Contacts of the helix formed by residues 433 - 443 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304C GLU* 3.4 16.4 - - - +
367C LYS* 3.6 17.7 - - - +
370C VAL* 4.8 1.1 - - - -
432C PRO* 1.3 77.2 - - - +
434C PHE* 1.3 63.1 + - - +
435C LYS* 3.4 10.4 + - - +
436C ALA* 3.1 23.9 + - + +
437C LEU* 3.1 22.7 + - - +
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Residues in contact with PHE 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ALA* 4.5 8.4 - - - +
300C MET* 3.4 57.0 - - + -
301C CYS* 3.3 25.1 - - - +
304C GLU* 2.7 17.9 + - + +
313C LEU* 4.4 0.4 - - + -
366C THR* 3.6 32.8 - - + -
369C ASP* 3.7 12.1 - - + -
370C VAL* 3.7 25.5 - - + +
373C PHE* 3.6 29.2 - + + -
432C PRO 4.1 0.2 + - - -
433C THR* 1.3 72.0 - - - +
435C LYS* 1.3 52.1 + - - +
437C LEU* 3.3 16.4 + - + +
438C ARG* 2.8 31.0 + - - +
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Residues in contact with LYS 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C CYS* 3.6 10.0 - - - -
304C GLU* 3.2 13.9 + - - +
433C THR* 3.5 10.1 - - - +
434C PHE* 1.3 77.3 - - - +
436C ALA* 1.3 60.4 + - - +
438C ARG* 3.4 12.9 + - - +
439C GLU* 2.9 46.8 + - + +
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Residues in contact with ALA 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C PRO* 4.3 10.5 - - + -
433C THR* 3.1 26.9 + - + +
435C LYS* 1.3 73.9 - - - +
437C LEU* 1.3 57.8 + - - +
439C GLU* 3.4 7.5 + - - +
440C ARG* 2.9 32.2 + - - +
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ALA* 4.6 2.5 - - + -
370C VAL* 4.2 14.6 - - + -
373C PHE* 3.8 31.2 - - + -
419C LEU* 3.6 33.4 - - + +
423C CYS* 3.8 13.2 - - - -
432C PRO* 3.6 23.8 - - + +
433C THR 3.1 19.4 + - - +
434C PHE* 3.5 21.8 - - + +
436C ALA* 1.3 74.4 - - - +
438C ARG* 1.3 59.7 + - - +
440C ARG* 4.1 3.5 - - - +
441C LEU* 2.9 37.5 + - + +
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Residues in contact with ARG 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C HIS* 6.0 1.2 + - - -
294C TRP* 3.4 26.5 - - + +
297C ALA* 3.9 14.8 - - + +
298C GLU* 2.6 35.0 + - - +
301C CYS* 3.5 33.7 - - - +
434C PHE 2.8 21.2 + - - +
435C LYS* 3.6 17.6 - - - +
436C ALA 3.3 0.2 - - - -
437C LEU* 1.3 73.2 - - - +
439C GLU* 1.3 93.2 + - - +
441C LEU* 4.7 0.4 - - - -
442C SER* 2.9 29.3 + - - -
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C LYS* 2.9 29.9 + - + +
436C ALA* 3.8 6.3 - - - +
438C ARG* 1.3 114.9 + - - +
440C ARG* 1.3 59.8 + - - +
442C SER* 3.1 24.2 - - - -
443C SER* 3.9 6.8 + - - -
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Residues in contact with ARG 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C SER* 2.6 33.9 + - - +
419C LEU* 3.7 25.1 - - + +
436C ALA 2.9 18.7 + - - +
437C LEU* 4.1 3.1 - - - +
439C GLU* 1.3 76.3 - - - +
441C LEU* 1.3 62.6 + - - +
443C SER* 3.5 23.5 + - - -
444C PHE* 3.3 30.8 - - + -
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LEU* 5.2 4.6 - - + +
293C ALA* 3.8 30.7 - - + +
294C TRP* 4.5 11.0 - - + +
297C ALA* 4.1 5.8 - - + -
373C PHE* 3.6 35.7 - - + -
377C LEU* 4.7 1.8 - - + -
416C VAL* 4.7 15.0 - - + -
419C LEU* 3.8 26.5 - - + -
437C LEU 2.9 21.2 + - - +
438C ARG 4.1 2.9 - - - +
440C ARG* 1.3 72.9 - - - +
442C SER* 1.3 58.3 + - - +
443C SER 3.1 0.9 - - - -
444C PHE* 2.9 36.8 + - + +
445C THR* 3.3 13.7 - - + +
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Residues in contact with SER 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C TRP* 3.8 17.1 + - - -
438C ARG* 2.9 15.8 + - - -
439C GLU* 3.1 21.8 - - - -
440C ARG 3.2 0.2 - - - -
441C LEU* 1.3 77.1 - - - +
443C SER* 1.3 56.7 + - - +
445C THR* 2.6 25.0 + - - -
447C HIS* 4.1 14.2 + - - -
448C HIS* 3.6 15.5 + - - +
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Residues in contact with SER 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C GLU 3.9 6.1 + - - -
440C ARG* 3.5 23.0 + - - -
441C LEU 3.1 0.6 - - - -
442C SER* 1.3 78.6 - - - +
444C PHE* 1.3 71.1 + - - +
445C THR 3.3 1.1 + - - +
448C HIS* 3.6 42.4 + - - +
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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