Contacts of the helix formed by residues 444 - 449 (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 THR 444 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B GLY* 3.5 1.1 - - - +
389B ARG* 3.3 46.9 - - - +
395B LEU* 3.2 19.1 - - - +
442B LEU* 3.5 22.2 - - + -
443B VAL* 1.3 70.9 - - - +
445B GLU* 1.3 62.3 + - - +
446B THR* 2.8 29.9 - - + +
447B THR* 2.9 28.2 + - - -
448B LEU* 3.8 1.7 + - - +
454B HIS* 4.0 12.5 - - + -
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG 3.0 16.4 + - - +
390B GLY* 3.9 14.6 - - - -
391B PRO* 4.3 9.3 - - + +
395B LEU* 3.5 8.3 - - - +
444B THR* 1.3 71.3 - - - +
446B THR* 1.3 54.6 + - - +
447B THR 2.5 17.4 + - - -
448B LEU* 2.7 23.8 + - + +
449B GLU* 3.2 26.0 + - + +
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG* 4.8 5.4 + - + -
444B THR* 2.8 30.5 - - + +
445B GLU* 1.3 76.5 + - - +
447B THR* 1.3 52.4 + - - +
449B GLU* 3.6 21.6 + - - -
450B ASN* 2.6 29.8 + - - +
452B LEU* 3.8 3.3 - - - +
454B HIS* 5.6 2.9 - - + +
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Residues in contact with THR 447 (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* 5.6 1.1 - - + -
442B LEU 4.6 0.2 + - - -
443B VAL* 3.8 10.2 - - + +
444B THR* 2.9 38.1 + - - -
445B GLU 2.5 6.9 + - - -
446B THR* 1.3 74.1 - - - +
448B LEU* 1.3 58.8 + - + -
450B ASN* 3.3 2.9 - - - -
451B GLY* 3.0 27.7 + - - -
452B LEU 2.9 25.6 + - - +
453B ILE* 3.5 23.3 - - + +
454B HIS* 5.5 0.2 + - - -
468B ILE* 3.7 17.0 - - + +
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Residues in contact with LEU 448 (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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391B PRO* 4.8 10.3 - - + -
394B GLU* 4.5 25.8 - - + +
395B LEU* 3.9 25.4 - - + -
397B GLN* 6.3 0.7 - - + -
398B VAL* 5.6 11.4 - - + -
443B VAL* 5.9 1.1 - - + -
444B THR 4.4 2.9 - - - +
445B GLU* 2.7 16.2 + - + +
447B THR* 1.3 77.1 - - + +
449B GLU* 1.3 56.0 + - - +
450B ASN 2.9 14.5 + - - +
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Residues in contact with GLU 449 (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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445B GLU* 3.2 27.9 + - + +
446B THR* 3.6 20.2 + - - -
448B LEU* 1.3 75.1 - - - +
450B ASN* 1.3 75.2 + - - +
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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