Contacts of the helix formed by residues 389 - 400 (chain E) in PDB entry 3HN3
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 ALA 389 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216E ARG* 3.4 28.4 - - + +
352E GLU* 2.8 18.0 + - - +
361E PHE* 3.8 24.2 - - + -
388E TYR* 1.3 75.0 - - - +
390E GLU* 1.3 65.7 + - - +
391E GLU* 3.5 15.9 - - - +
392E VAL* 2.9 22.8 + - + +
393E MET* 3.5 4.3 + - - +
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Residues in contact with GLU 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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29E TYR* 3.6 36.2 - - + -
122E ARG* 4.0 12.0 + - - -
124E GLY* 4.7 8.0 - - - +
148E PRO* 3.7 27.1 - - - +
216E ARG* 4.6 7.3 - - - +
388E TYR 3.4 1.9 + - - -
389E ALA* 1.3 74.5 - - - +
391E GLU* 1.3 69.1 + - - +
393E MET* 2.9 20.5 + - - +
394E GLN* 3.0 19.1 + - + +
436E ARG* 3.6 38.6 + - + +
437E ASP* 5.1 1.1 - - - +
440E HIS* 4.7 5.1 - - + +
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Residues in contact with GLU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.3 28.9 + - + +
216E ARG* 5.7 2.1 - - - +
217E SER* 3.4 22.2 + - - -
361E PHE* 3.5 43.2 - - + -
363E TRP* 3.9 20.6 - - + -
366E LEU* 4.3 2.7 - - + -
389E ALA* 3.5 6.7 - - + +
390E GLU* 1.3 90.7 + - - +
392E VAL* 1.3 61.4 + - - +
394E GLN* 3.3 11.9 + - - +
395E MET* 3.1 27.4 + - - +
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Residues in contact with VAL 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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350E LYS* 6.3 0.2 - - + -
352E GLU* 4.4 5.6 - - + +
361E PHE* 4.9 4.3 - - + -
366E LEU* 3.6 23.1 - - + -
370E PHE* 4.1 10.3 - - + -
381E PHE* 3.8 19.5 - - + -
388E TYR* 4.1 23.6 - - + -
389E ALA* 2.9 24.1 + - + +
391E GLU* 1.3 76.4 - - - +
393E MET* 1.3 77.4 + - + +
395E MET* 3.2 4.9 + - - +
396E CYS* 3.0 21.0 + - - -
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Residues in contact with MET 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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381E PHE* 4.3 1.6 - - + -
383E THR* 4.1 19.5 - - + -
388E TYR* 4.7 4.3 - - + +
389E ALA 4.1 9.0 - - - +
390E GLU* 2.9 7.2 + - - +
392E VAL* 1.3 95.2 - - + +
394E GLN* 1.3 65.0 + - - +
396E CYS* 3.2 17.7 + - - +
397E ASP* 3.0 25.6 + - - +
403E VAL* 4.1 23.8 - - + -
405E ASP* 4.3 8.3 - - - +
436E ARG* 4.2 17.5 - - - +
437E ASP* 4.2 1.6 - - - +
440E HIS* 3.3 34.7 + - + +
443E VAL* 4.2 14.1 - - - -
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Residues in contact with GLN 394 (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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29E TYR* 2.8 49.2 - - - +
323E PRO* 5.3 11.5 - - - +
390E GLU* 3.0 16.3 + - + +
391E GLU* 3.3 9.6 + - - +
393E MET* 1.3 75.0 - - - +
395E MET* 1.3 63.1 + - + +
397E ASP* 3.2 13.4 + - - +
398E ARG* 3.2 32.0 + - - +
440E HIS* 4.3 12.1 - - + -
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Residues in contact with MET 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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44B LEU* 3.9 19.1 - - + -
76B ASP* 4.1 0.7 - - - +
363E TRP* 5.7 0.2 - - + -
366E LEU* 3.8 28.3 - - + +
367E VAL* 4.3 12.1 - - + -
370E PHE* 3.5 43.3 - - + -
391E GLU 3.1 15.0 + - - +
392E VAL 3.4 7.6 - - - +
394E GLN* 1.3 74.7 - - + +
396E CYS* 1.3 59.4 + - - +
398E ARG* 3.1 16.4 + - - +
399E TYR* 2.8 64.5 + - + +
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Residues in contact with CYS 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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288E TRP* 3.9 0.2 - - - -
370E PHE* 3.7 11.0 - - - -
381E PHE* 3.4 37.0 - - - -
392E VAL 3.0 19.4 + - - -
393E MET* 3.2 12.8 + - - +
395E MET* 1.3 76.2 - - - +
397E ASP* 1.3 58.0 + - - +
400E GLY* 2.9 27.5 + - - -
401E ILE 3.3 23.3 + - - +
403E VAL* 3.4 16.8 - - + -
442E ALA* 3.5 14.2 - - + +
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Residues in contact with ASP 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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288E TRP* 2.9 26.7 + - - +
298E ALA* 3.5 4.7 - - - +
300E LEU* 3.6 17.6 - - + +
323E PRO* 5.4 6.6 - - + +
393E MET 3.0 13.3 + - - +
394E GLN* 3.4 10.5 - - - +
395E MET 3.2 0.4 - - - -
396E CYS* 1.3 76.9 - - - +
398E ARG* 1.3 58.5 + - + +
439E ASN 4.8 0.2 - - - +
440E HIS* 2.6 30.7 + - - +
441E PRO* 3.2 23.4 - - + +
442E ALA* 2.9 32.3 + - - +
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Residues in contact with ARG 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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44B LEU* 4.0 8.7 - - - +
76B ASP* 2.9 41.4 + - - -
298E ALA* 3.4 13.8 - - - +
300E LEU* 3.6 22.9 - - + -
394E GLN* 3.2 21.9 + - - +
395E MET* 3.1 16.0 + - - +
397E ASP* 1.3 77.9 - - + +
399E TYR* 1.3 76.9 + - + +
400E GLY 3.5 0.2 - - - -
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Residues in contact with TYR 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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76B ASP* 2.7 42.6 + - - +
291E TYR* 3.6 19.4 - - - +
297E PRO* 4.9 4.3 - - - +
298E ALA* 4.0 3.8 - - - +
367E VAL* 4.7 5.9 - - - +
370E PHE* 4.0 25.4 - + + -
371E ASN* 4.6 11.8 + - - -
374E ARG* 3.9 30.9 + - + +
395E MET* 2.8 40.9 + - + +
398E ARG* 1.3 94.4 - - + +
400E GLY* 1.3 61.0 + - - +
401E ILE* 3.4 17.4 - - + +
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Residues in contact with GLY 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TRP* 3.6 20.2 - - - -
289E TRP 4.4 0.9 - - - -
290E PRO* 3.4 8.3 - - - +
291E TYR* 2.8 31.3 + - - +
298E ALA* 3.5 10.8 - - - +
379E ASN 4.0 1.7 - - - +
396E CYS 2.9 10.0 + - - -
398E ARG 3.5 2.4 - - - -
399E TYR* 1.3 78.7 - - - +
401E ILE* 1.3 61.0 + - - +
402E VAL 3.6 2.6 + - - -
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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