Contacts of the helix formed by residues 416 - 429 (chain C) in PDB entry 3F7F
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
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Residue Dist Surf HB Arom Phob DC
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10C ASN* 6.1 2.0 - - - -
13C GLN* 4.4 25.4 - - - -
412C LYS 3.0 17.0 + - - -
413C SER 4.0 2.3 + - - -
414C ARG 3.7 1.2 - - - -
415C TYR* 1.3 81.5 - - - +
417C THR* 1.3 60.1 + - - -
418C GLN* 3.4 3.4 - - - -
419C ILE 3.3 1.6 + - - -
420C PHE* 3.0 26.9 + - - +
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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
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12C LEU 5.6 2.3 + - - -
13C GLN* 5.1 1.2 + - - +
15C TYR 3.8 15.1 + - - -
16C GLU* 2.8 35.3 + - - +
18C PRO* 3.2 22.9 - - + -
412C LYS* 3.7 19.5 + - - +
416C GLY* 1.3 69.1 - - - -
418C GLN* 1.3 67.3 + - - +
420C PHE* 4.4 6.1 - - - -
421C GLU* 3.0 42.3 + - + +
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Residues in contact with GLN 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASN* 3.0 34.9 + - - +
12C LEU* 5.0 6.8 + - + +
18C PRO* 3.4 30.9 + - + +
416C GLY 3.4 1.6 + - - -
417C THR* 1.3 78.9 - - - +
419C ILE* 1.3 59.5 + - - +
421C GLU* 4.2 1.0 - - - +
422C ARG* 3.3 20.8 + - - +
457C PHE* 3.4 17.9 - - + -
477C GLN* 3.5 17.3 - - - +
478C PRO* 3.2 22.4 + - - +
479C TYR* 3.8 16.1 - - - +
480C ASN* 3.2 9.9 + - - -
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Residues in contact with ILE 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASN* 4.5 15.0 - - + +
415C TYR* 3.6 38.1 - - + +
416C GLY 3.3 6.3 + - - +
417C THR 3.2 0.2 - - - -
418C GLN* 1.3 74.7 - - - +
420C PHE* 1.3 69.1 + - - +
422C ARG* 3.0 5.0 + - - +
423C ALA* 2.9 20.3 + - - +
450C LEU* 4.1 17.0 - - + +
453C VAL* 3.9 15.0 - - + +
454C LYS* 3.8 32.8 - - + +
457C PHE* 3.6 30.7 - - + -
480C ASN* 4.7 2.5 - - - +
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Residues in contact with PHE 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 3.6 36.1 - + - -
411C LEU* 4.2 10.3 - - + -
412C LYS* 3.7 60.1 - - + -
415C TYR* 4.6 1.3 - - + +
416C GLY 3.0 20.9 + - - +
417C THR* 4.0 4.7 - - - +
419C ILE* 1.3 76.4 - - - +
421C GLU* 1.3 63.3 + - + +
423C ALA* 3.1 5.5 + - - +
424C GLN* 3.0 49.1 + - - +
446C LEU* 3.9 20.2 - - + -
450C LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU 5.0 0.5 - - - +
17C LYS* 4.9 6.3 + - - -
18C PRO* 3.2 25.5 - - + +
412C LYS* 5.0 6.9 + - - +
417C THR* 3.0 33.7 + - + +
418C GLN 4.4 1.8 - - - +
420C PHE* 1.3 84.1 - - + +
422C ARG* 1.3 60.6 + - - +
424C GLN* 3.4 10.4 + - - +
425C GLN* 3.1 22.2 + - - +
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Residues in contact with ARG 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLN 3.3 19.1 + - - +
419C ILE 3.0 5.6 + - - +
421C GLU* 1.3 76.7 - - - +
423C ALA* 1.3 58.7 + - - +
425C GLN* 3.3 27.5 + - - +
426C ILE* 3.2 40.4 + - - +
453C VAL* 3.7 20.3 - - + +
457C PHE* 3.9 28.8 - - + -
477C GLN* 5.0 7.7 + - - +
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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
----------------------------------------------------------
419C ILE 2.9 7.5 + - - +
420C PHE 3.4 8.5 - - - +
422C ARG* 1.3 75.1 - - - +
424C GLN* 1.3 60.4 + - - +
425C GLN 3.0 4.7 - - - -
426C ILE 3.5 1.7 + - - -
427C LEU* 3.1 27.9 + - - +
446C LEU* 4.0 6.5 - - + -
449C ILE* 3.4 30.4 - - + +
450C LEU* 3.5 30.1 - - + +
453C VAL* 4.2 3.8 - - + +
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Residues in contact with GLN 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 3.3 30.1 - - - -
420C PHE* 3.0 37.9 + - + +
421C GLU* 3.4 10.1 + - - +
423C ALA* 1.3 75.3 - - - +
425C GLN* 1.3 61.9 + - - +
427C LEU* 3.7 8.1 - - - +
428C SER* 3.3 20.8 + - - -
442C TYR* 3.6 20.4 + - - +
446C LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 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 GLU 3.1 13.5 + - - +
422C ARG* 3.3 35.6 + - - +
423C ALA 3.0 0.2 - - - -
424C GLN* 1.3 74.2 - - - +
426C ILE* 1.3 68.1 + - - +
427C LEU 2.9 5.1 + - - -
428C SER* 2.9 19.0 + - - +
429C GLU* 3.0 36.6 + - + +
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Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 3.2 43.0 + - - +
423C ALA 3.9 4.9 - - - +
425C GLN* 1.3 79.3 - - - +
427C LEU* 1.3 59.3 + - - +
429C GLU* 4.1 11.4 - - - +
430C ASN* 3.0 33.6 + - - +
449C ILE* 4.3 24.0 - - + -
453C VAL* 4.1 15.9 - - + -
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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
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423C ALA 3.1 22.1 + - - +
424C GLN* 3.7 10.1 - - - +
425C GLN 2.9 0.8 + - - -
426C ILE* 1.3 75.7 - - - +
428C SER* 1.3 60.1 + - - +
430C ASN* 3.1 7.7 + - - -
431C LYS 3.2 0.2 + - - -
432C ILE* 2.8 72.6 + - + +
442C TYR* 3.1 36.6 - - + +
445C ASN* 4.0 16.2 - - + -
446C LEU* 3.7 24.2 - - + +
449C ILE* 4.5 13.9 - - + -
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Residues in contact with SER 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLN 3.3 11.2 + - - -
425C GLN* 2.9 17.5 + - - +
427C LEU* 1.3 74.0 - - - +
429C GLU* 1.3 55.2 + - - +
430C ASN 2.9 4.9 - - - -
431C LYS* 2.6 36.5 + - - +
432C ILE 4.3 7.2 - - - +
433C ILE* 4.8 12.0 - - - +
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Residues in contact with GLU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLN* 3.0 47.3 + - + +
426C ILE* 4.1 7.1 - - - +
428C SER* 1.3 77.6 + - - +
430C ASN* 1.3 70.5 + - - +
431C LYS* 3.3 8.8 + - - +
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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