Contacts of the helix formed by residues 433 - 444 (chain D) in PDB entry 4XKL
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 433 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LYS* 4.5 7.1 - - - -
420D PHE* 5.0 0.6 - - - -
429D PHE* 4.4 5.2 - - + -
430D PRO* 3.1 43.7 + - + +
431D ALA 4.2 1.8 - - - -
432D THR* 1.3 82.0 + - - +
434D LYS* 1.3 62.7 + - - +
435D GLN 3.5 1.8 - - - +
436D ILE* 3.6 48.6 - - + +
437D PHE* 3.3 20.8 + - - +
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Residues in contact with LYS 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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420D PHE* 4.6 15.9 - - + -
431D ALA 4.2 4.7 + - - +
432D THR 3.9 3.9 + - - +
433D GLU* 1.3 70.9 - - - +
435D GLN* 1.3 80.6 + - + +
437D PHE* 3.4 2.1 + - - +
438D GLU* 3.0 63.0 + - - +
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Residues in contact with GLN 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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45C PHE* 3.3 20.8 - - + -
46C ALA* 4.5 17.0 - - + -
65C SER* 6.0 0.3 - - - -
66C THR 3.0 26.3 + - - +
433D GLU 3.5 0.2 - - - -
434D LYS* 1.3 89.3 - - + +
436D ILE* 1.3 72.6 + - - +
438D GLU* 3.4 10.1 + - - +
439D ASP* 2.9 60.0 + - - +
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Residues in contact with ILE 436 (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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6C LYS* 3.9 24.9 - - + -
66C THR* 3.5 37.2 - - + +
68C HIS* 3.3 11.2 - - + -
429D PHE* 4.0 10.1 - - + -
433D GLU* 3.6 49.2 + - + +
434D LYS 3.3 0.4 - - - -
435D GLN* 1.3 96.9 - - - +
437D PHE* 1.3 62.1 + - - +
439D ASP* 3.4 2.0 + - - -
440D HIS* 3.0 19.1 + - - +
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Residues in contact with PHE 437 (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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420D PHE* 3.7 35.9 - + + -
421D ASN 3.6 17.3 - - - -
422D CYS* 3.6 27.8 - - + -
423D PRO* 4.7 3.6 - - + -
429D PHE* 3.5 38.1 - + + -
433D GLU 3.3 15.7 + - - +
434D LYS* 3.7 2.9 - - - +
436D ILE* 1.3 80.9 - - - +
438D GLU* 1.3 68.9 + - + +
440D HIS* 3.1 5.6 + - - +
441D VAL* 2.9 47.1 + - + +
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Residues in contact with GLU 438 (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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434D LYS* 3.0 55.5 + - - +
435D GLN* 3.8 6.0 - - - +
437D PHE* 1.3 87.0 - - + +
439D ASP* 1.3 59.9 + - - +
441D VAL* 3.4 7.0 + - - +
442D PHE* 2.9 29.4 + - - +
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Residues in contact with ASP 439 (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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44C ILE* 4.2 11.9 - - + +
45C PHE* 3.7 5.0 - - - -
46C ALA* 2.9 25.4 + - - -
47C GLY* 2.8 28.0 + - - -
66C THR 4.4 1.6 - - - +
68C HIS* 3.7 14.0 + - - +
435D GLN* 2.9 36.8 + - - +
436D ILE* 3.6 4.5 - - - +
438D GLU* 1.3 75.9 - - - +
440D HIS* 1.3 60.4 + - - +
442D PHE* 3.3 6.2 + - - +
443D CYS* 2.8 35.8 + - - -
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Residues in contact with HIS 440 (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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8C LEU* 3.2 48.0 + - + +
68C HIS* 3.5 26.6 + - - +
422D CYS* 3.3 17.1 - - + +
425D CYS* 3.7 7.4 - - - -
427D LYS* 4.0 8.2 + - + -
429D PHE* 3.5 23.5 - + + -
436D ILE 3.0 11.8 + - - +
437D PHE* 3.3 8.5 - + - +
439D ASP* 1.3 75.7 - - - +
441D VAL* 1.3 67.7 + - + +
443D CYS 3.2 9.5 + - - -
444D HIS* 3.1 10.1 + - - -
502D ZN 1.9 37.3 - - - -
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Residues in contact with VAL 441 (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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422D CYS* 4.3 1.1 - - - -
423D PRO* 4.3 18.8 - - + -
424D ILE* 4.5 13.9 - - + +
437D PHE* 2.9 48.4 + - + +
438D GLU* 3.8 7.6 - - - +
440D HIS* 1.3 81.9 - - + +
442D PHE* 1.3 60.4 + - - +
444D HIS* 3.3 22.9 - - - +
445D SER* 4.2 4.5 + - - -
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Residues in contact with PHE 442 (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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62A GLN* 4.7 7.0 - - + -
44C ILE* 3.7 29.4 - - + -
47C GLY* 3.6 39.9 - - - -
48C LYS* 3.9 11.2 - - - -
49C GLN* 4.5 3.1 - - + -
438D GLU 2.9 17.7 + - - +
439D ASP* 3.3 5.8 - - - +
441D VAL* 1.3 74.0 - - - +
443D CYS* 1.3 58.3 + - - +
445D SER* 2.9 35.5 + - - -
446D LEU* 3.9 34.4 - - + +
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Residues in contact with CYS 443 (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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8C LEU* 3.9 17.7 - - + +
44C ILE* 3.9 18.6 - - - -
68C HIS* 3.5 33.0 - - + -
70C VAL* 3.5 30.4 - - + +
439D ASP 2.8 26.0 + - - -
440D HIS* 3.2 9.8 + - - +
442D PHE* 1.3 73.6 - - - +
444D HIS* 1.3 62.1 + - - +
445D SER 3.2 0.5 + - - -
446D LEU* 3.2 23.6 + - - +
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Residues in contact with HIS 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.7 26.2 - - + +
9C THR* 5.1 2.5 - - + -
422D CYS* 3.5 4.1 - - - -
424D ILE* 3.5 48.6 - - + +
425D CYS* 4.0 10.1 - - + -
440D HIS* 3.1 20.7 + + - -
441D VAL* 3.3 12.5 + - - +
442D PHE 3.2 0.8 + - - -
443D CYS* 1.3 76.8 - - - +
445D SER* 1.3 62.3 + - - +
446D LEU 3.4 5.9 + - - +
502D ZN 2.2 35.4 - - - -
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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