Contacts of the helix formed by residues 441 - 455 (chain D) in PDB entry 3G4I
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 LYS 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393D SER* 4.2 17.5 + - - -
435D LEU 4.1 11.0 - - - +
436D ALA* 4.2 13.5 - - - +
438D ASP* 2.8 24.6 + - + +
440D SER* 1.3 90.3 + - - +
442D HIS* 1.3 63.1 + - - +
443D MET 3.4 2.2 - - - -
444D ASN* 3.3 17.6 + - + +
445D LEU* 3.0 27.0 + - + +
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Residues in contact with HIS 442 (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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438D ASP 4.0 1.2 + - - -
439D MET* 3.1 30.9 + - + +
440D SER 3.4 1.0 - - - -
441D LYS* 1.3 75.8 - - - +
443D MET* 1.3 84.4 + - + +
445D LEU* 3.3 5.7 + - - +
446D LEU* 2.9 44.9 + - + +
481D HIS* 2.7 38.9 + + + +
485D LEU* 4.2 1.6 - - - +
541D TYR 4.9 0.8 + - - -
542D ILE* 3.8 43.8 + - + +
546D LEU* 4.1 18.4 - - + -
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Residues in contact with MET 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D SER 4.9 3.2 + - - +
441D LYS 3.4 0.6 - - - -
442D HIS* 1.3 99.6 - - + +
444D ASN* 1.3 62.7 + - - +
446D LEU* 3.4 11.7 + - - +
447D ALA* 3.0 28.8 + - - +
541D TYR* 4.4 16.4 - - + +
542D ILE* 5.4 4.3 - - + -
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Residues in contact with ASN 444 (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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440D SER 5.5 2.3 + - - -
441D LYS* 3.3 19.6 + - + +
442D HIS 3.3 0.6 - - - -
443D MET* 1.3 78.0 - - - +
445D LEU* 1.3 65.1 + - - +
447D ALA* 3.4 8.2 + - - +
448D ASP* 3.1 30.3 + - - +
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Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ALA* 3.4 33.2 - - + +
441D LYS* 3.0 18.1 + - + +
442D HIS* 3.5 7.4 - - - +
444D ASN* 1.3 74.6 - - - +
446D LEU* 1.3 64.1 + - - +
448D ASP* 3.3 15.7 + - - +
449D LEU* 3.0 18.9 + - - +
474D GLN* 5.7 0.4 - - - -
477D GLN* 3.9 31.4 - - + +
478D ASN* 3.5 32.4 + - - +
481D HIS* 3.8 34.5 - - + +
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Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D HIS* 2.9 38.3 + - + +
443D MET* 3.7 13.5 - - - +
445D LEU* 1.3 76.8 - - - +
447D ALA* 1.3 57.2 + - - +
449D LEU* 3.2 4.9 + - + +
450D LYS* 2.9 47.3 + - - +
478D ASN* 4.3 2.4 + - - -
541D TYR 6.0 0.4 - - - +
545D PRO* 4.0 29.6 - - + +
546D LEU* 4.0 16.4 - - + +
549D THR* 3.6 33.7 - - + +
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Residues in contact with ALA 447 (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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443D MET 3.0 18.3 + - - +
444D ASN* 3.7 8.3 - - - +
445D LEU 3.3 0.2 - - - -
446D LEU* 1.3 77.2 - - - +
448D ASP* 1.3 61.5 + - - +
450D LYS* 3.5 10.7 + - - +
451D THR* 3.1 25.9 + - - -
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Residues in contact with ASP 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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444D ASN* 3.1 21.2 + - - +
445D LEU* 3.3 19.9 - - - +
447D ALA* 1.3 72.8 - - - +
449D LEU* 1.3 67.2 + - - +
451D THR* 3.3 8.5 + - - -
452D MET* 3.1 21.5 + - - +
474D GLN* 3.7 41.7 + - + +
477D GLN* 5.3 0.5 - - - +
478D ASN* 4.8 3.4 - - - +
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Residues in contact with LEU 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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445D LEU 3.0 10.9 + - - +
446D LEU* 3.5 9.4 - - + +
448D ASP* 1.3 79.3 - - - +
450D LYS* 1.3 57.7 + - - +
452D MET* 3.2 14.1 + - - +
453D VAL* 3.0 27.1 + - + +
474D GLN* 5.4 2.7 - - + +
475D VAL* 5.4 2.2 - - - -
478D ASN* 3.8 37.5 - - + +
546D LEU* 4.3 13.7 - - + -
549D THR* 3.7 22.9 - - + -
550D TRP* 4.1 24.0 - - + +
553D LEU* 4.0 29.8 - - + -
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Residues in contact with LYS 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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446D LEU* 2.9 42.8 + - + +
447D ALA* 3.8 8.3 - - - +
449D LEU* 1.3 74.3 - - - +
451D THR* 1.3 59.6 + - - +
453D VAL* 3.2 4.2 + - - +
454D GLU* 2.9 44.4 + - - +
545D PRO* 4.9 6.3 - - - +
549D THR* 3.7 32.8 - - + +
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Residues in contact with THR 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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447D ALA 3.1 13.3 + - - -
448D ASP* 3.3 10.4 + - - -
450D LYS* 1.3 78.4 - - - +
452D MET* 1.3 63.0 + - - +
454D GLU* 3.2 17.4 + - - +
455D THR* 3.1 34.1 + - + +
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Residues in contact with MET 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 ASP 3.1 12.5 + - - +
449D LEU* 3.3 15.0 - - + +
451D THR* 1.3 75.1 - - - +
453D VAL* 1.3 64.9 + - - +
455D THR* 3.2 8.1 + - - -
456D LYS* 2.9 23.6 + - - -
464D LEU* 4.7 2.2 - - + -
466D LEU* 4.2 9.6 - - + -
471D ASP* 3.5 45.3 - - + +
474D GLN* 3.7 18.2 - - + +
475D VAL* 3.5 26.2 - - + -
553D LEU* 3.8 23.3 - - + -
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Residues in contact with VAL 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LEU* 3.0 18.2 + - + +
450D LYS* 3.2 9.8 + - - +
452D MET* 1.3 76.2 - - - +
454D GLU* 1.3 65.4 + - + +
456D LYS* 3.2 24.9 + - + +
549D THR* 3.6 30.3 - - + +
552D ASP* 3.9 25.6 - - + +
553D LEU* 3.7 24.9 - - + +
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Residues in contact with GLU 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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450D LYS* 2.9 30.9 + - - +
451D THR* 3.5 15.6 + - - +
452D MET 3.2 0.2 - - - -
453D VAL* 1.3 79.3 - - + +
455D THR* 1.3 63.4 + - + +
456D LYS 3.5 1.1 + - - -
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Residues in contact with THR 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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451D THR* 3.1 24.9 + - + +
452D MET* 3.3 8.4 + - - -
453D VAL 3.2 0.2 - - - -
454D GLU* 1.3 82.7 - - + +
456D LYS* 1.3 63.5 + - - +
457D LYS* 3.5 19.2 + - - +
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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