Contacts of the helix formed by residues 430 - 442 (chain B) in PDB entry 4L28
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 THR 430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428B THR 3.6 2.6 + - - -
429B ILE* 1.3 76.7 - - + +
431B CYS* 1.3 63.1 + - - +
433B HIS* 3.2 28.4 + - + +
434B THR* 3.1 21.5 + - - +
475B PRO 2.7 26.5 + - - +
476B SER* 3.1 15.5 + - - -
477B ASP 3.1 12.8 + - - -
478B GLN* 4.7 1.3 - - - +
479B VAL* 3.7 1.8 - - - -
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Residues in contact with CYS 431 (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 THR* 1.3 77.6 + - - +
432B GLY* 1.3 61.2 + - - +
434B THR* 2.7 22.2 + - - -
435B ILE* 3.0 4.7 + - - +
464B MET* 3.3 38.6 - - + +
468B LEU* 5.2 1.8 - - + -
473B VAL* 4.1 21.3 - - - -
474B GLN 3.8 7.2 - - - +
475B PRO* 3.7 7.9 - - + +
477B ASP 3.0 18.5 + - - +
478B GLN 3.7 17.3 - - - -
479B VAL* 3.8 12.7 - - - +
482B VAL* 4.7 3.4 - - - -
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B CYS* 1.3 78.8 - - - +
433B HIS* 1.3 57.3 + - - +
435B ILE* 3.1 15.2 + - - +
436B GLU* 2.9 36.6 + - - +
468B LEU* 5.2 1.3 - - - -
475B PRO* 3.1 25.7 + - - +
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Residues in contact with HIS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ILE* 3.3 27.5 - - + +
430B THR* 3.2 29.2 + - + +
431B CYS 3.1 0.4 - - - -
432B GLY* 1.3 78.1 - - - +
434B THR* 1.3 57.3 + - - +
436B GLU* 3.0 22.8 + - + +
437B ILE* 2.9 54.9 + - + +
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Residues in contact with THR 434 (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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425B VAL* 4.9 12.8 - - + -
429B ILE* 3.5 30.7 - - + -
430B THR 3.1 16.2 - - - +
431B CYS* 2.7 14.9 + - - -
433B HIS* 1.3 75.5 - - - +
435B ILE* 1.3 61.5 + - - +
437B ILE* 3.8 7.1 - - - +
438B LEU* 2.9 45.4 + - - +
459B VAL* 5.5 7.1 - - + +
464B MET* 4.3 12.3 - - - +
479B VAL* 3.5 11.7 - - + -
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B CYS 3.0 6.8 + - - +
432B GLY* 3.3 11.7 - - - +
433B HIS 3.1 0.2 - - - -
434B THR* 1.3 85.3 + - - +
436B GLU* 1.3 65.1 + - + +
438B LEU* 4.0 1.0 - - + +
439B ARG* 3.0 46.2 + - - +
461B LEU* 4.3 8.7 - - + -
464B MET* 3.6 29.2 - - + -
465B LEU* 4.0 22.0 - - + -
468B LEU* 3.4 33.2 - - + -
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Residues in contact with GLU 436 (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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432B GLY 2.9 20.8 + - - +
433B HIS* 3.0 25.5 + - + +
435B ILE* 1.3 79.8 - - + +
437B ILE* 1.3 58.0 + - + +
439B ARG* 4.0 3.1 - - - +
440B GLU* 2.9 38.0 + - - +
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Residues in contact with ILE 437 (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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423B LEU* 3.7 29.2 - - + -
425B VAL* 5.6 10.5 - - + -
429B ILE* 6.0 2.9 - - + -
433B HIS* 2.9 47.3 + - + +
434B THR* 3.8 6.7 - - - +
436B GLU* 1.3 75.0 - - + +
438B LEU* 1.3 62.4 + - + +
440B GLU* 3.3 6.4 + - - +
441B LYS* 2.9 35.0 + - + +
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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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423B LEU* 5.6 6.1 - - + -
425B VAL* 6.1 2.2 - - + -
434B THR* 2.9 31.7 + - - +
435B ILE* 4.0 2.5 - - - +
437B ILE* 1.3 83.4 - - + +
439B ARG* 1.3 61.3 + - - +
441B LYS* 5.1 0.2 - - - -
442B GLY* 3.1 2.1 + - - -
443B PHE* 3.0 62.1 + - + +
445B GLN* 4.0 25.6 - - - +
446B ALA* 4.2 14.1 - - + +
459B VAL* 4.9 4.7 - - + +
460B THR 4.7 2.7 - - - -
461B LEU* 4.2 36.3 - - + +
464B MET* 5.9 1.6 - - + -
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Residues in contact with ARG 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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435B ILE* 3.0 36.0 + - - +
436B GLU* 4.1 2.9 - - - +
438B LEU* 1.3 77.6 - - - +
440B GLU* 1.3 65.1 + - - +
442B GLY* 3.1 12.6 + - - -
443B PHE 5.0 0.4 - - - -
461B LEU* 4.1 26.5 - - + +
465B LEU* 3.2 31.7 - - - +
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Residues in contact with GLU 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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436B GLU* 2.9 24.1 + - - +
437B ILE* 3.9 5.7 - - - +
439B ARG* 1.3 77.6 - - - +
441B LYS* 1.3 66.7 + - + +
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Residues in contact with LYS 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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423B LEU* 4.1 20.9 - - + -
437B ILE* 2.9 22.2 + - + +
438B LEU 4.6 0.2 - - - +
440B GLU* 1.3 85.2 - - + +
442B GLY* 1.3 62.3 + - - +
443B PHE* 3.2 35.1 - - + +
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU 3.1 6.0 + - - -
439B ARG* 3.1 11.3 + - - -
440B GLU 3.4 0.6 - - - -
441B LYS* 1.3 78.4 - - - +
443B PHE* 1.3 63.6 + - - +
444B ASN 4.1 0.2 + - - -
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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