Contacts of the helix formed by residues 416 - 429 (chain C) in PDB entry 2VF7
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 ASP 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366C LEU 5.3 5.6 - - - +
367C GLY* 5.5 9.6 - - - -
412C LEU* 3.6 29.5 - - + +
413C HIS* 3.2 12.4 + - - +
415C ALA* 1.3 89.7 - - - +
417C THR* 1.3 61.7 + - - +
418C GLU 3.3 2.7 - - - -
419C ALA* 3.3 15.8 + - + +
420C LEU 3.3 15.6 + - - -
531C VAL* 3.8 28.3 - - - +
532C SER* 4.7 4.0 + - - -
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Residues in contact with THR 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C LEU* 4.1 15.4 + - + +
413C HIS 3.8 3.3 + - - -
414C PRO* 3.5 27.1 - - - +
415C ALA 3.4 1.6 - - - -
416C ASP* 1.3 74.2 - - - +
418C GLU* 1.3 67.4 + - + +
420C LEU* 3.3 4.2 + - - +
421C LEU* 3.1 38.4 + - + +
440C ASP* 4.6 10.3 + - - +
442C ASP* 4.3 23.2 - - + +
443C VAL* 4.3 13.0 - - + +
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Residues in contact with GLU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C PRO 4.9 0.8 + - - -
415C ALA 4.8 5.5 + - - +
416C ASP* 3.3 0.8 - - - +
417C THR* 1.3 80.5 - - + +
419C ALA* 1.3 54.0 + - - +
421C LEU* 3.4 7.6 + - - +
422C SER* 2.8 41.6 + - - +
446C ARG* 2.8 41.9 + - - -
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Residues in contact with ALA 419 (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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365C HIS* 3.5 34.5 - - + +
366C LEU* 4.2 14.0 - - - +
415C ALA 5.5 0.4 + - - -
416C ASP* 3.3 19.6 + - + +
417C THR 3.3 0.6 - - - -
418C GLU* 1.3 77.7 - - - +
420C LEU* 1.3 61.4 + - - +
422C SER* 3.6 6.9 + - - -
423C ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 420 (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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366C LEU* 4.3 11.1 - - + +
387C ARG* 4.8 9.0 - - + -
390C LEU* 3.7 27.8 - - + -
408C PRO* 4.0 37.7 - - + +
409C SER* 4.2 6.3 - - - +
412C LEU* 3.8 29.4 - - + -
416C ASP 3.3 1.6 + - - -
417C THR* 3.3 7.9 + - - +
418C GLU 3.2 0.6 - - - -
419C ALA* 1.3 79.2 - - - +
421C LEU* 1.3 57.6 - - - +
423C ALA* 3.0 5.9 + - - +
424C LEU* 2.9 38.0 + - + +
443C VAL* 4.4 21.5 - - + -
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.3 15.7 - - + +
417C THR* 3.1 29.5 + - + +
418C GLU* 3.7 13.2 - - - +
420C LEU* 1.3 74.5 - - + +
422C SER* 1.3 57.0 + - - +
424C LEU* 3.6 9.4 + - + +
425C GLU* 3.0 26.2 + - - +
442C ASP 3.9 11.4 - - - +
443C VAL* 4.0 29.8 - - + -
446C ARG* 3.7 59.5 - - + +
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Residues in contact with SER 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C HIS* 5.4 9.6 + - - -
418C GLU* 2.8 23.1 + - - +
419C ALA* 3.8 7.5 - - - -
420C LEU 3.2 0.2 - - - -
421C LEU* 1.3 73.5 - - - +
423C ALA* 1.3 60.1 + - - +
425C GLU* 3.3 8.4 + - - +
426C ASN* 3.1 37.1 + - - +
446C ARG* 5.8 0.7 + - - -
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Residues in contact with ALA 423 (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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366C LEU* 3.6 33.2 - - + -
390C LEU* 4.2 10.3 - - + -
394C LEU* 3.6 22.5 - - + +
419C ALA 3.2 12.3 + - - +
420C LEU* 3.0 9.3 + - - +
422C SER* 1.3 75.6 - - - +
424C LEU* 1.3 63.9 + - - +
426C ASN* 3.4 4.3 + - - +
427C LEU* 3.2 21.3 + - - +
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Residues in contact with LEU 424 (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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38C LEU* 3.7 30.7 - - + -
390C LEU* 4.1 22.9 - - + -
405C LEU* 4.1 28.3 - - + -
408C PRO* 4.9 6.5 - - + -
420C LEU* 2.9 32.6 + - + +
421C LEU* 3.8 14.8 - - + +
423C ALA* 1.3 75.7 - - - +
425C GLU* 1.3 61.7 + - - +
427C LEU* 3.5 6.4 + - + +
428C LYS* 3.2 17.7 + - - +
434C LEU* 3.2 26.4 - - + +
436C VAL* 4.6 7.4 - - + -
443C VAL* 4.8 8.7 - - + -
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Residues in contact with GLU 425 (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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421C LEU 3.0 15.8 + - - +
422C SER* 3.4 13.2 - - - +
423C ALA 3.2 0.2 - - - -
424C LEU* 1.3 76.6 - - - +
426C ASN* 1.3 56.2 + - - +
428C LYS* 3.3 29.4 + - - +
429C ARG* 3.1 68.9 + - - +
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Residues in contact with ASN 426 (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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394C LEU* 3.7 22.2 - - + +
422C SER* 3.1 22.8 + - - +
423C ALA* 3.8 4.1 - - - +
424C LEU 3.4 0.2 - - - -
425C GLU* 1.3 72.1 - - - +
427C LEU* 1.3 65.3 + - - +
429C ARG* 3.2 29.5 + - - +
430C GLY* 3.1 18.9 + - - -
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Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 5.0 4.3 - - + -
390C LEU* 4.0 23.1 - - + -
393C GLN* 3.9 26.7 - - + +
394C LEU* 3.5 18.0 - - + +
403C TYR* 3.7 48.2 - - + +
405C LEU* 5.3 0.9 - - + -
423C ALA 3.2 8.3 + - - +
424C LEU* 3.5 15.5 - - + +
426C ASN* 1.3 71.6 - - - +
428C LYS* 1.3 66.6 - - - +
430C GLY* 3.4 7.4 + - - -
432C ASN* 3.3 28.9 + - - +
434C LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 4.0 12.8 + - - +
37C ALA* 3.8 14.4 - - - +
38C LEU* 3.8 23.3 - - + +
424C LEU 3.2 10.3 + - - +
425C GLU* 3.3 32.6 + - - +
427C LEU* 1.3 79.5 - - - +
429C ARG* 1.3 68.5 + - - +
431C GLY* 3.1 17.8 + - - -
432C ASN* 3.1 29.2 + - - +
434C LEU* 4.2 8.7 - - + +
448C ASP* 3.1 21.9 + - - +
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Residues in contact with ARG 429 (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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425C GLU* 3.1 48.1 + - - +
426C ASN* 3.2 28.5 + - - +
428C LYS* 1.3 85.0 - - - +
430C GLY* 1.3 55.8 + - - +
431C GLY 3.3 4.4 + - - -
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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