Contacts of the helix formed by residues 434 - 446 (chain B) in PDB entry 5OIV
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 GLN 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.4 0.2 - - - -
31B ALA* 3.5 15.6 + - - +
32B ALA* 3.5 6.5 - - - +
36B TYR* 3.7 8.9 - - - -
417B PHE* 2.9 16.8 + - - +
419B GLU* 3.7 32.2 - - - +
431B SER* 3.5 24.7 - - - +
432B MET 3.2 0.4 - - - -
433B GLN* 1.3 75.3 - - - +
435B SER* 1.3 67.0 + - - +
436B TRP* 3.6 33.0 - - + +
437B THR* 3.0 15.3 + - - +
438B ALA* 3.2 11.8 + - - +
502B GOL 2.9 27.7 + - - -
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Residues in contact with SER 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.0 9.9 - - - -
20B LEU* 3.6 20.0 - - - +
23B ASN* 2.8 24.3 + - - +
29B THR* 3.8 1.5 - - - +
30B THR 2.7 28.0 + - - -
31B ALA* 2.9 14.5 + - - -
43B ALA* 6.3 0.4 - - - -
47B VAL* 3.8 14.6 - - - -
433B GLN 3.5 1.2 + - - -
434B GLN* 1.3 71.4 - - - +
436B TRP* 1.4 58.4 + - - +
438B ALA* 3.2 2.3 + - - +
439B ALA* 2.9 26.9 + - - +
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Residues in contact with TRP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 4.7 0.4 + - - +
42B TRP* 3.4 51.4 - + - -
43B ALA* 3.7 21.5 - - + +
46B PHE* 3.6 36.7 - + + +
47B VAL* 4.8 2.2 - - - +
180B GLY 5.5 0.4 - - - -
376B TRP* 5.2 2.0 - + - -
381B TRP* 3.9 25.0 - + - -
383B VAL* 3.6 41.2 - - + +
419B GLU 4.6 3.2 + - - -
434B GLN* 3.4 26.3 - - + +
435B SER* 1.4 78.6 - - - +
437B THR* 1.3 69.7 + - - +
439B ALA* 3.7 8.8 - - - +
440B ALA* 3.0 26.7 + - - +
502B GOL 3.8 22.7 - - - -
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Residues in contact with THR 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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382B PRO* 3.9 29.7 - - + +
412B ALA* 5.3 4.7 - - + -
417B PHE* 3.7 24.7 - - + -
418B ALA 2.7 31.0 + - - +
419B GLU* 4.2 1.9 + - - -
421B TYR* 4.9 3.4 - - - +
434B GLN* 3.0 11.1 + - - +
436B TRP* 1.3 88.5 + - - +
438B ALA* 1.3 65.0 + - - +
440B ALA* 3.3 3.2 + - - +
441B VAL* 3.1 27.7 + - + +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.7 20.0 - - + +
19B LEU* 3.6 30.3 - - + -
20B LEU* 4.3 4.0 - - + -
417B PHE* 3.6 23.1 - - + -
434B GLN 3.2 3.2 + - - +
435B SER 3.2 4.6 + - - +
437B THR* 1.3 78.1 - - - +
439B ALA* 1.3 59.0 + - - +
441B VAL* 3.2 2.9 + - - +
442B LEU* 2.9 33.9 + - - +
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Residues in contact with ALA 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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20B LEU* 4.5 5.1 - - + +
46B PHE* 3.2 34.8 - - + +
47B VAL* 4.3 3.4 - - - -
49B ILE* 4.9 1.7 - - + +
50B GLY* 3.6 20.5 - - - -
435B SER 2.9 17.1 + - - +
436B TRP* 3.7 6.7 - - - +
437B THR 3.2 0.2 - - - -
438B ALA* 1.3 77.9 - - - +
440B ALA* 1.3 62.9 + - - +
442B LEU* 3.2 2.1 + - - +
443B ASP* 2.9 26.0 + - - +
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Residues in contact with ALA 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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49B ILE* 6.3 0.2 - - - -
382B PRO* 4.3 9.0 - - + +
383B VAL* 5.4 0.9 - - - -
386B TRP* 3.8 35.6 - - + +
436B TRP 3.0 17.6 + - - +
437B THR* 3.3 7.6 + - - +
439B ALA* 1.3 74.5 - - - +
441B VAL* 1.3 63.9 + - - +
443B ASP* 3.3 1.8 + - - +
444B TRP* 2.9 43.3 + - + -
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Residues in contact with VAL 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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12B LEU* 3.7 20.9 - - + -
16B ALA* 4.3 7.0 - - + -
409B LEU* 4.2 2.5 - - + -
412B ALA* 3.6 30.1 - - + -
417B PHE* 4.0 17.9 - - + -
437B THR* 3.1 15.3 + - + +
438B ALA 3.2 6.7 + - - +
440B ALA* 1.3 76.4 - - - +
442B LEU* 1.3 59.7 + - - +
444B TRP* 3.3 15.5 + - + +
445B LEU* 2.9 54.3 + - + +
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Residues in contact with LEU 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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13B ALA* 3.7 30.7 - - + +
16B ALA* 3.7 8.5 - - + -
17B ALA* 3.9 16.4 - - + +
20B LEU* 3.6 31.0 - - + -
50B GLY* 3.6 17.7 - - - +
53B PRO* 4.3 15.6 - - + +
54B LEU* 4.0 25.1 - - + -
438B ALA 2.9 17.4 + - - +
439B ALA 3.7 3.6 - - - +
441B VAL* 1.3 79.5 - - - +
443B ASP* 1.3 63.4 + - - +
445B LEU* 3.7 9.6 + - + +
446B GLY* 3.7 8.7 + - - +
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Residues in contact with ASP 443 (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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502A GOL 5.3 1.2 + - - -
49B ILE* 3.6 22.3 - - + +
50B GLY* 5.1 0.4 - - - -
53B PRO* 5.0 4.0 - - - +
125B ARG* 2.9 42.1 + - - +
129B HIS* 4.7 2.1 + - - -
386B TRP* 2.7 41.3 + - - +
390B TRP* 5.4 1.4 - - - -
439B ALA 2.9 16.2 + - - +
440B ALA 3.8 0.2 - - - +
442B LEU* 1.3 78.3 - - - +
444B TRP* 1.3 66.8 + - - +
446B GLY* 3.6 8.8 + - - -
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Residues in contact with TRP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 4.2 10.5 - - + -
385B THR* 3.6 30.7 - - + -
386B TRP* 3.3 39.5 - + + -
389B SER* 3.3 19.9 + - - -
405B ARG* 2.5 71.1 + - + +
408B GLY* 3.7 25.6 - - - -
409B LEU* 3.8 25.8 - - + -
412B ALA* 5.3 0.7 - - + -
440B ALA* 2.9 35.0 + - + +
441B VAL* 3.7 10.1 - - + +
443B ASP* 1.3 80.9 - - - +
445B LEU* 1.3 57.8 + - - +
446B GLY* 3.2 0.9 + - - -
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Residues in contact with LEU 445 (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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9B PRO* 3.5 46.0 - - + +
12B LEU* 4.2 6.7 - - + -
13B ALA* 3.6 27.4 - - + +
405B ARG* 3.8 10.5 + - - +
409B LEU* 3.8 26.7 - - + -
441B VAL* 2.9 34.8 + - + +
442B LEU* 3.7 3.3 + - - +
443B ASP 3.5 0.4 - - - -
444B TRP* 1.3 77.4 - - - +
446B GLY* 1.3 70.1 + - - +
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Residues in contact with GLY 446 (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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502A GOL 4.5 21.2 + - - -
13B ALA* 5.9 1.7 - - - +
53B PRO* 6.5 1.3 - - - -
129B HIS* 6.5 0.4 - - - -
442B LEU 3.7 7.0 + - - +
443B ASP 3.6 10.2 + - - -
444B TRP 3.1 4.8 - - - -
445B LEU* 1.3 88.5 - - - +
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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