Contacts of the helix formed by residues 439 - 453 (chain C) in PDB entry 6AH0
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 PRO 439 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C ASP 6.2 2.0 - - - -
437C HIS 3.9 2.6 - - - -
438C ILE* 1.3 71.0 - - - +
440C SER* 1.3 65.4 + - - +
442C LYS* 4.4 1.2 + - - -
443C VAL* 3.6 19.7 + - - -
444C GLY 4.8 1.1 - - - +
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Residues in contact with SER 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C GLU* 5.8 3.4 - - - +
129C ILE 4.3 10.8 - - - -
130C ARG* 4.3 13.0 - - - +
131C ASN 5.2 2.7 - - - +
223C ASP* 5.6 10.8 - - - +
438C ILE 3.2 5.0 - - - -
439C PRO* 1.3 75.7 - - - +
441C PRO* 1.3 60.6 - - - +
444C GLY* 3.0 27.2 + - - -
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Residues in contact with PRO 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C SER 4.2 12.5 - - - +
127C GLU* 5.7 0.6 - - - -
129C ILE 4.1 10.2 - - - +
130C ARG* 5.3 0.2 - - - -
131C ASN 5.8 0.2 - - - -
440C SER* 1.3 71.4 - - - +
442C LYS* 1.3 63.8 + - - +
444C GLY* 3.3 12.0 + - - -
445C ALA 4.4 2.1 + - - -
466C SER 5.3 1.2 - - - +
468C CYS* 5.7 5.5 - - - -
547C GLY* 5.4 14.1 - - - +
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Residues in contact with LYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C SER 4.3 7.3 + - - -
127C GLU* 5.9 0.6 - - - +
439C PRO 4.4 1.4 + - - -
440C SER 3.4 0.6 - - - -
441C PRO* 1.3 77.1 - - - +
443C VAL* 1.3 62.0 + - - +
445C ALA 4.8 1.0 + - - -
466C SER 3.9 16.3 - - - +
467C ASP 5.5 5.2 - - - -
468C CYS* 6.5 0.4 - - - +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C PRO* 3.6 19.6 + - - -
442C LYS* 1.3 77.1 - - - +
444C GLY* 1.3 67.0 + - - +
445C ALA 3.0 2.9 + - - -
446C LYS* 3.1 14.9 + - - -
447C PRO 4.2 2.6 - - - -
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Residues in contact with GLY 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ASP* 6.0 5.6 - - - -
439C PRO* 4.8 1.4 - - - +
440C SER 3.0 20.0 + - - -
441C PRO* 3.5 8.1 - - - -
442C LYS 3.2 1.2 - - - -
443C VAL* 1.3 74.1 - - - +
445C ALA* 1.3 59.8 + - - -
446C LYS 3.6 0.2 + - - -
447C PRO* 3.7 2.9 - - - +
448C LYS* 3.3 16.3 + - - -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C PRO 4.4 3.8 + - - -
442C LYS 4.8 1.2 + - - -
443C VAL 3.0 2.2 + - - -
444C GLY* 1.3 69.8 - - - +
446C LYS* 1.3 62.0 + - - +
448C LYS* 3.6 1.6 - - - +
449C ILE* 2.6 35.7 + - - +
465C MET 5.1 5.2 - - - -
466C SER* 5.0 14.6 + - - +
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Residues in contact with LYS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C VAL 3.1 10.8 + - - -
445C ALA* 1.3 76.9 - - - +
447C PRO* 1.3 62.5 - - - +
449C ILE 4.3 1.2 + - - -
450C GLU* 4.4 5.9 + - - -
466C SER* 5.0 7.4 + - - +
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Residues in contact with PRO 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C GLU 5.6 3.4 - - - +
250C ARG 5.5 8.1 - - - +
443C VAL 4.2 3.0 - - - -
444C GLY 3.7 4.9 - - - +
445C ALA 3.3 0.2 - - - -
446C LYS* 1.3 77.5 - - - +
448C LYS* 1.3 60.7 + - - +
450C GLU* 4.2 5.2 + - - -
451C HIS* 4.3 5.0 + - - -
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Residues in contact with LYS 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C GLU 5.9 2.5 - - - -
444C GLY 3.3 14.1 + - - -
445C ALA* 3.2 4.4 + - - +
447C PRO* 1.3 75.0 - - - +
449C ILE* 1.3 59.0 + - - +
451C HIS* 3.4 3.8 + - - -
452C THR* 2.9 25.7 + - - -
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Residues in contact with ILE 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ALA* 2.6 24.8 + - - +
448C LYS* 1.3 67.8 - - - +
450C GLU* 1.3 60.4 + - - +
452C THR* 4.6 1.1 - - - +
453C TYR* 2.5 37.9 + - - +
456C GLY* 4.3 6.0 - - - -
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Residues in contact with GLU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C LYS 4.4 6.3 + - - -
447C PRO 4.2 4.7 + - - -
448C LYS 3.4 1.0 - - - -
449C ILE* 1.3 76.8 - - - +
451C HIS* 1.3 62.2 + - - +
453C TYR 3.6 9.7 - - - +
456C GLY* 4.4 18.1 + - - -
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Residues in contact with HIS 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447C PRO 4.3 5.0 + - - -
448C LYS 3.4 5.8 + - - -
450C GLU* 1.3 79.7 - - - +
452C THR* 1.3 59.9 + - - +
453C TYR 4.8 1.0 - - - +
578C ARG* 4.7 6.8 + - - -
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C LYS 2.9 16.4 + - - -
449C ILE* 4.3 1.1 - - - +
451C HIS* 1.3 76.6 - - - +
453C TYR* 1.3 53.9 + - - +
577C PHE* 2.6 14.5 - - - -
578C ARG* 2.5 33.8 + - - +
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Residues in contact with TYR 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C ILE* 2.5 26.5 + - - +
450C GLU 3.6 8.0 - - - +
451C HIS 4.8 0.8 - - - +
452C THR* 1.3 72.6 - - - +
454C THR* 1.3 61.7 + - - +
455C GLY 3.4 2.5 - - - -
456C GLY* 3.0 20.5 + - - +
575C GLN 5.1 4.0 - - - -
577C PHE* 4.3 5.2 - - - +
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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