Contacts of the helix formed by residues 497 - 502 (chain D) in PDB entry 2W93
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 SER 497 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501C THR* 2.6 27.5 + - - -
494D ASP* 2.9 40.9 + - - -
495D HIS 3.1 0.4 - - - -
496D LEU* 1.3 76.3 - - - +
498D LEU* 1.3 57.7 + - - +
499D LEU 3.4 0.4 - - - -
500D PRO* 3.3 11.8 - - - +
501D THR* 2.9 35.6 + - - -
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Residues in contact with LEU 498 (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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501C THR* 3.7 20.4 - - + -
502C PHE* 4.5 4.7 - - + -
447D LEU* 3.7 30.3 - - + -
451D VAL* 3.7 24.7 - - + -
454D ILE* 4.5 3.4 - - + -
493D TRP* 4.5 12.3 - - + -
494D ASP 4.3 2.0 - - - +
495D HIS* 3.0 32.6 + - + +
497D SER* 1.3 78.4 + - - +
499D LEU* 1.3 64.5 + - - +
501D THR* 3.3 4.3 + - - -
502D PHE* 3.0 47.6 + - + -
535D MET* 3.9 15.3 - - + -
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Residues in contact with LEU 499 (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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454D ILE* 3.5 28.0 - - + -
458D ILE* 3.7 13.7 - - + +
466D LEU* 4.7 3.1 - - + -
495D HIS 4.7 0.4 + - - -
496D LEU 4.3 2.5 + - - +
498D LEU* 1.3 77.1 - - - +
500D PRO* 1.4 71.4 - - + +
502D PHE 3.2 9.0 + - - -
503D GLY 3.2 0.5 + - - -
504D ALA* 2.9 28.9 + - + +
507D TYR* 4.0 20.6 - - + -
508D GLU 4.1 4.9 - - - +
509D THR* 4.1 6.3 - - + -
533D ILE* 4.0 25.6 - - + -
534D ARG 4.3 3.6 - - - -
535D MET* 3.9 41.3 - - + +
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Residues in contact with PRO 500 (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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494C ASP* 4.1 9.8 - - - +
496D LEU 3.7 8.7 - - - +
497D SER* 3.3 26.9 - - - +
499D LEU* 1.4 94.5 - - + +
501D THR* 1.3 61.0 + - - +
503D GLY* 2.9 13.9 + - - -
504D ALA* 4.0 13.6 - - + +
507D TYR* 3.7 31.4 - - + +
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Residues in contact with THR 501 (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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493C TRP* 3.5 4.0 - - - +
494C ASP* 2.8 43.8 + - - +
497C SER* 3.5 12.6 - - - -
498C LEU* 3.5 34.8 - - + +
501C THR* 2.8 30.0 + - + +
497D SER* 2.9 20.2 + - - -
498D LEU* 3.3 5.6 + - - -
500D PRO* 1.3 77.6 - - - +
502D PHE* 1.3 64.3 + - + +
503D GLY 3.2 0.4 + - - -
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Residues in contact with PHE 502 (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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451C VAL* 4.8 3.6 - - + -
491C GLN* 3.0 28.9 + - - +
492C GLY 3.5 4.8 - - - +
493C TRP* 3.5 50.3 - + - +
498C LEU* 4.4 14.1 - - + -
502C PHE* 5.5 1.8 - + - -
451D VAL* 3.5 37.2 - - + -
452D GLN* 4.0 14.1 - - + -
454D ILE* 4.0 11.2 - - + -
455D SER* 4.0 17.5 - - - -
458D ILE* 3.7 17.1 - - + +
498D LEU* 3.0 37.4 + - + +
500D PRO 3.1 0.4 - - - -
501D THR* 1.3 79.7 - - + +
503D GLY* 1.3 58.3 + - - +
504D ALA 3.5 2.0 + - - -
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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