Contacts of the helix formed by residues 380 - 392 (chain C) in PDB entry 6UZA
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 HIS 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C VAL* 4.4 15.3 - - + +
333C LEU* 3.8 23.3 - - + +
334C ASP* 3.5 38.2 + - + -
376C LYS 3.4 17.0 + - - +
377C PHE 4.0 2.9 - - - +
378C VAL 3.3 1.6 - - - -
379C ALA* 1.3 78.1 - - - +
381C PRO* 1.3 79.8 - - + +
382C ASN* 3.4 48.4 + - + -
383C CYS* 3.0 5.2 + - - +
384C GLN* 3.0 22.3 + - - +
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Residues in contact with PRO 381 (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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379C ALA 4.1 5.2 - - - +
380C HIS* 1.3 100.3 - - + +
382C ASN* 1.3 61.8 + - - +
384C GLN* 3.9 9.3 - - + +
385C GLN* 3.0 32.6 + - - +
313D GLU* 4.5 25.3 - - + +
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Residues in contact with ASN 382 (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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333C LEU* 3.3 37.4 + - + +
334C ASP* 4.5 6.5 + - - +
336C CYS* 4.6 6.9 + - - +
342C VAL* 3.6 8.8 - - + +
346C LEU* 3.4 14.9 - - - +
380C HIS* 3.2 21.4 + - + -
381C PRO* 1.3 79.6 - - - +
383C CYS* 1.3 55.7 + - - +
385C GLN* 3.3 27.8 + - - +
386C GLN 4.1 0.5 + - - -
267D PHE* 3.3 30.5 - - + -
271D ARG* 5.2 3.1 + - - +
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Residues in contact with CYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 4.8 0.2 - - - +
346C LEU* 4.0 15.5 - - + +
366C LEU* 3.7 41.5 - - - -
377C PHE 3.5 22.0 - - - +
378C VAL* 4.0 15.9 - - - +
380C HIS* 3.0 10.6 + - + +
382C ASN* 1.3 77.6 - - - +
384C GLN* 1.3 59.9 + - - +
385C GLN 3.2 1.3 - - - -
386C GLN* 3.2 3.5 + - - +
387C LEU* 3.0 35.0 + - - +
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Residues in contact with GLN 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C VAL 2.9 21.9 - - - +
379C ALA* 4.5 4.7 - - - +
380C HIS 3.0 18.8 + - - +
381C PRO* 3.3 7.8 + - + +
383C CYS* 1.3 76.9 - - - +
385C GLN* 1.3 57.2 + - - +
387C LEU* 4.3 9.9 - - - +
388C LEU* 2.9 46.4 + - + +
743C LYS* 3.6 28.8 + - + +
746C ARG* 3.1 33.8 - - - +
747C ALA* 4.6 5.4 - - - +
750C TRP* 4.3 13.3 - - + -
313D GLU* 5.3 5.4 - - - +
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Residues in contact with GLN 385 (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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339C THR* 5.4 5.1 + - - -
342C VAL* 3.7 18.6 - - - +
381C PRO 3.0 21.0 + - - +
382C ASN* 3.3 23.3 + - - +
384C GLN* 1.3 77.2 - - - +
386C GLN* 1.3 70.0 + - - +
388C LEU* 4.3 7.0 - - - +
389C SER* 3.1 23.0 + - - -
399C ARG* 5.0 3.8 + - - +
267D PHE* 4.1 25.5 - - + -
313D GLU* 5.4 9.3 + - + +
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Residues in contact with GLN 386 (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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342C VAL* 4.7 3.3 - - - +
343C GLU* 4.3 13.9 - - - +
346C LEU* 3.4 31.4 - - + +
347C ASN* 3.3 37.5 + - - +
361C PRO* 3.7 20.5 - - + +
363C LEU* 4.1 10.7 - - - +
366C LEU* 4.3 4.6 - - + +
382C ASN 4.3 0.2 - - - +
383C CYS* 3.2 9.0 + - - +
384C GLN 3.2 0.4 - - - -
385C GLN* 1.3 90.2 + - - +
387C LEU* 1.3 67.7 + - + +
389C SER* 3.3 14.2 + - - -
390C ILE* 3.5 17.1 + - + +
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Residues in contact with LEU 387 (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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363C LEU* 4.4 9.4 - - + -
366C LEU* 3.8 15.7 - - + -
378C VAL* 4.6 2.5 - - + -
383C CYS* 3.0 36.1 + - - +
384C GLN* 3.3 7.2 + - - +
386C GLN* 1.3 75.5 - - + +
388C LEU* 1.3 60.2 + - - +
390C ILE* 3.2 6.8 + - + +
391C TRP* 3.0 27.5 + - - +
747C ALA* 4.2 20.6 - - + -
750C TRP* 3.8 22.6 - - + -
751C PHE* 3.7 37.5 - - + -
754C PHE* 3.9 15.8 - - + -
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Residues in contact with LEU 388 (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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384C GLN* 2.9 29.5 + - + +
385C GLN* 4.6 3.4 - - - +
387C LEU* 1.3 76.3 - - - +
389C SER* 1.3 58.1 + - - +
390C ILE 3.2 0.2 - - - -
391C TRP* 4.1 5.8 - - + -
392C TYR* 2.9 61.2 + - + +
399C ARG* 3.4 25.1 + - - +
746C ARG* 5.6 4.9 - - - +
750C TRP* 3.6 31.9 - - + -
1005C Y01 5.0 2.7 - - - +
313D GLU* 5.8 4.3 - - - +
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Residues in contact with SER 389 (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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385C GLN 3.1 15.4 + - - -
386C GLN* 3.3 11.3 + - - -
387C LEU 3.2 0.6 - - - -
388C LEU* 1.3 80.1 - - - +
390C ILE* 1.3 59.6 + - - +
392C TYR* 4.1 5.0 - - - +
393C GLU* 3.9 17.0 - - - +
399C ARG* 4.6 8.9 + - - +
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Residues in contact with ILE 390 (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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360C ARG* 3.7 46.2 - - + +
361C PRO* 4.3 21.1 - - + -
363C LEU* 3.8 35.0 - - + -
386C GLN* 3.5 17.3 - - + +
387C LEU* 3.2 8.0 + - + +
388C LEU 3.2 0.2 - - - -
389C SER* 1.3 78.4 - - - +
391C TRP* 1.3 66.2 + - - +
392C TYR 3.5 0.2 - - - -
393C GLU* 3.5 12.7 - - - +
439C PRO* 3.4 16.8 - - - +
754C PHE* 3.9 21.8 - - + -
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Residues in contact with TRP 391 (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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387C LEU 3.0 17.1 + - - +
388C LEU* 3.4 11.9 + - + +
390C ILE* 1.3 79.1 - - - +
392C TYR* 1.3 81.3 + + - +
393C GLU 3.2 4.9 + - - -
395C LEU* 5.4 0.3 - - - +
439C PRO* 3.6 29.3 - - + +
440C PHE* 3.4 52.6 + + + +
443C PHE* 3.7 32.3 - + + -
616C ALA* 5.4 0.2 - - + -
749C LEU* 4.4 4.9 - - + -
750C TRP* 3.6 39.5 - + + -
753C TYR* 3.9 23.8 - + + -
754C PHE* 4.0 11.4 - + + -
1005C Y01 3.0 32.5 + - - -
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Residues in contact with TYR 392 (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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388C LEU* 2.9 44.5 + - + +
389C SER* 4.1 7.9 - - - +
391C TRP* 1.3 83.1 - + - +
393C GLU* 1.3 64.4 + - - +
394C ASN 3.7 0.9 - - - -
395C LEU* 3.8 26.9 + - + +
398C LEU 4.3 7.6 - - - -
399C ARG* 3.6 47.1 - - + +
406C LYS* 3.4 19.2 + - - -
440C PHE* 3.7 40.2 - + - -
1005C Y01 2.4 30.0 + - - +
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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