Contacts of the helix formed by residues 395 - 404 (chain B) in PDB entry 3E20
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 SER 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B TYR* 5.3 5.8 - - - -
280B GLU* 3.6 16.1 + - - +
281B LYS* 3.4 37.9 - - - +
392B SER 4.1 0.4 + - - -
393B ASP 3.5 0.2 - - - -
394B ARG* 1.3 82.8 - - - +
396B GLN* 1.3 66.4 + - - +
397B GLU* 3.9 3.2 - - - +
398B GLY* 3.0 23.2 + - - -
399B MET* 3.0 22.0 + - - +
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Residues in contact with GLN 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLY 4.8 0.4 - - - +
577A TYR* 3.2 32.4 - - + -
578A SER* 2.9 39.0 - - - +
647A ASP* 3.2 28.8 + - - +
281B LYS* 5.3 4.1 - - - +
395B SER* 1.3 73.9 - - - +
397B GLU* 1.3 75.3 + - - +
399B MET* 3.4 5.8 + - + +
400B GLN* 3.0 33.0 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LYS* 3.0 56.3 + - - +
284B ILE* 3.7 22.0 - - + +
285B GLN* 3.5 33.7 - - + +
288B PHE* 4.1 11.7 - - + -
395B SER* 3.9 3.8 - - - +
396B GLN* 1.3 86.4 + - - +
398B GLY* 1.3 52.2 + - - +
400B GLN* 3.1 11.4 + - - +
401B PHE* 2.7 36.2 + - - +
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Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 3.6 15.3 - - - -
391B VAL* 5.6 0.9 - - - -
392B SER 3.7 15.9 - - - -
393B ASP* 4.0 2.5 - - - -
395B SER* 3.0 20.2 + - - -
397B GLU* 1.3 76.0 - - - +
399B MET* 1.3 51.7 + - - +
401B PHE* 2.9 3.8 + - - -
402B VAL* 2.7 42.9 + - - +
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Residues in contact with MET 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLY* 4.0 14.3 - - - +
578A SER* 5.3 9.2 - - - -
393B ASP* 3.9 37.2 - - - +
395B SER 3.0 12.7 + - - +
396B GLN* 3.8 9.4 - - + +
398B GLY* 1.3 73.5 - - - +
400B GLN* 1.3 58.0 + - - +
402B VAL* 3.8 4.9 - - - +
403B LYS* 2.8 51.2 + - + +
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ILE* 4.3 7.3 + - - +
573A LEU* 4.1 3.2 - - - +
574A THR* 2.6 50.0 + - - +
576A GLY* 3.4 10.9 + - - -
577A TYR* 3.5 40.0 - - + +
285B GLN* 5.6 0.5 - - - +
288B PHE* 3.8 25.5 - - + -
396B GLN* 3.0 24.9 + - + +
397B GLU* 3.2 9.7 - - - +
399B MET* 1.3 74.8 - - - +
401B PHE* 1.3 58.4 + - - +
402B VAL 2.9 0.2 + - - -
404B GLY* 2.7 35.2 + - - -
405B PHE* 3.6 3.0 + - - -
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Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ILE* 3.8 18.2 - - + -
287B PHE* 4.3 30.3 - + - -
288B PHE* 4.7 0.2 - - - -
318B LEU* 3.2 49.1 - - + -
320B PHE 4.4 0.2 - - - -
391B VAL* 3.8 29.2 - - + -
397B GLU 2.7 19.7 + - - +
398B GLY 3.4 3.1 - - - +
400B GLN* 1.3 73.3 - - - +
402B VAL* 1.3 62.4 + - + +
405B PHE* 3.5 21.5 + - + -
407B GLY* 3.0 44.5 + - - -
408B ILE 4.5 1.8 - - - -
409B GLY* 3.6 13.7 - - - -
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B PHE* 3.4 59.5 - - + -
391B VAL* 5.8 0.9 - - + -
392B SER 5.4 0.2 - - - -
393B ASP* 3.8 11.9 - - + +
398B GLY* 2.7 23.2 + - - +
399B MET* 3.8 7.4 - - - +
400B GLN 2.9 1.0 + - - -
401B PHE* 1.3 78.7 - - + +
403B LYS* 1.3 66.3 + - + +
404B GLY 3.2 1.3 - - - -
406B GLY* 3.4 9.7 + - - -
407B GLY* 3.3 20.2 + - - -
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A THR* 3.7 14.4 - - + +
576A GLY* 4.4 9.9 - - - -
591A SER* 5.0 9.9 + - - +
592A PHE 6.1 1.3 - - - +
624A GLU* 4.5 16.4 + - - -
399B MET* 2.8 35.3 + - + +
402B VAL* 1.3 78.1 - - + +
404B GLY* 1.3 59.2 + - - +
406B GLY 4.8 0.8 + - - -
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Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A THR 4.9 1.3 - - - -
575A THR* 3.8 23.1 - - - -
576A GLY 4.1 3.5 - - - +
611A MET* 5.5 1.4 - - - +
300B PHE* 4.5 5.2 - - - -
400B GLN 2.7 14.7 + - - -
403B LYS* 1.3 80.5 - - - +
405B PHE* 1.3 76.5 + - - +
406B GLY 3.7 1.9 + - - -
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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