Contacts of the helix formed by residues 393 - 399 (chain E) in PDB entry 3GHG
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 GLN 393 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377E THR 4.8 0.2 + - - -
378E TYR* 3.1 29.1 + - - +
379E ASP 5.1 0.8 - - - -
380E ARG 4.6 0.8 - - - +
381E ASP* 4.0 33.8 - - - +
383E ASP* 3.2 15.9 - - - +
385E TRP* 3.9 0.9 - - - -
389E ASP 4.1 6.5 - - - +
390E PRO* 3.3 22.4 - - - +
391E ARG 3.1 12.0 - - - +
392E LYS* 1.3 77.3 - - - +
394E CYS* 1.3 68.1 + - - +
395E SER* 4.5 4.0 - - - +
396E LYS* 3.2 29.3 + - + +
397E GLU* 3.6 2.8 + - - +
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Residues in contact with CYS 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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383E ASP* 3.3 19.3 + - + -
385E TRP* 3.5 12.0 - - - -
393E GLN* 1.3 70.1 - - - +
395E SER* 1.3 55.2 + - - +
397E GLU* 2.8 24.8 + - - +
398E ASP* 3.1 14.6 + - - +
404E TYR* 3.4 24.9 - - + -
406E ARG* 3.2 24.5 - - - -
407E CYS* 2.0 51.3 - - + -
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Residues in contact with SER 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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376E SER* 4.3 4.9 - - - -
377E THR* 3.0 14.7 - - - -
378E TYR* 2.7 37.2 + - - +
380E ARG 5.2 0.7 - - - -
383E ASP* 4.8 1.8 + - - +
393E GLN* 3.3 6.6 - - - +
394E CYS* 1.3 78.0 - - - +
396E LYS* 1.3 64.1 + - - +
397E GLU 3.2 0.7 + - - -
399E GLY* 3.7 15.2 + - - -
400E GLY 3.1 20.4 + - - +
404E TYR* 3.6 22.9 - - - -
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Residues in contact with LYS 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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378E TYR* 3.9 32.5 - - + +
390E PRO* 3.3 42.9 + - - +
391E ARG* 4.0 16.4 - - + +
393E GLN* 3.2 32.3 + - + +
394E CYS 3.1 0.2 + - - -
395E SER* 1.3 80.0 - - - +
397E GLU* 1.3 62.7 + - + +
399E GLY* 4.6 2.6 + - - -
429E HIS* 3.7 22.4 + - + +
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Residues in contact with GLU 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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385E TRP* 3.9 9.6 - - + -
391E ARG* 3.1 31.9 - - - +
392E LYS* 3.7 21.1 + - - +
393E GLN 4.0 3.1 - - - +
394E CYS* 2.8 14.4 + - - +
396E LYS* 1.3 73.8 - - + +
398E ASP* 1.3 57.0 + - - +
399E GLY* 3.2 10.2 + - - -
429E HIS* 4.2 28.1 + - + +
431E THR* 2.8 49.1 + - + +
433E ASP* 3.7 10.0 - - - +
3P ARG* 3.5 18.7 + - - +
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Residues in contact with ASP 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 CYS 3.1 8.7 + - - +
397E GLU* 1.3 73.1 - - - +
399E GLY* 1.3 58.5 + - - +
404E TYR* 3.6 20.3 + - + +
407E CYS* 3.4 12.0 - - - +
408E HIS* 2.9 34.1 + - - +
411E ASN* 2.7 30.5 + - - +
414E GLY* 3.9 0.2 - - - -
431E THR* 3.3 14.4 + - - -
432E ASP* 3.4 5.4 + - - +
433E ASP* 3.0 30.9 + - - +
1P GLY 3.6 1.7 + - - -
3P ARG* 3.1 19.4 + - - -
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Residues in contact with GLY 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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262E PHE 3.3 10.8 - - - +
263E GLY* 5.1 1.6 - - - -
395E SER 3.7 6.3 + - - -
396E LYS 5.2 1.8 - - - -
397E GLU 3.2 8.1 + - - -
398E ASP* 1.3 79.0 - - - +
400E GLY* 1.3 58.6 + - - +
404E TYR* 4.1 0.7 - - - -
413E ASN 3.2 17.0 - - - +
414E GLY* 3.5 6.9 - - - -
415E ARG* 3.7 27.1 - - - +
433E ASP* 4.2 0.4 - - - -
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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