Contacts of the helix formed by residues 416 - 433 (chain C) in PDB entry 2VK8
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 GLY 416 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.8 1.9 - - - -
387C GLU* 2.9 11.6 + - - -
415C ILE* 1.3 73.6 - - - +
417C PHE* 1.3 65.2 + - - +
418C THR 3.0 3.7 + - - -
419C THR* 3.2 6.7 + - - -
420C GLY 4.0 0.2 + - - -
446C SER* 3.6 17.9 - - - -
449C LEU* 4.3 1.3 - - - -
450C THR* 2.8 44.6 + - - +
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Residues in contact with PHE 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.5 39.0 - + + +
59C ASP* 3.5 40.8 - - + -
63C ARG* 4.1 9.9 - - - -
387C GLU* 4.3 2.7 - - - +
407C ILE* 3.9 19.1 - - + -
409C GLN* 3.5 48.2 - - + +
414C SER 3.0 20.4 + - - +
415C ILE 3.3 1.0 + - - -
416C GLY* 1.3 75.9 - - - +
418C THR* 1.3 72.2 + - + +
420C GLY 3.2 4.0 + - - -
421C ALA* 2.9 45.9 + - + -
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Residues in contact with THR 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ILE* 3.6 19.1 - - + -
386C ALA 3.9 4.5 - - - +
387C GLU* 2.7 52.9 + - - +
407C ILE 5.5 0.2 - - - +
409C GLN 6.2 0.4 - - - +
417C PHE* 1.3 87.0 - - + +
419C THR* 1.3 61.3 + - - +
421C ALA* 3.7 6.7 - - - -
422C THR* 2.7 35.0 + - - -
440C LEU* 3.5 19.4 - - - +
442C ILE* 3.4 13.7 - - - +
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Residues in contact with THR 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLY 3.2 2.0 + - - -
418C THR* 1.3 79.1 + - - +
420C GLY* 1.3 62.3 + - - +
422C THR* 4.6 0.2 - - - -
423C LEU* 3.4 5.9 + - - +
440C LEU* 4.5 10.5 - - + -
442C ILE* 3.2 20.1 - - - +
447C LEU* 4.1 11.5 - - + +
450C THR* 2.8 43.7 + - - +
451C VAL 4.6 0.2 - - - +
453C GLU* 4.2 6.8 - - + +
454C ILE* 4.1 17.9 - - + -
457C MET* 3.2 38.4 - - + +
466C LEU* 6.3 0.2 - - + -
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Residues in contact with GLY 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN* 3.9 12.1 - - - -
56C TYR* 3.8 15.1 - - - -
57C ALA* 3.1 24.1 - - - +
416C GLY 4.0 2.6 + - - -
417C PHE 3.2 6.7 + - - -
419C THR* 1.3 77.7 - - - +
421C ALA* 1.3 65.2 + - - +
423C LEU* 3.0 11.6 + - - +
424C GLY 3.1 2.6 + - - -
450C THR* 5.0 1.0 - - - -
453C GLU* 4.5 11.5 - - - +
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR 3.5 11.4 + - - +
60C GLY* 3.8 12.5 - - - -
385C ILE* 4.2 11.4 - - + -
407C ILE* 4.8 3.6 - - + -
417C PHE* 2.9 48.1 + - + +
418C THR* 4.0 6.1 - - - +
420C GLY* 1.3 74.8 - - - +
422C THR* 1.3 52.7 + - - +
424C GLY* 3.3 0.5 + - - -
425C ALA* 2.8 37.1 + - - +
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Residues in contact with THR 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ILE* 3.6 16.6 - - - +
418C THR 2.7 24.1 + - - -
419C THR 3.7 5.2 - - - -
421C ALA* 1.3 74.6 - - - +
423C LEU* 1.3 58.6 + - - +
425C ALA* 3.8 0.7 - - - +
426C ALA* 2.9 32.7 + - - +
438C VAL* 4.0 10.1 - - + +
440C LEU* 3.4 25.9 - - + +
457C MET* 4.0 13.5 - - + -
464C PRO* 3.7 29.6 - - + -
466C LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 4.4 0.7 - - + -
48C ASN* 3.2 30.7 - - - +
57C ALA* 4.0 8.5 - - + -
419C THR 3.4 9.5 + - - +
420C GLY 3.0 8.6 + - - +
422C THR* 1.3 78.1 - - - +
424C GLY* 1.3 62.1 + - - +
426C ALA* 3.2 5.8 + - - +
427C PHE* 3.0 53.2 + - + -
453C GLU* 3.8 14.8 - - + -
456C THR* 3.7 15.0 - - + -
457C MET* 3.6 41.6 - - + +
462C LEU* 3.6 13.5 - - + -
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Residues in contact with GLY 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.9 14.8 - - - -
57C ALA* 3.2 25.7 - - - +
61C TYR* 3.5 19.0 - - - -
420C GLY 3.1 10.1 + - - -
421C ALA 3.7 1.1 - - - -
423C LEU* 1.3 76.6 - - - +
425C ALA* 1.3 62.3 + - - +
427C PHE 3.3 1.4 + - - -
428C ALA 3.0 18.2 + - - -
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLY 3.8 11.2 - - - +
64C ILE* 3.8 22.5 - - + +
383C VAL* 4.2 9.6 - - + -
385C ILE* 3.9 20.4 - - + -
407C ILE* 4.4 2.9 - - + -
421C ALA 2.8 21.2 + - - +
422C THR 3.9 1.6 - - - +
424C GLY* 1.3 71.7 - - - +
426C ALA* 1.3 56.2 + - - +
428C ALA* 3.4 1.8 + - - +
429C ALA* 2.8 32.4 + - - +
438C VAL* 4.2 5.8 - - + -
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C THR 2.9 19.6 + - - +
423C LEU* 3.2 4.7 + - - +
425C ALA* 1.3 74.1 - - - +
427C PHE* 1.3 60.3 + - - +
429C ALA* 3.9 0.5 - - - +
430C GLU* 3.0 30.3 + - - +
438C VAL* 3.8 21.3 - - + +
457C MET* 6.1 0.2 - - + -
462C LEU* 3.9 27.0 - - + +
463C LYS 5.3 1.1 - - - +
464C PRO* 4.8 11.2 - - + -
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Residues in contact with PHE 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 3.8 14.8 - - + +
23C PHE* 3.5 26.5 - + - -
44C ARG* 3.4 35.4 + - - +
46C ALA* 3.8 14.8 - - + -
61C TYR* 3.9 6.3 - - + -
423C LEU* 3.0 45.4 + - + -
424C GLY 3.6 5.8 - - - +
426C ALA* 1.3 74.4 - - - +
428C ALA* 1.3 63.1 + - - +
430C GLU* 3.3 4.0 + - - +
431C GLU* 3.1 28.6 + - - +
456C THR* 4.7 0.4 - - + -
460C TRP* 3.5 45.8 - + + -
462C LEU* 3.8 17.6 - - + +
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 3.7 22.9 - - + +
64C ILE* 3.7 27.8 - - + -
65C LYS* 3.9 18.5 - - + +
424C GLY 3.0 13.7 + - - +
425C ALA 3.8 0.2 - - - +
427C PHE* 1.3 78.7 - - - +
429C ALA* 1.3 62.3 + - - +
431C GLU* 3.1 5.5 + - - +
432C ILE* 3.0 28.0 + - - +
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.2 5.3 - - + +
383C VAL* 4.8 3.4 - - + -
425C ALA 2.8 22.1 + - - +
426C ALA 3.9 3.1 - - - +
428C ALA* 1.3 70.5 - - - +
430C GLU* 1.3 57.0 + - - +
432C ILE* 3.1 6.1 + - - +
433C ASP 2.8 40.3 + - - +
436C LYS* 4.2 31.0 - - + +
438C VAL* 3.9 19.1 - - + -
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Residues in contact with GLU 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 2.7 42.7 + - - -
426C ALA 3.0 19.4 + - - +
427C PHE 3.5 2.9 - - - +
428C ALA 3.3 0.2 - - - -
429C ALA* 1.3 76.7 - - - +
431C GLU* 1.3 61.1 + - - +
434C PRO* 3.7 38.6 - - + +
460C TRP 4.5 7.3 - - - +
461C GLY 5.1 2.9 - - - +
462C LEU* 3.9 18.1 - - + +
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Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASN* 3.8 16.3 - - + +
21C THR* 2.7 28.9 + - - -
44C ARG* 3.0 18.4 + - - +
61C TYR* 2.5 29.0 + - - -
65C LYS* 2.9 23.7 + - - +
427C PHE 3.1 13.3 + - - +
428C ALA 3.1 6.0 + - - +
430C GLU* 1.3 76.9 - - - +
432C ILE* 1.3 62.5 + - - +
434C PRO* 5.7 0.3 - - - +
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Residues in contact with ILE 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.7 35.7 - - + +
65C LYS* 4.3 18.4 - - + -
428C ALA 3.0 17.8 + - - +
429C ALA* 3.7 5.8 - - - +
431C GLU* 1.3 79.9 - - - +
433C ASP* 1.3 63.1 + - + +
434C PRO* 4.6 1.0 - - - +
436C LYS* 3.9 23.1 - - + -
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Residues in contact with ASP 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ALA 2.8 22.3 + - - +
431C GLU 3.7 0.8 - - - -
432C ILE* 1.3 80.2 - - + +
434C PRO* 1.3 68.1 - - - +
435C LYS* 2.9 26.6 + - - +
436C LYS* 2.9 45.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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