Contacts of the helix formed by residues 397 - 408 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A LEU* 2.8 43.4 - - - +
394A GLU* 3.0 27.3 + - - +
395A LEU 2.9 2.0 + - - -
396A ARG* 1.3 78.1 - - - +
398A VAL* 1.3 66.6 + - + +
399A CYS 3.2 1.5 + - - -
400A GLN* 3.6 19.1 + - - +
401A GLY* 3.6 6.6 + - - -
448A LEU* 6.3 0.9 - - + -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU 5.5 1.1 - - - +
395A LEU* 3.8 6.7 - - + +
397A GLN* 1.3 76.6 - - - +
399A CYS* 1.3 58.1 + - - +
400A GLN 3.1 0.7 - - - -
401A GLY* 2.7 6.6 + - - +
402A LEU* 2.7 40.5 + - + +
405A GLU* 5.9 1.1 - - - +
443A VAL* 3.6 34.1 - - + -
447A THR* 5.6 1.1 - - + -
448A LEU* 5.6 11.2 - - + -
468A ILE* 3.7 25.8 - - + -
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Residues in contact with CYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.2 6.3 - - - +
386A ASP 4.3 6.7 - - - -
387A VAL* 3.3 33.7 - - - -
395A LEU 3.5 12.1 - - - -
396A ARG* 3.5 11.4 - - - +
398A VAL* 1.3 82.9 - - - +
400A GLN* 1.3 51.2 + - - +
402A LEU* 3.1 7.7 + - - +
403A PHE* 2.6 36.2 + - - +
417A TYR* 3.3 36.5 - - + -
443A VAL* 4.5 12.6 - - - -
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ARG* 3.9 25.8 + - - +
397A GLN* 3.6 14.8 + - - +
398A VAL 3.1 0.6 - - - -
399A CYS* 1.3 72.1 - - - +
401A GLY* 1.3 61.8 + - - +
402A LEU 3.0 1.6 - - - -
403A PHE* 3.9 8.7 - - + -
404A ASN* 2.5 38.1 + - - +
417A TYR* 3.6 24.5 - - + +
418A LEU* 5.0 7.3 - - - +
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLN 3.6 4.8 + - - -
398A VAL* 2.7 15.8 + - - -
400A GLN* 1.3 79.4 - - - +
402A LEU* 1.3 51.4 + - - +
404A ASN* 4.4 2.0 - - - +
405A GLU* 2.7 37.4 + - - +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.1 19.7 - - + -
398A VAL* 2.7 12.4 + - + +
399A CYS* 3.3 8.5 - - - +
401A GLY* 1.3 77.2 - - - +
403A PHE* 1.3 58.3 + - - +
404A ASN 2.9 1.1 - - - -
405A GLU* 2.5 52.8 + - - +
406A LEU* 2.5 40.9 + - + +
441A VAL* 4.6 12.3 - - + -
443A VAL* 4.8 7.4 - - + -
453A ILE* 5.8 0.4 - - + -
468A ILE* 4.3 32.5 - - + -
471A LEU* 4.7 15.3 - - + -
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.7 0.6 - - - +
399A CYS 2.6 20.7 + - - +
400A GLN* 4.0 4.0 - - + -
402A LEU* 1.3 73.3 - - - +
404A ASN* 1.3 66.0 - - - +
406A LEU* 3.8 0.4 + - - +
407A LEU* 2.8 59.0 + - + +
413A VAL* 3.7 38.0 - - + +
415A PRO* 3.3 38.4 - - + -
417A TYR* 3.3 18.4 - - + +
121C PHE* 4.6 2.5 - - + -
122C ARG* 4.4 14.1 - - - -
123C GLU* 3.0 33.7 - - + -
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Residues in contact with ASN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLN* 2.5 31.0 + - - +
401A GLY* 4.4 2.9 - - - +
402A LEU 2.9 0.2 - - - -
403A PHE* 1.3 89.3 - - - +
405A GLU* 1.3 58.5 + - - +
407A LEU* 2.9 8.3 + - - +
408A GLU* 2.7 51.0 + - + +
121C PHE* 6.0 6.5 - - - +
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A VAL* 5.9 1.4 - - - +
401A GLY 2.7 25.5 + - - +
402A LEU* 2.5 36.1 + - + +
404A ASN* 1.3 76.9 - - - +
406A LEU* 1.3 64.4 + - + +
408A GLU* 3.3 8.5 + - - +
409A ASN* 3.2 23.4 + - - -
468A ILE 6.0 0.2 - - - -
469A SER* 5.0 12.5 - - - +
471A LEU* 5.5 0.9 - - - +
472A LYS* 3.9 34.9 + - + +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A VAL* 4.7 3.8 - - + -
385A LEU* 5.4 2.9 - - + -
402A LEU* 2.5 66.3 + - + +
403A PHE 3.9 0.7 - - - +
405A GLU* 1.3 74.6 - - - +
407A LEU* 1.3 59.7 + - - +
409A ASN* 3.2 12.3 + - - +
410A GLY 3.4 0.3 + - - -
411A ILE* 3.0 42.0 + - + +
413A VAL* 3.3 27.6 - - + -
471A LEU* 4.7 7.6 - - + -
472A LYS* 4.5 15.7 - - + -
475A LEU* 3.4 31.6 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PHE* 2.8 61.2 + - + +
404A ASN* 2.9 7.9 + - - +
406A LEU* 1.3 73.9 - - - +
408A GLU* 1.3 55.5 + - + +
409A ASN 2.7 15.8 + - - -
410A GLY* 3.1 11.2 + - - +
411A ILE 3.2 23.6 - - - +
412A SER* 4.5 2.9 - - - -
413A VAL* 4.3 9.2 - - + +
120C VAL* 3.5 31.6 - - + +
121C PHE* 4.2 22.7 - - + -
123C GLU* 5.4 2.0 - - + +
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ASN* 2.7 37.3 + - + +
405A GLU* 3.3 9.3 + - - +
407A LEU* 1.3 71.2 - - - +
409A ASN* 1.3 69.7 + - - +
121C PHE* 4.4 19.5 - - - -
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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