Contacts of the helix formed by residues 449 - 457 (chain B) in PDB entry 6G4O
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 GLY 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B TYR* 3.9 11.5 - - - +
445B GLU 3.1 0.8 + - - -
446B PHE 3.0 8.3 + - - -
447B VAL 3.3 0.8 - - - -
448B PHE* 1.3 79.1 - - - +
450B LEU* 1.3 65.3 + - - +
451B PRO* 3.3 2.2 - - - -
452B LEU* 3.2 23.4 + - - +
453B VAL* 4.4 0.7 - - - +
466B SER* 3.1 19.1 - - - -
470B MET* 3.3 18.3 - - - +
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Residues in contact with LEU 450 (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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128B ASP* 3.9 16.6 - - + +
129B VAL* 3.6 36.1 - - + +
131B ASN 4.9 2.0 - - - +
134B TYR* 3.7 28.5 - - + -
445B GLU* 3.6 19.1 - - + +
448B PHE* 3.3 13.2 + - + +
449B GLY* 1.3 71.7 - - - +
451B PRO* 1.3 64.8 - - + +
452B LEU 3.0 11.0 + - - -
453B VAL* 3.1 24.6 + - - +
456B LEU* 3.8 18.9 - - + +
458B TYR* 3.8 13.9 - - - +
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Residues in contact with PRO 451 (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 3.0 17.0 - - - +
446B PHE* 3.6 31.0 - - + -
449B GLY 3.5 3.1 - - - -
450B LEU* 1.3 91.3 - - + +
452B LEU* 1.3 60.2 + - - -
453B VAL 3.3 2.2 - - - +
454B LYS* 3.4 12.6 + - - -
458B TYR* 3.4 39.9 - - + +
462B GLU 3.2 25.1 - - - +
463B GLU* 3.5 8.9 - - - +
466B SER* 3.6 9.4 - - - +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.3 28.4 - - + +
134B TYR* 5.3 1.1 - - + -
138B THR* 3.9 24.5 - - + +
449B GLY* 3.2 18.6 - - - +
450B LEU 3.0 1.6 + - - -
451B PRO* 1.3 78.9 - - - +
453B VAL* 1.3 59.8 + - + +
454B LYS* 3.4 19.3 + - - +
463B GLU* 3.4 31.3 - - + +
466B SER* 4.3 9.0 - - - +
467B ARG* 3.4 50.0 + - + +
470B MET* 4.6 6.5 - - - -
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Residues in contact with VAL 453 (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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23B LEU* 4.7 5.6 - - + -
134B TYR* 3.7 41.7 - - + +
449B GLY 4.4 0.4 - - - +
450B LEU* 3.1 25.1 + - - +
451B PRO 4.2 4.5 - - - +
452B LEU* 1.3 78.4 - - - +
454B LYS* 1.3 67.6 + - - +
455B GLU* 4.4 7.0 - - + +
456B LEU* 3.4 36.2 + - + +
457B ASN 4.1 2.4 + - - -
458B TYR* 4.6 2.6 + - - -
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Residues in contact with LYS 454 (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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451B PRO 3.4 19.6 + - - -
452B LEU 3.4 17.7 + - - +
453B VAL* 1.3 76.3 - - - +
455B GLU* 1.3 59.1 + - - +
456B LEU 3.1 0.2 - - - -
457B ASN* 3.0 26.3 + - - +
458B TYR 5.8 5.8 + - - +
460B ALA* 6.2 1.7 - - - +
463B GLU* 2.5 31.4 + - - +
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Residues in contact with GLU 455 (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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453B VAL* 3.4 5.5 - - + +
454B LYS* 1.3 77.6 - - - +
456B LEU* 1.3 66.5 + - + +
457B ASN* 3.3 3.1 + - - +
604B NAG 2.8 67.7 + - + +
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Residues in contact with LEU 456 (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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134B TYR* 5.9 0.7 - - + +
429B ASN* 3.3 15.6 + - - -
450B LEU* 3.8 39.0 - - + +
453B VAL* 3.8 28.5 - - + +
454B LYS 3.1 2.0 - - - -
455B GLU* 1.3 83.3 - - + +
457B ASN* 1.3 72.0 + - - +
458B TYR* 3.6 17.7 - - + +
604B NAG 4.9 8.7 - - + +
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Residues in contact with ASN 457 (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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428B SER* 4.6 2.6 + - - -
429B ASN* 3.5 18.8 + - + +
453B VAL 4.1 1.0 + - - -
454B LYS 3.0 20.1 + - - +
455B GLU* 4.0 3.2 - - - +
456B LEU* 1.3 80.9 - - - +
458B TYR* 1.3 62.9 + - - +
604B NAG 1.4 70.3 + - - +
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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