Contacts of the helix formed by residues 397 - 408 (chain B) in PDB entry 2G4C
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 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B LEU* 2.8 42.9 - - - +
394B GLU* 3.0 28.8 + - - +
395B LEU 2.9 1.8 + - - -
396B ARG* 1.3 78.8 - - - +
398B VAL* 1.3 65.8 + - - +
399B CYS 3.2 1.5 + - - -
400B GLN* 3.6 18.8 + - - +
401B GLY* 3.6 6.6 + - - -
448B LEU* 6.3 0.4 - - + -
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Residues in contact with VAL 398 (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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394B GLU 5.5 0.7 - - - +
395B LEU* 3.8 7.2 - - + +
397B GLN* 1.3 77.5 - - + +
399B CYS* 1.3 57.1 + - - +
400B GLN 3.1 0.9 - - - -
401B GLY* 2.7 23.4 + - - +
402B LEU* 2.7 23.5 + - + +
405B GLU* 5.9 1.3 - - - +
443B VAL* 3.6 33.4 - - + -
447B THR* 5.6 1.6 - - + -
448B LEU* 5.6 11.4 - - + -
468B ILE* 3.7 25.4 - - + -
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Residues in contact with CYS 399 (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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385B LEU* 4.2 5.6 - - + +
386B ASP 4.3 7.0 - - - -
387B VAL* 3.3 34.5 - - - -
395B LEU 3.5 13.0 - - - -
396B ARG* 3.5 10.8 - - - +
397B GLN 3.2 0.2 - - - -
398B VAL* 1.3 82.8 - - - +
400B GLN* 1.3 53.0 + - - +
402B LEU* 3.1 8.5 + - - +
403B PHE* 2.6 35.5 + - - +
417B TYR* 3.3 35.4 - - + -
443B VAL* 4.5 11.9 - - - -
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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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396B ARG* 3.9 25.0 + - - +
397B GLN* 3.6 13.7 + - - +
398B VAL 3.1 0.4 - - - -
399B CYS* 1.3 72.3 - - - +
401B GLY* 1.3 64.1 + - - +
402B LEU 3.0 2.2 - - - -
403B PHE* 3.9 7.9 - - + -
404B ASN* 2.5 37.4 + - - +
417B TYR* 3.6 25.8 - - + +
418B LEU* 5.0 6.9 - - - +
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Residues in contact with GLY 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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397B GLN 3.6 5.4 + - - -
398B VAL* 2.7 15.8 + - - -
400B GLN* 1.3 78.5 - - - +
402B LEU* 1.3 51.0 + - - +
404B ASN* 4.4 2.3 - - - +
405B GLU* 2.7 37.7 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 4.1 19.7 - - + -
398B VAL* 2.7 12.6 + - + +
399B CYS* 3.3 9.2 - - - +
401B GLY* 1.3 76.2 - - - +
403B PHE* 1.3 58.4 + - - +
404B ASN 2.9 1.3 - - - -
405B GLU* 2.5 38.7 + - - +
406B LEU* 2.5 55.3 + - + +
441B VAL* 4.6 11.9 - - + -
443B VAL* 4.8 7.6 - - + -
453B ILE* 5.8 0.9 - - + -
468B ILE* 4.2 32.1 - - + -
471B LEU* 4.7 15.5 - - + -
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Residues in contact with PHE 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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385B LEU* 4.7 0.8 - - - +
399B CYS 2.6 20.7 + - - +
400B GLN* 4.0 3.8 - - + -
402B LEU* 1.3 74.6 - - - +
404B ASN* 1.3 67.3 + - - +
406B LEU 3.8 0.2 + - - -
407B LEU* 2.8 57.6 + - + +
413B VAL* 3.7 37.1 - - + +
415B PRO* 3.2 38.4 - - + -
417B TYR* 3.3 17.7 - - + +
121D PHE* 4.7 2.2 - - + -
122D ARG* 4.4 15.3 - - - -
123D GLU* 3.0 34.1 - - + -
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Residues in contact with ASN 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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400B GLN* 2.5 30.5 + - - +
401B GLY* 4.4 2.9 - - - +
402B LEU 2.9 0.4 - - - -
403B PHE* 1.3 87.4 - - - +
405B GLU* 1.3 56.9 + - - +
407B LEU* 2.9 7.7 + - - +
408B GLU* 2.7 51.9 + - + +
121D PHE* 6.0 6.7 - - - +
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Residues in contact with GLU 405 (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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398B VAL* 5.9 1.2 - - - +
401B GLY 2.7 25.3 + - - +
402B LEU* 2.5 35.3 + - + +
404B ASN* 1.3 75.8 - - - +
406B LEU* 1.3 63.6 + - - +
408B GLU* 3.3 9.4 + - - +
409B ASN* 3.2 23.6 + - - +
469B SER* 5.0 12.4 - - - +
471B LEU* 5.5 1.0 - - - +
472B LYS* 3.9 34.3 + - + +
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Residues in contact with LEU 406 (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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383B VAL* 4.7 3.6 - - + -
385B LEU* 5.4 3.1 - - + -
402B LEU* 2.5 67.0 + - + +
403B PHE 3.9 1.1 - - - +
405B GLU* 1.3 73.7 - - - +
407B LEU* 1.3 59.8 + - - +
409B ASN* 3.2 11.8 + - - +
410B GLY 3.4 0.5 + - - -
411B ILE* 3.0 41.1 + - + +
413B VAL* 3.3 26.7 - - + -
471B LEU* 4.7 7.4 - - + -
472B LYS* 4.5 16.2 - - + +
475B LEU* 3.4 32.1 - - + -
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Residues in contact with LEU 407 (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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403B PHE* 2.8 59.2 + - + +
404B ASN* 2.9 8.6 + - - +
406B LEU* 1.3 72.9 - - - +
408B GLU* 1.3 53.3 + - - +
409B ASN 2.7 16.7 + - - -
410B GLY* 3.2 11.3 + - - +
411B ILE 3.2 24.2 - - - +
412B SER* 4.5 3.1 - - - -
413B VAL* 4.3 9.2 - - + +
120D VAL* 3.6 32.6 - - + +
121D PHE* 4.3 22.7 - - + -
123D GLU* 5.4 1.8 - - + +
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Residues in contact with GLU 408 (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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404B ASN* 2.7 38.6 + - + +
405B GLU* 3.3 9.6 + - - +
407B LEU* 1.3 69.8 - - - +
409B ASN* 1.3 67.2 + - - +
121D PHE* 4.4 19.6 - - - -
484D ASN* 5.9 1.4 + - - -
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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