Contacts of the helix formed by residues 447 - 456 (chain D) in PDB entry 4C1M
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 THR 447 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446D GLU* 1.3 86.8 + - + +
448D VAL* 1.3 66.3 + - - +
449D GLY* 3.4 4.5 + - - -
450D GLN* 3.0 39.6 + - - +
451D LEU* 2.9 23.0 + - - +
465D MET* 4.8 5.4 - - - -
471D PRO* 4.7 0.2 - - - +
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D THR* 1.3 73.8 - - - +
449D GLY* 1.3 56.6 + - - +
451D LEU* 3.3 4.3 + - - +
452D GLY* 2.8 29.3 + - - -
458D LEU* 3.8 7.6 - - + +
461D ALA* 3.6 3.9 - - - +
462D ARG* 3.7 44.0 - - + +
465D MET* 3.8 36.4 - - + +
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Residues in contact with GLY 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D THR* 3.2 5.4 + - - -
448D VAL* 1.3 82.3 - - - +
450D GLN* 1.3 62.9 + - - +
452D GLY* 3.1 2.3 + - - -
453D THR* 3.1 24.5 + - - -
458D LEU* 4.5 8.5 - - - -
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Residues in contact with GLN 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D GLN 4.5 1.4 - - - +
445D PRO* 3.5 17.2 - - + +
446D GLU* 3.1 26.1 + - - +
447D THR* 3.0 32.7 + - - +
449D GLY* 1.3 70.0 - - - +
451D LEU* 1.4 64.2 + - - +
453D THR* 3.2 10.4 + - - +
454D VAL* 3.0 27.0 + - + +
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D TYR* 4.2 16.6 - - + +
445D PRO* 3.4 26.8 - - + +
447D THR 2.9 13.6 + - - +
448D VAL* 3.5 9.4 - - - +
450D GLN* 1.4 76.4 - - - +
452D GLY* 1.3 57.3 + - - +
454D VAL* 3.5 1.5 + - + +
455D LEU* 3.0 46.2 + - + +
461D ALA* 3.6 30.5 - - + +
464D LEU* 4.1 8.7 - - + -
465D MET* 4.4 6.1 - - + +
471D PRO* 4.1 13.5 - - + -
474D ILE* 4.0 24.9 - - + -
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Residues in contact with GLY 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D VAL 2.8 15.2 + - - -
449D GLY 3.1 4.9 + - - -
450D GLN 3.1 0.4 - - - -
451D LEU* 1.3 72.9 - - - +
453D THR* 1.3 58.1 + - - +
456D ARG* 2.9 23.4 + - - -
457D ASN 2.9 11.9 + - - -
458D LEU* 4.0 18.3 + - - -
461D ALA* 3.6 12.1 - - - +
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Residues in contact with THR 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D GLY 3.1 12.3 + - - -
450D GLN* 3.5 10.9 - - - +
452D GLY* 1.3 73.1 - - - +
454D VAL* 1.3 70.1 - - + +
456D ARG* 3.0 21.0 + - - +
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Residues in contact with VAL 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D TYR* 3.6 21.5 - - + +
437D ARG* 3.5 35.2 - - - +
443D PRO* 5.2 6.1 - - + +
445D PRO* 4.1 22.2 - - + -
450D GLN* 3.0 19.7 + - + +
451D LEU* 3.9 4.0 - - + +
453D THR* 1.3 79.4 - - + +
455D LEU* 1.3 64.3 + - + +
456D ARG* 3.5 4.7 + - - +
483D GLU* 4.5 1.8 - - - +
484D PRO* 3.8 14.6 - - - +
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Residues in contact with LEU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D GLN* 2.9 27.9 + - - +
433D TYR* 4.7 4.5 - - + +
451D LEU* 3.0 46.8 + - + +
454D VAL* 1.3 77.7 - - + +
456D ARG* 1.4 65.7 + - - +
457D ASN* 3.9 11.9 - - + +
460D LEU* 4.1 5.8 - - + -
461D ALA* 4.0 15.5 - - - +
464D LEU* 3.7 22.4 - - + -
479D GLY 5.0 0.7 - - - +
482D SER* 3.5 34.8 - - - +
483D GLU* 3.9 16.4 - - + +
484D PRO* 3.4 8.1 - - - +
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Residues in contact with ARG 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D GLN* 4.4 2.4 - - - +
452D GLY 2.9 10.1 + - - -
453D THR* 3.0 15.2 + - - +
454D VAL 4.4 2.9 + - - +
455D LEU* 1.4 78.0 - - - +
457D ASN* 1.3 59.7 + - - +
484D PRO* 3.6 32.7 + - + +
485D LEU 4.6 9.3 + - - -
631D GOL 5.4 5.5 + - - -
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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