Contacts of the helix formed by residues 440 - 450 (chain B) in PDB entry 3T9K
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 CYS 440 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B CYS* 3.3 9.2 - - + +
423B CYS* 3.6 7.6 - - - -
425B GLU* 3.5 32.1 - - + -
428B PRO* 3.7 10.5 - - + +
429B GLU 4.7 0.7 - - - +
430B TRP* 4.2 0.7 - - - -
439B LEU* 1.3 77.7 - - - +
441B ILE* 1.3 62.9 + - + +
442B GLN* 3.8 11.0 - - - -
443B CYS* 3.4 15.8 + - - -
444B SER* 3.0 25.1 + - - -
506B LYS* 4.5 1.3 - - - -
999B ZN 2.3 34.8 - - - -
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Residues in contact with ILE 441 (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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429B GLU 5.5 0.2 - - - +
430B TRP* 3.7 38.3 - - + +
440B CYS* 1.3 75.5 - - + +
442B GLN* 1.3 65.4 + - + +
444B SER* 2.9 20.2 + - - +
445B GLY* 3.1 8.1 + - - -
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Residues in contact with GLN 442 (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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706A GLN* 4.0 11.7 + - - +
440B CYS* 3.3 10.4 - - - -
441B ILE* 1.3 84.3 - - + +
443B CYS* 1.3 63.1 + - - +
445B GLY* 3.3 3.6 + - - -
446B ILE* 3.2 21.5 + - + +
499B PRO 4.5 0.9 - - - +
501B CYS 4.1 3.9 + - - +
502B SER 4.6 0.6 - - - -
503B ARG* 3.4 45.6 + - + +
506B LYS* 2.8 40.8 + - + +
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Residues in contact with CYS 443 (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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420B CYS* 3.7 11.9 - - - -
422B ASP* 3.9 17.3 - - - +
423B CYS* 3.8 13.2 - - - -
439B LEU* 4.3 3.8 - - + -
440B CYS* 3.4 5.6 + - - +
442B GLN* 1.3 78.9 - - - +
444B SER* 1.3 53.2 + - - +
446B ILE* 3.2 4.7 + - - +
447B HIS* 2.8 40.4 + - - -
506B LYS* 3.9 14.6 - - - -
510B ILE* 3.9 19.7 - - + +
999B ZN 2.3 35.2 - - - -
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Residues in contact with SER 444 (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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430B TRP* 3.5 34.3 - - - -
439B LEU* 4.1 15.2 - - - +
440B CYS 3.0 16.0 + - - -
441B ILE* 2.9 17.7 + - - +
443B CYS* 1.3 73.3 - - - +
445B GLY* 1.3 67.5 + - - +
447B HIS* 3.4 3.0 + - - +
448B ARG* 3.1 29.5 + - - +
457B VAL* 3.7 17.1 - - - +
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Residues in contact with GLY 445 (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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441B ILE 3.1 8.7 + - - -
442B GLN 3.3 4.9 + - - -
444B SER* 1.3 82.9 + - - +
446B ILE* 1.3 59.7 + - - +
448B ARG* 3.5 22.6 + - - +
449B SER* 3.4 21.5 + - - -
503B ARG* 3.6 13.8 + - - -
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Residues in contact with ILE 446 (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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442B GLN* 3.2 18.1 + - + +
443B CYS* 3.2 7.8 + - - +
445B GLY* 1.3 73.4 - - - +
447B HIS* 1.3 65.7 + - - +
449B SER* 3.1 20.6 + - - -
450B LEU* 3.5 12.0 + - + +
503B ARG* 3.8 31.4 - - + +
506B LYS* 3.7 18.6 - - + -
507B GLU* 3.7 47.1 - - + +
510B ILE* 3.7 31.2 - - + -
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Residues in contact with HIS 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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422B ASP* 2.6 30.7 - - - -
432B SER* 4.3 0.4 - - - -
435B LEU* 3.8 10.5 - - + +
437B VAL* 5.1 0.2 - - - +
439B LEU* 3.5 23.6 - - + +
443B CYS 2.8 26.0 + - - +
444B SER 3.6 8.3 - - - +
446B ILE* 1.3 70.9 - - - +
448B ARG* 1.3 64.0 + - - +
450B LEU* 3.1 30.9 + - + +
451B GLY 4.0 2.3 + - - +
455B SER* 2.8 37.1 - - - +
457B VAL* 3.6 15.0 - - + -
510B ILE* 4.1 8.5 - - + +
514B TYR* 3.3 30.1 + + - -
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Residues in contact with ARG 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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430B TRP* 4.0 20.4 - - - -
444B SER* 3.1 20.5 + - - +
445B GLY* 3.6 22.9 - - - +
446B ILE 3.2 0.4 - - - -
447B HIS* 1.3 77.5 - - - +
449B SER* 1.3 56.5 + - - +
451B GLY* 2.9 24.1 + - - -
455B SER 5.2 2.5 - - - +
457B VAL* 3.7 38.5 + - + +
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Residues in contact with SER 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 GLY 3.4 10.3 + - - -
446B ILE* 3.1 12.9 + - - -
448B ARG* 1.3 75.5 - - - +
450B LEU* 1.3 60.6 + - - +
451B GLY 3.3 0.6 + - - -
503B ARG* 4.4 12.3 + - - -
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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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446B ILE* 3.7 13.5 - - + +
447B HIS* 3.2 32.1 - - + +
448B ARG 3.0 1.6 + - - -
449B SER* 1.3 79.1 - - - +
451B GLY* 1.3 57.1 + - - +
453B HIS* 4.2 2.8 - - - -
454B PHE* 3.3 46.2 - - + +
455B SER* 4.6 1.1 - - - -
510B ILE* 4.0 27.1 - - + -
511B HIS* 4.7 15.0 - - + +
514B TYR* 4.6 13.7 - - + -
515B VAL* 4.1 18.4 - - + -
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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