Contacts of the helix formed by residues 389 - 401 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E ALA 4.5 1.1 - - - -
20E ALA* 3.3 27.4 - - - +
22E ALA* 3.7 4.9 - - + -
23E ASP* 3.1 27.8 - - - -
24E THR 3.7 26.2 - - - -
25E PHE* 4.4 14.7 - + + -
28E HIS* 3.6 38.3 + + + +
388E MET* 1.3 69.2 - - - +
390E HIS* 1.3 60.0 + - - +
391E ARG* 3.3 24.2 - - + -
392E LYS* 3.4 34.0 + - + -
393E LEU* 2.9 30.7 + - - +
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Residues in contact with HIS 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA* 6.1 1.4 - - + +
43E ASN* 5.7 3.6 - - - -
385E GLU* 3.2 27.0 + - + -
386E ALA* 4.6 4.3 - - - -
388E MET* 3.1 36.7 + - + +
389E PHE* 1.3 72.1 - - - +
391E ARG* 1.3 53.1 + - - +
393E LEU* 3.0 9.7 + - - +
394E PHE* 2.6 37.2 + - - +
420E TYR* 3.6 21.9 + - + +
444E ARG* 4.0 17.1 + - + +
445E PRO 4.2 4.5 - - - -
446E ARG* 3.6 64.1 - - + +
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Residues in contact with ARG 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA 3.8 8.8 + - - +
21E MET* 3.9 4.4 + - - +
22E ALA 3.8 6.9 - - - +
23E ASP* 2.9 49.1 + - - +
389E PHE* 3.3 25.2 - - + -
390E HIS* 1.3 78.5 - - - +
392E LYS* 1.3 68.6 + - - +
394E PHE* 3.7 6.7 - - - +
395E GLU* 3.2 49.8 + - - +
417E GLU* 5.7 4.3 - - - +
420E TYR* 4.7 12.5 - - + -
446E ARG* 5.2 2.1 - - - +
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Residues in contact with LYS 392 (chain E).
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 5.8 3.6 - - - +
24E THR 5.7 0.2 - - - -
25E PHE* 3.1 38.3 - - + +
389E PHE* 3.4 40.7 + - + -
390E HIS 3.2 0.6 - - - -
391E ARG* 1.3 90.0 - - - +
393E LEU* 1.3 61.6 + - - +
395E GLU* 3.7 10.1 + - - +
396E GLU* 3.2 55.3 + - - +
25F PHE* 4.4 8.2 - - - +
392F LYS* 3.0 28.8 - - - +
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Residues in contact with LEU 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ASN* 5.9 4.3 - - + +
352E LEU 6.1 0.2 - - - +
353E ASP 5.6 4.9 - - - +
354E GLY* 6.2 0.7 - - - -
388E MET* 3.8 32.3 - - + -
389E PHE 2.9 18.6 + - - +
390E HIS* 3.5 8.7 - - - +
392E LYS* 1.3 77.6 - - - +
394E PHE* 1.3 57.6 + - - +
396E GLU* 3.3 17.5 + - - +
397E LEU* 3.0 40.3 + - + +
444E ARG* 4.1 31.4 - - + +
26F LEU* 4.9 14.1 - - + -
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Residues in contact with PHE 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E HIS 2.6 19.4 + - - +
391E ARG* 3.7 6.1 - - - +
392E LYS 3.4 0.2 - - - -
393E LEU* 1.3 74.3 - - - +
395E GLU* 1.3 62.5 + - + +
397E LEU* 3.3 10.0 + - - +
398E VAL* 3.0 48.0 + - + +
413E MET* 3.5 28.5 - - + -
416E VAL* 3.5 22.0 - - + -
417E GLU* 3.5 28.0 - - + -
420E TYR* 3.5 26.0 - + + +
443E TYR* 3.2 37.7 - + + -
444E ARG* 6.3 0.2 - - - -
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Residues in contact with GLU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E ARG* 3.2 43.9 + - - +
392E LYS* 3.9 11.0 - - - +
393E LEU 3.3 0.2 - - - -
394E PHE* 1.3 84.8 - - + +
396E GLU* 1.3 57.7 + - + +
398E VAL* 3.4 8.2 + - - +
399E ARG* 2.9 29.2 + - - +
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Residues in contact with GLU 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E LYS* 3.2 41.5 + - + +
393E LEU* 3.3 17.7 + - + +
394E PHE 3.3 0.4 - - - -
395E GLU* 1.3 73.9 - - + +
397E LEU* 1.3 59.8 + - - +
399E ARG* 3.4 7.6 + - - +
400E ALA* 3.0 30.7 + - - +
24F THR* 3.6 28.5 - - + +
25F PHE* 3.4 18.5 + - - +
26F LEU* 3.3 29.3 + - + +
392F LYS* 4.0 2.6 + - - -
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Residues in contact with LEU 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ASN* 3.6 35.9 - - + +
318E ARG* 4.7 1.7 - - - -
393E LEU* 3.0 39.3 + - + +
394E PHE* 3.3 6.3 + - - +
396E GLU* 1.3 74.0 - - - +
398E VAL* 1.3 61.9 + - - +
400E ALA* 3.9 2.9 + - - +
401E SER* 3.1 24.8 + - - -
442E ARG* 3.4 20.4 + - - +
443E TYR* 3.5 30.1 - - + +
444E ARG* 4.1 14.6 - - + +
26F LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E PHE* 3.0 42.8 + - + +
395E GLU* 3.6 9.6 - - - +
396E GLU 3.3 0.2 - - - -
397E LEU* 1.3 74.1 - - - +
399E ARG* 1.3 65.4 + - - +
401E SER* 3.3 5.2 + - - -
402E SER* 3.0 25.7 + - - -
413E MET* 3.8 39.9 - - + +
443E TYR* 4.1 8.3 - - + -
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Residues in contact with ARG 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E GLU 2.9 17.9 + - - +
396E GLU* 3.6 9.2 - - - +
398E VAL* 1.3 78.0 - - - +
400E ALA* 1.3 61.8 + - - +
402E SER* 3.1 27.4 + - - -
403E HIS* 5.5 0.5 - - - -
23F ASP* 3.4 32.5 + - - -
24F THR* 3.6 15.0 + - + +
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Residues in contact with ALA 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E ARG* 3.7 38.6 - - + +
396E GLU 3.0 17.3 + - - +
397E LEU* 4.1 4.9 - - - +
398E VAL 3.2 0.2 - - - -
399E ARG* 1.3 77.5 - - - +
401E SER* 1.3 58.6 + - - +
402E SER 3.5 0.2 - - - -
403E HIS* 3.1 19.9 + - - -
24F THR* 6.4 0.4 - - + -
26F LEU* 4.1 10.1 - - + -
27F GLU* 6.0 1.6 - - - +
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Residues in contact with SER 401 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E ARG 4.8 2.5 - - - -
397E LEU 3.1 11.9 + - - -
398E VAL 3.3 5.5 + - - -
400E ALA* 1.3 77.8 - - - +
402E SER* 1.3 61.6 + - - +
403E HIS* 3.2 13.5 - - - -
404E SER* 3.4 24.0 + - - +
409E GLU* 4.1 6.0 - - - +
413E MET* 6.0 1.2 - - - +
442E ARG* 3.9 22.0 + - - -
443E TYR* 2.6 29.1 + - - -
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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