Contacts of the helix formed by residues 433 - 442 (chain B) in PDB entry 5H2U
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 433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B GLU* 3.4 18.6 - - - +
367B LYS* 3.7 22.9 - - - +
370B VAL* 4.7 0.4 - - - -
432B PRO* 1.3 77.2 - - - +
434B PHE* 1.3 60.4 + - - +
435B LYS* 3.7 6.7 + - - +
436B ALA* 3.2 21.9 + - - +
437B LEU* 2.9 28.5 + - - +
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Residues in contact with PHE 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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297B ALA* 4.5 8.3 - - - +
300B MET* 3.5 50.9 - - + -
301B CYS* 2.9 31.5 - - - +
304B GLU* 2.7 30.0 + - - +
313B LEU* 4.3 0.4 - - + -
366B THR* 3.7 20.2 - - + -
369B ASP* 3.5 24.5 - - + -
370B VAL* 3.5 17.3 - - + -
373B PHE* 3.6 30.1 - + + -
433B THR* 1.3 69.8 - - - +
435B LYS* 1.3 63.6 + - - +
437B LEU* 3.8 16.7 - - + +
438B ARG* 3.0 17.8 + - - +
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Residues in contact with LYS 435 (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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361A ARG* 3.8 12.1 - - - +
301B CYS* 3.5 11.3 - - - -
304B GLU* 3.0 12.9 + - - +
433B THR* 3.2 9.4 - - - +
434B PHE* 1.3 76.0 - - - +
436B ALA* 1.3 62.3 + - - +
438B ARG* 3.5 19.1 + - - +
439B GLU* 2.9 56.0 + - - +
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Residues in contact with ALA 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 PRO* 4.3 2.5 - - + -
433B THR* 3.2 25.3 + - - +
435B LYS* 1.3 77.1 - - - +
437B LEU* 1.3 64.6 + - - +
439B GLU* 3.3 15.2 + - - +
440B ARG* 3.1 52.7 + - - +
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Residues in contact with LEU 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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297B ALA* 5.0 1.1 - - + -
370B VAL* 3.9 22.7 - - + -
373B PHE* 3.8 28.0 - - + -
377B LEU* 5.7 0.4 - - + -
419B LEU* 3.7 28.0 - - + +
423B CYS* 3.7 20.4 - - - -
432B PRO* 3.7 15.7 - - + +
433B THR 2.9 20.7 + - - +
434B PHE* 3.8 27.8 - - + +
436B ALA* 1.3 74.7 - - - +
438B ARG* 1.3 58.2 + - - +
440B ARG* 3.3 7.2 + - - +
441B LEU* 2.9 35.7 + - + +
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Residues in contact with ARG 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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294B TRP* 3.5 25.3 - - + +
297B ALA* 3.9 15.7 - - + +
298B GLU* 3.5 39.3 + - + -
301B CYS* 3.6 30.5 - - - +
434B PHE 3.0 19.1 + - - +
435B LYS* 3.7 27.4 + - - +
437B LEU* 1.3 74.1 - - - +
439B GLU* 1.3 74.7 + - - +
441B LEU* 3.4 2.1 + - - +
442B SER* 3.1 20.4 + - - -
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Residues in contact with GLU 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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361A ARG* 3.0 43.9 + - - +
363A HIS* 5.5 5.9 - - + -
435B LYS* 2.9 47.2 + - - +
436B ALA* 3.5 17.1 - - - +
438B ARG* 1.3 91.4 + - - +
440B ARG* 1.3 63.7 + - + +
442B SER* 3.7 15.3 - - - -
443B SER* 4.1 6.1 + - - -
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Residues in contact with ARG 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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361A ARG* 5.4 3.2 + - - +
363A HIS* 3.2 38.1 + - + -
419B LEU* 3.8 34.3 - - + +
422B THR* 5.3 1.2 + - - -
432B PRO* 4.0 25.1 - - - +
436B ALA* 3.1 32.9 + - - +
437B LEU 3.7 3.8 - - - +
439B GLU* 1.3 75.5 - - + +
441B LEU* 1.3 63.2 + - - +
442B SER 3.1 3.1 + - - -
443B SER* 3.3 15.8 + - - -
444B PHE* 3.3 21.2 - - + -
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Residues in contact with LEU 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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290B LEU* 4.9 5.3 - - + +
293B ALA* 4.1 23.3 - - + +
294B TRP* 4.3 14.1 - - + -
297B ALA* 4.0 12.3 - - + -
373B PHE* 3.7 36.3 - - + -
377B LEU* 4.7 7.0 - - + -
416B VAL* 4.7 14.6 - - + -
419B LEU* 4.0 20.9 - - + -
437B LEU 2.9 21.7 + - - +
438B ARG 3.9 3.6 - - - +
440B ARG* 1.3 74.4 - - - +
442B SER* 1.3 62.5 + - - +
443B SER 3.2 0.2 - - - -
444B PHE* 3.2 27.4 + - + +
445B THR* 3.4 14.7 - - - +
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Residues in contact with SER 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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294B TRP* 3.9 17.3 + - - -
438B ARG 3.1 12.9 + - - -
439B GLU* 3.7 14.6 - - - -
440B ARG 3.1 1.0 - - - -
441B LEU* 1.3 77.0 - - - +
443B SER* 1.3 60.4 + - - +
444B PHE 3.1 0.7 - - - -
445B THR* 2.7 25.7 + - - -
447B HIS* 3.5 7.8 + - - +
448B HIS* 3.1 29.6 + - - -
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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