Contacts of the helix formed by residues 3449 - 3459 (chain F) in PDB entry 6X34
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 LYS3449 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3445F TYR* 3.4 19.2 + - + +
3446F TRP 3.7 9.4 - - - +
3447F SER 4.5 2.0 - - - -
3448F LYS* 1.3 76.9 - - + +
3450F HIS* 1.3 63.9 + - - +
3451F ASN* 3.2 3.7 + - + +
3452F PHE* 3.4 34.1 + - + +
3453F LYS 3.5 8.1 + - - -
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Residues in contact with HIS3450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3447F SER 5.1 4.0 - - - +
3448F LYS 3.6 5.6 + - - +
3449F LYS* 1.3 70.9 - - - +
3451F ASN* 1.3 63.0 + - - +
3453F LYS* 3.9 7.1 - - - +
3454F ARG* 3.2 25.8 + - - +
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Residues in contact with ASN3451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3449F LYS* 3.2 3.4 - - + +
3450F HIS* 1.3 78.2 - - - +
3452F PHE* 1.3 70.6 + - + +
3454F ARG* 4.1 2.8 - - - +
3455F GLU* 3.1 26.9 + - - +
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Residues in contact with PHE3452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3398F GLU* 6.3 2.9 - - + -
3399F PHE* 6.4 2.0 - - + -
3445F TYR* 4.5 18.2 - - + +
3446F TRP* 5.6 3.9 - - + +
3449F LYS* 3.4 28.5 + - + +
3451F ASN* 1.3 83.0 - - + +
3453F LYS* 1.3 64.8 + - - +
3455F GLU* 4.0 4.6 - - + +
3456F GLU* 3.1 25.5 + - - +
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Residues in contact with LYS3453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3446F TRP* 3.3 40.3 + - + +
3447F SER* 5.5 1.1 - - - -
3449F LYS 3.5 5.9 + - - +
3450F HIS* 4.0 9.4 - - - +
3451F ASN 3.3 0.4 - - - -
3452F PHE* 1.3 77.7 - - - +
3454F ARG* 1.3 63.9 + - - +
3456F GLU* 3.5 12.4 + - - +
3457F GLN* 3.6 13.9 + - - +
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Residues in contact with ARG3454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3450F HIS 3.2 17.3 + - - +
3451F ASN* 4.3 3.4 - - - +
3453F LYS* 1.3 77.2 - - - +
3455F GLU* 1.3 62.2 + - - +
3457F GLN* 3.7 3.2 + - - +
3458F ASN* 3.3 22.9 + - - +
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Residues in contact with GLU3455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399F PHE* 3.7 30.3 - - + +
3451F ASN 3.1 20.2 + - - +
3452F PHE* 4.3 5.2 - - + +
3454F ARG* 1.3 75.6 - - - +
3456F GLU* 1.3 64.7 + - - +
3458F ASN* 3.9 7.2 - - - +
3459F PHE* 3.6 19.1 + - - +
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Residues in contact with GLU3456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399F PHE* 5.2 2.2 - - - +
3403F CYS* 4.3 12.8 - - + +
3446F TRP* 4.3 26.7 - - + -
3452F PHE 3.1 19.6 + - - +
3453F LYS* 3.8 6.1 - - - +
3454F ARG 3.3 0.4 - - - -
3455F GLU* 1.3 80.7 - - - +
3457F GLN* 1.3 60.8 + - - +
3458F ASN 3.4 0.5 + - - -
3459F PHE* 3.6 8.0 + - - +
3460F VAL* 3.3 15.9 + - - +
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Residues in contact with GLN3457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3453F LYS 3.6 10.8 + - - +
3454F ARG* 4.5 2.9 - - - +
3455F GLU 3.5 0.2 - - - -
3456F GLU* 1.3 76.7 - - - +
3458F ASN* 1.3 64.0 + - - +
3459F PHE 3.4 0.2 - - - -
3460F VAL* 3.6 21.8 + - + +
3461F VAL* 4.2 5.0 + - - +
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Residues in contact with ASN3458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3454F ARG 3.3 18.8 + - - +
3455F GLU* 4.0 9.0 - - - +
3456F GLU 3.2 1.0 - - - -
3457F GLN* 1.3 79.5 - - - +
3459F PHE* 1.3 61.5 + - - +
3460F VAL 3.5 0.5 + - - -
3461F VAL* 3.8 15.5 + - - +
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Residues in contact with PHE3459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399F PHE* 4.6 3.1 - - + +
3400F SER* 3.7 43.1 - - - -
3403F CYS* 3.6 32.1 - - + -
3404F ARG* 4.6 11.0 - - + -
3455F GLU 3.6 9.9 + - - +
3456F GLU 3.6 1.8 + - - +
3457F GLN 3.4 0.4 - - - -
3458F ASN* 1.3 76.5 - - - +
3460F VAL* 1.3 65.0 + - - +
3461F VAL 3.4 7.9 - - - +
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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