Contacts of the helix formed by residues 389 - 401 (chain F) in PDB entry 3SRF
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 PHE 389 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F ALA 4.2 3.8 - - - -
20F ALA* 3.5 29.2 - - - -
22F ALA* 4.4 2.5 - - + -
23F ASP* 3.7 16.8 - - - -
24F THR 4.1 19.5 - - - -
25F PHE* 3.8 23.5 - + + -
28F HIS* 3.7 27.5 + + + +
388F MET* 1.3 72.7 - - - +
390F HIS* 1.3 65.0 + - - +
391F ARG* 3.5 29.1 + - + -
392F LYS* 3.6 39.6 - - + +
393F LEU* 3.1 24.3 + - - +
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Residues in contact with HIS 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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20F ALA* 6.0 2.6 - - + +
43F ASN* 5.9 2.0 - - - -
385F GLU* 2.9 27.5 + - + -
386F ALA 4.8 2.7 - - - -
388F MET* 3.5 36.0 + - + +
389F PHE* 1.3 72.9 - - - +
391F ARG* 1.3 56.1 + - - +
393F LEU* 3.3 7.8 + - - +
394F PHE* 2.8 36.7 + - - +
420F TYR* 3.6 22.5 + + + +
444F ARG* 3.4 19.7 + - + +
445F PRO 3.8 7.0 - - - -
446F ARG* 3.8 54.2 + - + +
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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
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20F ALA* 3.3 23.6 + - + +
21F MET* 3.6 11.7 + - - +
23F ASP* 3.2 46.1 + - - +
389F PHE* 3.5 19.1 - - + -
390F HIS* 1.3 77.0 - - - +
392F LYS* 1.3 66.0 + - - +
394F PHE* 3.4 7.3 + - - +
395F GLU* 3.2 49.1 + - + +
417F GLU* 5.9 2.9 - - - +
420F TYR* 4.8 9.8 - - + -
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Residues in contact with LYS 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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25E PHE* 4.6 4.0 - - - +
392E LYS* 3.0 42.7 - - - +
396E GLU* 4.0 2.8 + - - -
23F ASP 6.0 1.1 - - - +
25F PHE* 3.5 22.8 - - + +
389F PHE* 3.5 43.0 + - + +
390F HIS 3.3 0.2 - - - -
391F ARG* 1.3 79.6 - - - +
393F LEU* 1.3 65.0 + - - +
395F GLU* 3.5 13.6 + - - +
396F GLU* 3.2 52.2 + - + +
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 4.7 15.3 - - + -
317F ASN* 5.5 6.3 - - - +
353F ASP 5.9 2.5 - - - +
354F GLY* 6.4 0.9 - - - -
388F MET* 3.6 30.7 - - + -
389F PHE 3.1 18.4 + - - +
390F HIS* 3.7 7.4 - - - +
392F LYS* 1.3 73.3 - - - +
394F PHE* 1.3 60.0 + - - +
396F GLU* 3.2 12.1 + - - +
397F LEU* 2.9 52.0 + - + +
443F TYR 5.6 0.2 - - - +
444F ARG* 4.1 25.8 - - + +
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Residues in contact with PHE 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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390F HIS 2.8 20.4 + - - +
391F ARG* 3.6 6.3 - - - +
393F LEU* 1.3 73.5 - - - +
395F GLU* 1.3 63.4 + - + +
397F LEU* 3.4 4.8 + - - +
398F VAL* 3.0 56.9 + - + +
413F MET* 3.5 28.5 - - + -
416F VAL* 3.7 27.6 - - + -
417F GLU* 3.4 35.9 - - + -
420F TYR* 3.8 14.4 - + + +
443F TYR* 3.5 38.6 + + + +
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Residues in contact with GLU 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 40.3 + - + +
392F LYS* 3.7 13.8 - - - +
393F LEU 3.3 0.4 - - - -
394F PHE* 1.3 83.2 - - + +
396F GLU* 1.3 59.7 + - + +
398F VAL* 3.5 7.7 + - - +
399F ARG* 2.9 27.9 + - - +
417F GLU* 6.1 0.7 - - - +
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Residues in contact with GLU 396 (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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24E THR* 3.6 35.5 - - + +
25E PHE* 3.4 16.1 + - - +
26E LEU* 3.2 29.7 + - + +
392F LYS* 3.2 46.8 + - + +
393F LEU* 3.2 11.3 + - - +
394F PHE 3.2 0.4 - - - -
395F GLU* 1.3 78.3 - - + +
397F LEU* 1.3 57.9 + - - +
399F ARG* 3.5 7.7 - - - +
400F ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 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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26E LEU* 3.8 21.5 - - + -
317F ASN* 3.4 35.7 - - + +
318F ARG* 4.3 3.4 - - - +
393F LEU* 2.9 43.7 + - + +
394F PHE* 3.8 4.0 - - - +
396F GLU* 1.3 72.3 - - - +
398F VAL* 1.3 62.0 - - - +
400F ALA* 3.6 2.9 + - - +
401F SER* 2.8 27.4 + - - -
442F ARG* 3.4 24.3 + - - +
443F TYR* 3.9 33.6 - - + +
444F ARG* 4.2 5.4 - - + -
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Residues in contact with VAL 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 PHE* 3.0 44.2 + - + +
395F GLU* 3.7 7.0 - - - +
396F GLU 3.3 0.2 - - - -
397F LEU* 1.3 74.7 - - - +
399F ARG* 1.3 65.8 + - - +
401F SER* 3.2 7.9 + - - -
402F SER* 3.1 25.6 + - - -
413F MET* 3.7 42.3 - - + +
443F TYR* 4.1 5.4 - - + -
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Residues in contact with ARG 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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23E ASP* 4.3 20.4 + - - -
24E THR* 4.7 11.8 + - + +
395F GLU 2.9 20.0 + - - +
396F GLU* 3.5 10.3 - - - +
398F VAL* 1.3 77.4 - - - +
400F ALA* 1.3 59.5 + - - +
402F SER* 2.9 28.8 + - - -
403F HIS* 5.3 0.5 - - - -
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Residues in contact with ALA 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 6.5 0.2 - - + -
26E LEU* 4.3 8.7 - - + -
27E GLU* 5.4 3.6 - - - +
318F ARG* 3.7 36.8 - - + +
396F GLU 3.0 18.6 + - - +
397F LEU* 3.9 5.2 - - - +
398F VAL 3.3 0.2 - - - -
399F ARG* 1.3 77.4 - - - +
401F SER* 1.3 58.1 + - - +
403F HIS* 3.1 23.0 + - - -
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Residues in contact with SER 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ARG 5.1 1.3 - - - -
397F LEU 2.8 20.3 + - - -
398F VAL* 3.2 6.3 + - - -
400F ALA* 1.3 76.2 - - - +
402F SER* 1.3 59.3 + - - +
403F HIS* 3.2 7.4 - - - -
404F SER* 3.0 32.6 + - - +
409F GLU* 3.9 8.5 - - - +
413F MET* 5.0 1.7 - - - -
442F ARG* 4.1 17.0 - - - -
443F TYR* 3.0 26.7 + - - -
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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