Contacts of the helix formed by residues 443 - 452 (chain C) in PDB entry 6CP3
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 443 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLN* 5.1 0.5 - - - +
151C GLY* 3.2 34.6 + - - +
152C LEU 3.3 17.7 + - - -
153C LYS* 4.1 11.8 - - + +
156C ASP* 4.4 9.8 + - - +
157C ALA 5.7 0.4 + - - -
385C LEU* 4.3 22.6 - - + +
438C LEU* 3.7 20.4 - - + +
439C ALA 3.1 17.3 + - - +
440C THR* 3.1 14.4 + - - +
442C GLU* 1.3 79.9 - - - +
444C VAL* 1.3 65.6 + - - +
445C PRO 3.5 2.5 - - - -
446C LEU* 3.3 8.4 + - - +
447C ILE* 3.1 29.5 + - + +
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Residues in contact with VAL 444 (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 ALA* 3.7 32.5 - - + +
385C LEU* 4.0 21.8 - - + +
388C VAL* 3.8 21.0 - - + +
440C THR* 3.2 23.2 + - + +
443C GLN* 1.3 77.1 - - - +
445C PRO* 1.4 64.0 - - + +
447C ILE 3.9 0.3 - - - -
448C TYR* 2.9 27.1 + - - +
485C ILE* 4.7 10.8 - - + -
491C LEU* 3.9 19.7 - - + -
499C LEU* 4.8 5.2 - - + -
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Residues in contact with PRO 445 (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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441C GLU 3.4 20.4 - - - +
442C GLU* 4.5 2.5 - - - -
443C GLN 3.8 1.8 - - - +
444C VAL* 1.4 92.8 - - + +
446C LEU* 1.3 57.3 + - + +
448C TYR* 3.6 8.1 - - + +
449C ALA* 2.8 30.0 + - - +
470C PHE* 3.7 27.8 - - + -
474C LEU* 3.8 17.5 - - + -
481C LEU* 6.0 0.2 - - + -
482C LEU* 4.6 1.8 - - + -
485C ILE* 4.5 10.8 - - + -
499C LEU* 3.8 26.2 - - + -
503C THR* 5.1 0.7 + - - -
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Residues in contact with LEU 446 (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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153C LYS* 4.7 7.6 - - + -
429C LEU* 4.0 23.3 - - + +
438C LEU* 4.2 5.4 - - + -
442C GLU 3.4 23.3 - - - +
443C GLN* 3.3 8.1 + - - +
445C PRO* 1.3 76.0 - - + +
447C ILE* 1.3 65.9 + - + +
449C ALA* 3.3 8.5 + - + +
450C GLY* 2.9 23.2 + - - -
455C LEU* 4.8 1.3 - - + +
466C PHE* 6.3 1.6 - - + -
467C GLU* 3.5 53.4 - - + +
470C PHE* 4.3 21.1 - - + -
471C LEU* 5.0 8.5 - - + -
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Residues in contact with ILE 447 (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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153C LYS* 5.4 4.9 - - + +
157C ALA* 4.3 19.3 - - + -
385C LEU* 4.3 12.8 - - + -
388C VAL* 3.4 30.7 - - + +
389C ALA* 3.8 19.3 - - + -
392C LEU* 4.0 17.5 - - + -
426C LEU* 5.5 3.8 - - + -
429C LEU* 5.2 7.6 - - + -
430C LEU* 4.8 15.5 - - + -
443C GLN* 3.1 20.6 + - + +
446C LEU* 1.3 79.6 - - + +
448C TYR* 1.3 57.4 + - - +
450C GLY* 3.0 2.3 + - - +
451C VAL* 2.9 31.9 + - + +
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Residues in contact with TYR 448 (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 VAL* 3.9 27.0 - - + +
444C VAL 2.9 19.3 + - - +
445C PRO 3.6 3.6 - - - +
447C ILE* 1.3 77.7 - - - +
449C ALA* 1.3 59.9 + - - +
450C GLY 3.4 0.2 + - - -
451C VAL* 4.2 2.2 - - + -
452C ASN* 3.2 47.3 + - - +
454C HIS* 3.9 14.9 + + - -
496C LEU* 3.9 22.3 + - + +
499C LEU* 3.6 23.3 - - + -
500C LYS* 3.3 53.8 + - + +
503C THR* 3.9 12.8 - - - -
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Residues in contact with ALA 449 (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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445C PRO 2.8 18.6 + - - +
446C LEU* 3.6 10.3 - - + +
448C TYR* 1.3 76.2 - - - +
450C GLY* 1.3 63.6 + - - +
452C ASN 4.1 0.5 + - - -
454C HIS* 3.6 24.6 + - + -
455C LEU* 3.3 35.3 + - + +
466C PHE* 6.2 0.4 - - + -
470C PHE* 5.4 7.9 - - + -
503C THR* 4.3 17.7 - - + -
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Residues in contact with GLY 450 (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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422C ARG* 3.5 20.4 - - - +
426C LEU* 3.7 25.1 - - - +
429C LEU* 4.5 0.4 - - - -
446C LEU 2.9 14.1 + - - -
447C ILE 3.0 4.2 + - - -
449C ALA* 1.3 80.8 - - - +
451C VAL* 1.3 63.8 + - - +
452C ASN 3.3 0.7 + - - -
453C GLY* 3.9 2.9 + - - -
455C LEU* 3.8 13.8 - - - +
456C ASP* 5.5 0.2 - - - +
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Residues in contact with VAL 451 (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 VAL* 3.4 27.8 - - - +
389C ALA* 5.0 0.4 - - - -
392C LEU* 4.0 30.1 - - + -
395C PHE* 6.3 0.4 - - + -
422C ARG* 2.9 34.3 + - - +
426C LEU* 5.0 2.0 - - + -
447C ILE* 2.9 19.2 + - + +
448C TYR* 3.8 3.6 - - - +
450C GLY* 1.3 77.1 - - - +
452C ASN* 1.3 83.4 + - - +
453C GLY 3.5 0.4 - - - -
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Residues in contact with ASN 452 (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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422C ARG* 4.9 1.6 - - - +
448C TYR* 3.2 46.3 + - - +
450C GLY 3.3 1.2 - - - -
451C VAL* 1.3 93.5 - - - +
453C GLY* 1.3 56.1 + - - +
454C HIS* 3.0 36.8 + - + +
500C LYS* 6.0 1.1 - - - +
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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