Contacts of the helix formed by residues 451 - 461 (chain A) in PDB entry 6HBU
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 GLU 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A MET* 4.1 18.9 - - + +
447A LEU 4.8 4.5 + - - +
448A PHE 4.3 5.0 - - - +
449A VAL 3.2 2.2 - - - +
450A VAL* 1.3 94.8 - - + +
452A LYS* 1.3 58.6 + - - +
453A LYS 3.4 2.0 - - - +
454A LEU* 3.4 32.6 - - + +
455A PHE* 3.1 26.2 + - - +
469A TYR* 3.8 15.2 + - - +
473A LYS* 4.4 10.3 - - - +
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Residues in contact with LYS 452 (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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448A PHE 3.8 14.1 + - - +
449A VAL 3.3 16.9 + - - +
450A VAL 3.5 1.6 + - - -
451A GLU* 1.3 75.9 - - - +
453A LYS* 1.3 61.0 + - - +
455A PHE* 3.3 7.8 + - + +
456A ILE* 2.9 50.1 + - + +
530A GLY* 3.7 24.1 + - - -
531A GLN* 3.6 19.9 - - - +
532A SER* 2.8 28.1 + - - +
651A LEU* 4.1 16.8 - - + +
182B PHE* 3.7 25.0 - - + +
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Residues in contact with LYS 453 (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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129A VAL* 3.9 33.1 - - + +
450A VAL 5.2 1.0 + - - +
451A GLU* 3.4 0.6 - - - +
452A LYS* 1.3 78.0 - - - +
454A LEU* 1.3 58.0 + - - +
456A ILE* 3.5 8.5 + - + +
457A HIS* 3.1 28.5 + - - +
181B GLN* 2.8 57.1 + - + +
182B PHE* 3.7 23.1 - - + -
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Residues in contact with LEU 454 (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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129A VAL* 3.8 32.3 - - + +
130A VAL* 4.7 1.1 - - - +
131A MET* 3.7 47.8 - - + +
383A ARG* 4.1 9.4 - - - +
451A GLU* 3.4 32.7 + - + +
452A LYS 3.3 0.2 - - - -
453A LYS* 1.3 76.5 - - - +
455A PHE* 1.3 60.9 + - - +
457A HIS* 3.9 2.2 - - - +
458A GLU* 3.1 55.9 + - + +
464A TYR* 4.4 0.4 - - - -
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Residues in contact with PHE 455 (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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448A PHE 5.9 0.7 - - - +
451A GLU 3.1 20.2 + - - +
452A LYS* 3.3 7.6 + - + +
454A LEU* 1.3 75.9 - - - +
456A ILE* 1.3 74.0 + - + +
459A TYR* 3.0 26.3 + - + +
464A TYR* 3.4 24.9 + + - -
466A VAL* 4.3 17.5 - - + -
469A TYR* 3.5 43.2 + + + +
648A LEU* 3.9 44.2 - - + -
651A LEU* 4.4 7.9 - - + -
653A LYS* 3.8 26.5 - - - -
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Residues in contact with ILE 456 (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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452A LYS* 2.9 48.8 + - + +
453A LYS* 4.0 9.4 - - + +
455A PHE* 1.3 80.6 - - + +
457A HIS* 1.3 62.0 + - - +
459A TYR* 4.1 0.5 - - - +
460A ILE* 3.2 30.8 + - + +
651A LEU* 4.3 15.0 - - + -
652A LYS 4.9 7.6 - - - +
653A LYS* 3.4 47.3 - - + +
182B PHE* 4.2 14.1 - - + -
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Residues in contact with HIS 457 (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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96A ARG* 5.0 2.9 - - - -
123A TYR 4.9 1.4 + - - -
125A VAL* 3.7 39.3 + - + +
129A VAL* 3.7 43.8 + - + +
198A MET* 6.1 3.4 - - + -
199A GLU* 3.9 21.8 + - - -
453A LYS* 3.1 20.6 + - - +
454A LEU* 4.1 3.2 - - - +
456A ILE* 1.3 77.9 - - - +
458A GLU* 1.3 70.8 + - + +
460A ILE* 3.3 11.4 - - + +
461A SER* 2.9 42.8 + - - -
463A TYR* 5.1 5.4 - - - -
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Residues in contact with GLU 458 (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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131A MET* 5.8 0.2 - - - +
142A PHE* 4.2 0.9 - - - -
383A ARG* 2.8 40.7 + - - -
454A LEU* 3.1 39.9 + - + +
457A HIS* 1.3 80.0 - - + +
459A TYR* 1.3 61.3 + - - +
461A SER* 3.9 2.0 - - - -
462A GLY 3.5 1.7 + - - -
463A TYR* 3.0 67.7 + - + +
464A TYR* 3.2 29.3 + - + +
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Residues in contact with TYR 459 (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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118A LYS* 3.3 30.4 + - - -
367A ILE* 5.6 3.3 - - - +
369A TYR* 3.4 25.3 + - - -
455A PHE* 3.0 29.6 + + + +
456A ILE 4.1 2.7 - - - +
458A GLU* 1.3 76.5 - - - +
460A ILE* 1.3 65.8 + - + +
461A SER 3.2 0.4 - - - -
462A GLY* 3.0 15.1 + - - -
464A TYR* 3.4 26.4 + + + -
466A VAL* 3.5 32.4 - - + +
649A LEU* 4.7 7.9 - - - +
653A LYS* 3.7 36.8 - - + -
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Residues in contact with ILE 460 (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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96A ARG* 3.3 56.1 + - + +
118A LYS* 3.3 24.0 - - - +
456A ILE* 3.2 22.2 + - + +
457A HIS* 3.3 16.2 - - + +
459A TYR* 1.3 80.8 - - + +
461A SER* 1.3 56.9 + - - +
462A GLY 3.3 0.2 - - - -
653A LYS* 3.7 39.0 - - + +
654A TYR* 6.5 0.9 - - + -
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.5 19.7 + - - +
118A LYS* 3.0 18.6 - - - +
123A TYR 4.8 0.9 + - - -
147A ARG* 3.3 24.4 + - - +
199A GLU* 3.9 6.4 + - - -
457A HIS* 2.9 33.4 + - - -
458A GLU 4.2 0.2 - - - -
459A TYR 3.2 0.4 - - - -
460A ILE* 1.3 77.7 - - - +
462A GLY* 1.3 59.7 + - - +
463A TYR* 3.7 23.6 - - - -
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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