Contacts of the helix formed by residues 429 - 436 (chain D) in PDB entry 4K9P
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 GLY 429 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 5.2 0.3 - - - +
427D GLY 3.0 0.8 - - - -
428D ASP* 1.3 79.1 - - - +
430D SER* 1.3 63.8 - - - +
431D ALA 3.1 2.8 + - - -
432D ASN* 3.4 20.3 + - - +
433D TYR* 3.3 17.2 - - - -
458D TYR* 3.8 26.6 + - - -
478D VAL* 4.7 3.6 - - - -
602D TPP 3.3 12.9 + - - -
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Residues in contact with SER 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D GLU* 3.2 45.6 + - - +
377D THR* 5.0 0.3 - - - +
403D LEU* 3.3 25.0 - - - +
404D GLY* 4.3 2.3 + - - -
407D LEU* 6.0 0.7 - - - +
426D ILE* 3.9 5.2 - - - -
427D GLY 3.3 0.2 + - - -
429D GLY* 1.3 72.0 - - - +
431D ALA* 1.3 63.0 + - - +
433D TYR* 3.2 29.6 + - - +
434D SER 4.5 0.7 + - - -
602D TPP 2.8 26.4 + - - -
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D LEU* 4.0 13.8 - - + +
426D ILE* 3.4 14.6 - - + +
427D GLY 3.1 17.6 + - - +
428D ASP 4.1 0.7 - - - +
429D GLY 3.1 0.4 - - - -
430D SER* 1.3 80.6 - - - +
432D ASN* 1.3 61.8 + - - +
433D TYR 3.4 0.3 + - - -
434D SER 3.8 1.4 + - - -
435D ILE* 3.4 28.5 + - + +
452D ILE* 4.3 14.4 - - + -
483D PHE* 3.8 25.6 - - + -
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Residues in contact with ASN 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.5 39.3 - - + +
46B GLN* 4.7 1.0 - - - +
436B SER* 3.8 17.7 + - - -
490B TYR* 3.1 28.7 + - - +
428D ASP 3.0 23.4 + - - -
429D GLY* 3.4 12.8 + - - +
430D SER 3.2 1.0 - - - -
431D ALA* 1.3 76.1 - - - +
433D TYR* 1.3 64.5 + - - +
434D SER 3.3 0.8 + - - -
435D ILE* 3.8 10.8 + - - +
478D VAL* 5.4 0.6 - - - +
481D ILE* 3.4 20.1 - - - +
483D PHE* 3.7 13.5 - - - -
486D LEU* 4.4 1.0 - - - +
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Residues in contact with TYR 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 2.8 25.4 + - - -
45B LEU 3.5 20.9 - - - -
46B GLN* 3.8 24.5 + - + +
47B GLU* 3.6 20.9 - - - -
77B ASN* 4.0 5.8 - - - +
46D GLN* 5.3 4.0 - - - +
48D ALA* 5.2 4.0 - - - +
403D LEU* 3.7 22.2 - - + +
404D GLY* 3.5 20.9 - - - -
429D GLY 3.3 19.1 - - - -
430D SER* 3.2 20.4 - - - +
431D ALA 3.3 1.0 - - - -
432D ASN* 1.3 77.9 - - - +
434D SER* 1.3 62.3 + - - +
458D TYR* 4.1 5.1 + + - -
602D TPP 3.4 47.5 + - + +
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Residues in contact with SER 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA* 4.2 14.4 - - - +
49D CYS* 3.8 19.6 - - - -
404D GLY* 3.0 29.4 + - - -
407D LEU* 3.9 8.4 - - - +
408D PRO* 3.7 16.4 - - - +
430D SER 4.5 1.0 + - - -
431D ALA 3.8 5.2 + - - -
433D TYR* 1.3 78.6 + - - +
435D ILE* 1.3 65.9 + - - +
436D SER 3.1 5.2 + - - -
437D ALA* 3.1 17.8 + - - +
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ILE* 3.5 31.2 - - + -
490B TYR* 4.0 13.5 - - + +
407D LEU* 4.5 8.7 - - + -
431D ALA* 3.4 27.6 + - + +
432D ASN* 4.2 7.6 - - - +
433D TYR 3.7 0.2 - - - -
434D SER* 1.3 77.6 - - - +
436D SER* 1.3 67.6 + - - +
437D ALA 3.2 0.7 + - - -
438D LEU* 3.2 41.1 + - + +
452D ILE* 6.3 0.7 - - + -
483D PHE* 4.9 4.7 - - + -
486D LEU* 4.1 35.0 - - + -
490D TYR* 4.0 9.4 - - + -
518D LEU* 5.6 3.1 - - + -
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Residues in contact with SER 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ASN 4.2 13.0 + - - -
435B ILE* 5.1 0.2 - - - -
45D LEU* 3.9 20.9 + - - +
46D GLN* 3.7 14.2 - - - +
49D CYS* 3.5 14.9 - - - -
434D SER* 3.1 1.0 + - - -
435D ILE* 1.3 78.0 - - - +
437D ALA* 1.3 65.7 + - - +
438D LEU 3.0 2.7 - - - -
439D TRP* 3.0 22.2 + - - +
440D THR* 4.3 1.0 + - - -
490D TYR* 3.6 30.5 - - - -
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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