Contacts of the helix formed by residues 457 - 469 (chain D) in PDB entry 1D7W
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 ASN 457 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394D GLN* 2.7 45.0 + - - +
395D ASN* 6.2 0.8 - - - +
452D GLY* 2.8 8.2 + - - -
455D LEU* 3.0 7.7 - - + +
456D ARG* 1.3 81.6 + - - +
458D LEU* 1.3 62.9 + - - +
459D LYS* 3.3 17.2 + - - +
460D LEU* 2.9 27.6 + - + +
461D ALA* 3.1 20.8 + - - +
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Residues in contact with LEU 458 (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* 4.1 28.3 - - + +
449D GLY* 4.7 6.5 - - - +
452D GLY* 4.0 12.6 + - - -
457D ASN* 1.3 71.2 + - - +
459D LYS* 1.3 61.0 + - - +
461D ALA* 3.2 0.6 + - + -
462D ARG* 2.9 76.3 + - + +
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Residues in contact with LYS 459 (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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395D ASN* 5.1 16.4 - - + +
457D ASN* 3.3 12.3 + - - +
458D LEU* 1.3 79.3 - - - +
460D LEU* 1.4 62.9 + - - +
462D ARG* 3.4 14.2 + - - +
463D LYS* 3.3 52.4 + - - +
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Residues in contact with LEU 460 (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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68B ILE* 3.9 27.8 - - + -
394D GLN* 3.8 33.9 - - + +
397D ILE* 5.2 0.9 - - + -
455D LEU* 3.8 7.9 - - + -
457D ASN* 2.9 25.3 + - - +
459D LYS* 1.4 75.0 - - + +
461D ALA* 1.3 65.7 + - - +
463D LYS* 3.2 13.6 + - + +
464D LEU* 2.9 35.4 + - + +
482D SER* 3.6 37.9 - - - +
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Residues in contact with ALA 461 (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* 3.8 10.1 - - + +
451D LEU* 3.6 27.4 - - + +
452D GLY* 3.4 37.9 - - - +
455D LEU* 4.1 3.6 - - + +
457D ASN 3.1 6.4 + - - +
458D LEU 3.6 5.6 - - - +
460D LEU* 1.3 75.5 - - - +
462D ARG* 1.3 52.6 + - - +
464D LEU* 3.3 2.1 + - - +
465D MET* 2.7 35.0 + - - +
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Residues in contact with ARG 462 (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* 3.9 20.5 - - + +
458D LEU* 2.9 51.1 + - + +
459D LYS* 3.5 12.0 - - - +
460D LEU 3.2 0.4 - - - -
461D ALA* 1.3 76.1 - - - +
463D LYS* 1.3 51.6 + - + +
465D MET* 3.2 3.1 + - - +
466D GLU* 2.8 37.4 + - - +
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Residues in contact with LYS 463 (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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67B GLU* 3.1 27.0 + - + +
68B ILE* 3.9 20.2 - - + +
459D LYS* 3.3 49.8 + - - +
460D LEU* 3.2 16.9 + - + +
462D ARG* 1.3 77.1 - - + +
464D LEU* 1.3 57.9 + - - +
466D GLU* 3.3 16.1 + - - +
467D GLN* 3.0 33.6 + - - +
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Residues in contact with LEU 464 (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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68B ILE* 3.3 23.6 - - + -
451D LEU* 3.9 14.1 - - + -
455D LEU* 3.4 33.4 - - + -
460D LEU* 2.9 24.9 + - + +
461D ALA 3.5 6.3 - - - +
463D LYS* 1.3 74.0 - - - +
465D MET* 1.3 59.1 + - - +
467D GLN 3.1 1.4 + - - -
468D TYR* 2.9 47.2 + - + +
474D ILE* 4.1 19.5 - - + -
478D MET* 3.9 22.0 - - + -
479D GLY* 5.7 0.4 - - - -
482D SER* 3.9 12.6 - - - +
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Residues in contact with MET 465 (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 GLU 3.9 6.7 - - - +
447D THR* 3.8 7.2 - - - -
448D VAL* 3.5 52.3 - - + +
451D LEU* 4.6 5.3 - - + +
461D ALA 2.7 19.1 + - - +
462D ARG* 3.6 4.3 - - - +
464D LEU* 1.3 71.0 - - - +
466D GLU* 1.3 59.0 + - - +
468D TYR* 5.3 0.2 - - - -
469D GLY* 2.6 57.5 + - - +
470D THR* 3.8 1.8 - - - +
471D PRO* 3.7 28.7 - - + -
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Residues in contact with GLU 466 (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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67B GLU* 4.3 14.0 - - - +
462D ARG 2.8 20.0 + - - +
463D LYS* 3.6 13.9 - - - +
464D LEU 3.2 0.2 - - - -
465D MET* 1.3 73.9 - - - +
467D GLN* 1.3 79.2 + - - +
469D GLY 4.9 0.3 + - - -
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Residues in contact with GLN 467 (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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57B PRO 4.7 2.9 - - - +
59B ALA* 3.2 24.8 + - - +
63B ALA* 3.4 14.3 - - - +
64B VAL* 3.3 38.3 + - + +
67B GLU* 3.3 33.8 - - + +
68B ILE* 4.2 9.0 - - + -
463D LYS 3.0 19.6 + - - +
464D LEU* 3.1 4.0 + - - +
466D GLU* 1.3 93.4 + - - +
468D TYR* 1.3 74.3 - - + +
469D GLY 3.8 0.2 - - - -
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Residues in contact with TYR 468 (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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56B PHE* 3.7 17.4 - - - +
57B PRO* 4.4 6.9 - - - +
59B ALA* 4.6 8.7 - - + +
64B VAL* 3.5 25.7 - - + +
422D MET* 3.4 19.1 - - - -
426D ARG* 4.2 8.1 - - - -
464D LEU* 2.9 41.6 + - + +
467D GLN* 1.3 84.8 - - + +
469D GLY* 1.3 55.0 + - - +
470D THR* 3.1 26.8 + - - +
473D ASN* 3.1 32.9 + - + +
474D ILE* 3.7 20.0 - - + +
475D ASP* 2.6 40.6 + - - +
478D MET* 3.7 3.6 - - + +
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Residues in contact with GLY 469 (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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56B PHE* 3.8 30.8 - - - -
57B PRO* 6.1 0.7 - - - -
465D MET* 2.6 40.0 + - - +
466D GLU 4.7 0.2 - - - -
467D GLN 3.8 0.8 - - - -
468D TYR* 1.3 69.4 - - - +
470D THR* 1.3 58.7 + - - +
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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