Contacts of the helix formed by residues 919 - 925 (chain D) in PDB entry 3O33
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 GLU 919 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917D CYS 3.7 3.2 + - - -
918D HIS* 1.3 82.1 + - + +
920D MET* 1.3 85.3 + - + +
921D SER 3.1 4.7 + - - -
922D LEU* 3.5 31.1 + - + +
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Residues in contact with MET 920 (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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918D HIS* 3.0 29.3 + - + +
919D GLU* 1.3 116.7 - - + +
921D SER* 1.3 57.3 + - - +
922D LEU 3.4 1.3 + - - -
923D ALA* 4.8 0.7 + - - +
924D PHE* 3.3 24.9 - - - -
989D ALA* 3.8 38.2 - - - +
992D LYS* 4.0 28.7 - - + -
993D LEU* 4.0 10.7 - - + +
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Residues in contact with SER 921 (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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915D LEU 2.8 33.0 + - - -
916D TYR 3.5 0.5 + - - -
918D HIS 2.9 11.3 + - - -
920D MET* 1.3 78.0 - - - +
922D LEU* 1.3 56.3 + - - +
923D ALA 3.3 2.7 - - - -
924D PHE* 2.8 25.6 + - - -
925D GLN* 2.9 30.9 + - - +
945D LEU* 4.1 9.2 - - - -
993D LEU* 3.9 21.7 - - - +
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Residues in contact with LEU 922 (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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831D VAL 5.7 4.0 - - - +
918D HIS 5.3 0.2 - - - +
919D GLU* 3.5 24.0 - - + +
920D MET 3.4 1.6 - - - -
921D SER* 1.3 79.1 + - - +
923D ALA* 1.3 60.2 + - - +
924D PHE 3.1 1.4 + - - -
925D GLN* 3.8 30.6 + - - +
926D ASP 5.1 1.0 + - - -
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Residues in contact with ALA 923 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920D MET 4.8 1.0 + - - -
921D SER 3.3 1.0 - - - -
922D LEU* 1.3 76.5 - - - +
924D PHE* 1.3 85.0 + - + +
925D GLN 3.7 0.4 - - - -
926D ASP 4.4 7.8 - - - +
928D VAL* 5.0 10.0 - - - +
986D VAL* 4.3 22.0 - - + -
989D ALA* 5.9 2.0 - - + -
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Residues in contact with PHE 924 (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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920D MET 3.3 27.4 - - - -
921D SER* 2.8 8.9 + - - +
923D ALA* 1.3 92.1 - - + +
925D GLN* 1.3 57.5 + - - +
926D ASP 3.5 4.9 - - - -
943D MET 6.0 0.2 - - - -
944D ASP* 3.5 6.6 - - - +
945D LEU* 3.0 30.4 + - + +
972D ILE* 3.9 28.5 - - + -
973D PHE* 5.9 0.7 - + - -
976D CYS* 3.7 39.3 - - + -
980D ASN* 5.4 0.4 - - - -
986D VAL* 3.9 19.1 - - + -
989D ALA* 4.2 3.8 - - + -
990D GLY* 3.8 22.7 - - - -
993D LEU* 3.7 18.6 - - + -
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Residues in contact with GLN 925 (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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831D VAL* 4.7 9.9 + - - +
916D TYR* 3.5 46.6 + - + -
918D HIS 4.9 0.4 + - - -
921D SER* 2.9 34.2 + - - +
922D LEU* 3.8 34.9 + - - +
923D ALA 3.7 0.8 - - - -
924D PHE* 1.3 79.0 - - - +
926D ASP* 1.3 69.8 + - - +
944D ASP* 3.9 0.2 - - - -
945D LEU* 4.0 9.6 - - + -
946D SER* 3.0 31.9 + - - -
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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