Contacts of the helix formed by residues 437 - 445 (chain B) in PDB entry 4K9N
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 ALA 437 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 5.6 0.4 - - - -
49B CYS* 3.7 16.4 - - + -
53B ILE* 4.8 2.9 - - + -
407B LEU* 3.7 13.5 - - + -
408B PRO* 3.8 28.0 - - + -
411B ILE* 3.0 19.9 - - + +
434B SER 3.0 15.6 + - - +
436B SER* 1.3 79.7 + - - +
438B LEU* 1.3 62.1 + - - +
440B THR* 2.9 19.7 + - - +
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Residues in contact with LEU 438 (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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407B LEU* 3.9 13.4 - - + +
411B ILE* 4.5 3.6 - - - -
435B ILE* 3.2 37.2 + - + +
436B SER 3.1 0.6 - - - -
437B ALA* 1.3 78.4 - - - +
439B TRP* 1.3 61.5 + - - +
441B ALA* 3.1 6.2 + - - +
442B ALA 3.1 17.0 + - - -
450B PHE* 3.7 40.8 - - + -
486B LEU* 4.6 4.7 - - + +
487B ALA* 4.2 25.1 - - - +
490B TYR* 3.9 13.5 - - + -
492B VAL* 3.5 18.9 - - + +
518B LEU* 4.3 15.0 - - + -
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Residues in contact with TRP 439 (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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43B LEU* 3.6 48.0 - - + -
45B LEU* 3.6 31.9 - - + -
436B SER 3.1 13.9 + - - +
437B ALA 3.1 0.4 - - - -
438B LEU* 1.3 80.7 - - - +
440B THR* 1.3 65.4 + - - +
442B ALA* 3.3 1.6 + - - +
443B GLN* 2.9 59.5 + - + +
444B TYR* 4.8 3.1 - + - -
490B TYR* 3.7 23.5 - + + +
477D ASP 3.9 6.5 - - - -
478D VAL* 3.8 17.3 - - + -
479D PRO* 2.7 29.0 + - + -
480D GLY 4.1 8.7 - - - -
481D ILE* 3.6 24.3 - - + +
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Residues in contact with THR 440 (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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42B ILE* 3.8 16.8 - - + -
43B LEU 2.9 27.1 + - - +
44B ALA* 3.4 18.0 - - - +
45B LEU 4.7 0.5 + - - -
53B ILE* 3.9 16.7 - - + +
411B ILE* 4.4 8.5 - - + -
436B SER 5.0 0.3 + - - -
437B ALA* 2.9 12.7 + - - -
439B TRP* 1.3 82.7 - - - +
441B ALA* 1.3 65.5 + - - +
444B TYR* 3.1 39.3 + - + +
446B ILE* 4.1 2.8 - - + +
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Residues in contact with ALA 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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411B ILE* 3.8 24.3 - - + +
437B ALA 3.5 2.4 + - - -
438B LEU 3.1 9.8 + - - +
440B THR* 1.3 79.2 - - - +
442B ALA* 1.3 57.3 + - - +
445B ASN* 3.0 10.0 + - - -
446B ILE* 3.0 49.8 + - - +
450B PHE* 4.4 8.1 - - + -
492B VAL* 4.9 0.9 - - + -
516B PRO* 3.7 17.9 - - + +
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Residues in contact with ALA 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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438B LEU 3.1 8.3 + - - +
439B TRP* 3.7 4.5 - - + +
441B ALA* 1.3 77.0 - - - +
443B GLN* 1.3 70.6 + - + +
445B ASN* 3.4 11.8 + - - +
490B TYR 3.3 26.7 - - - +
491B GLY* 3.6 21.3 - - - +
492B VAL* 4.0 3.1 - - + -
516B PRO* 4.1 10.7 - - - +
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Residues in contact with GLN 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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439B TRP* 2.9 58.5 + - + +
442B ALA* 1.3 81.5 - - - +
444B TYR* 1.3 75.9 + - + +
445B ASN* 3.8 0.7 + - - +
479D PRO* 3.2 36.8 + - - +
480D GLY* 4.2 7.3 + - - -
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Residues in contact with TYR 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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41B TYR* 3.3 21.4 + - - -
42B ILE* 3.9 17.7 - - + -
43B LEU* 2.9 51.0 + - + +
415B LEU* 6.0 0.9 - - + -
439B TRP* 4.8 3.5 - + - -
440B THR* 3.1 30.4 + - + +
443B GLN* 1.3 89.0 - - + +
445B ASN* 1.3 72.4 + - - +
446B ILE* 3.3 18.8 + - + +
475D GLY* 5.8 0.3 - - - -
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Residues in contact with ASN 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 ALA 3.0 8.9 + - - -
442B ALA 3.4 8.9 + - - +
443B GLN 3.4 0.8 - - - +
444B TYR* 1.3 82.2 - - - +
446B ILE* 1.3 59.8 + - - +
447B PRO* 3.4 10.6 - - - +
514B LYS 3.6 21.9 + - - +
515B GLY* 3.7 11.4 - - - -
516B PRO* 4.2 4.3 - - - +
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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