRP* 4.1 22.9 - - + +
384F MET* 3.8 10.0 - - - -
385F ASN 2.9 17.6 + - - +
386F TYR* 3.8 15.9 - - + +
388F LYS* 1.3 75.6 - - - +
390F SER* 1.3 65.8 + - - +
392F GLY* 3.0 12.5 + - - -
393F LEU* 3.2 34.3 + - + -
210G A 4.9 2.9 - - - -
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Residues in contact with SER 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F TYR* 2.8 38.1 + - - -
387F GLU* 2.9 24.3 + - - -
389F LEU* 1.3 84.4 - - - +
391F ARG* 1.3 60.6 + - - +
393F LEU* 3.1 9.0 + - - +
394F ARG* 2.9 47.2 + - - +
412F TYR* 3.9 7.4 + - - -
303H G 5.5 0.6 - - - -
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Residues in contact with ARG 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F GLU 4.2 4.9 - - - +
388F LYS 3.1 13.9 + - - +
390F SER* 1.3 81.2 + - - +
392F GLY* 1.3 62.6 + - - +
394F ARG* 3.2 29.4 + - - +
395F TYR* 3.2 47.9 + - + +
210G A 5.0 0.9 - - - +
211G T 3.2 31.6 + - + +
212G C 3.7 4.0 - - - +
305H G 3.3 39.2 + - - +
306H G 2.7 47.7 + - - -
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Residues in contact with GLY 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F LEU* 4.3 9.4 - - - -
388F LYS 3.4 4.7 + - - -
389F LEU* 3.0 9.2 + - - -
391F ARG* 1.3 80.6 - - - +
393F LEU* 1.3 61.6 + - - +
395F TYR* 3.2 25.6 + - - +
396F TYR* 3.7 12.3 + - - -
209G C 4.3 25.6 - - - +
210G A 5.5 1.9 + - - -
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F LEU* 3.4 20.6 - - + -
341F LEU* 3.9 24.7 - - + -
365F LEU* 5.1 4.0 - - + -
386F TYR* 5.2 0.7 - - + -
389F LEU* 3.2 28.8 + - + +
390F SER* 3.1 9.3 + - - +
392F GLY* 1.3 76.9 - - - +
394F ARG* 1.3 63.3 + - - +
396F TYR* 2.9 35.6 + - + +
397F TYR* 3.7 10.1 + - - -
402F ILE* 3.9 10.7 - - + +
412F TYR* 3.6 50.3 - - + +
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Residues in contact with ARG 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F GLU 4.4 4.0 + - - -
390F SER* 2.9 45.8 + - - +
391F ARG* 3.2 28.1 + - - +
393F LEU* 1.3 76.8 - - - +
395F TYR* 1.3 60.5 + - - +
397F TYR* 3.1 47.9 + - + +
398F ASP* 4.4 1.4 + - - +
412F TYR* 4.9 2.3 + - - +
213G C 4.9 2.4 - - - +
303H G 4.1 19.9 + - - +
304H A 3.2 48.8 + - + +
305H G 3.0 43.7 + - + +
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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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391F ARG* 3.2 61.9 + - + +
392F GLY* 3.2 15.1 + - - +
393F LEU 3.1 1.0 - - - -
394F ARG* 1.3 76.6 - - - +
396F TYR* 1.3 62.1 + - + +
397F TYR 3.6 0.2 + - - -
398F ASP* 4.0 6.2 + - - +
399F LYS* 3.5 39.8 + - + +
209G C 4.9 23.5 + + + +
210G A 3.5 18.8 + - - -
306H G 5.0 0.3 + - - -
307H A 3.2 24.9 + - - -
308H T 3.8 5.4 + - - +
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Residues in contact with TYR 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F GLN* 4.8 1.6 - - - -
337F LEU* 3.3 12.7 + - + +
338F TRP* 2.9 52.8 + + + -
392F GLY 3.7 17.7 - - - -
393F LEU* 2.9 32.1 + - + +
395F TYR* 1.3 80.0 - - + +
397F TYR* 1.3 64.6 + - - +
398F ASP 3.2 0.7 - - - -
399F LYS* 2.9 28.6 + - - +
400F ASN 3.0 10.4 + - - -
401F ILE* 3.4 26.4 + - + -
402F ILE* 3.6 28.5 - - + +
209G C 2.6 32.1 + - - -
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Residues in contact with TYR 397 (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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393F LEU 3.9 8.5 - - - -
394F ARG* 3.1 37.7 + - + +
396F TYR* 1.3 77.7 - - - +
398F ASP* 1.3 62.4 + - - +
400F ASN* 3.3 9.2 + - - +
402F ILE* 3.1 20.0 - - + -
403F HIS* 3.4 26.8 + + + -
404F LYS* 3.3 23.7 - - + +
412F TYR* 3.2 26.6 - + - -
304H A 2.4 45.0 + - - -
305H G 3.8 21.8 - - - +
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Residues in contact with ASP 398 (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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394F ARG 4.4 1.0 + - - +
395F TYR 4.0 7.9 + - - +
396F TYR 3.2 0.4 - - - -
397F TYR* 1.3 81.0 - - - +
399F LYS* 1.3 62.2 + - + +
400F ASN* 3.2 14.4 + - - -
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Residues in contact with LYS 399 (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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395F TYR* 3.5 38.7 + - + +
396F TYR* 2.9 25.5 + - - +
398F ASP* 1.3 78.2 - - + +
400F ASN* 1.3 71.2 + - - +
401F ILE* 3.3 23.1 + - + +
208G A 5.4 14.5 + - - +
209G C 5.6 1.6 + - - -
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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