Contacts of the helix formed by residues 731 - 743 (chain D) in PDB entry 3LZB
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 ALA 731 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730D LYS* 1.3 77.4 - - - +
732D ASN* 1.3 65.4 + - - +
733D LYS* 4.0 11.7 - - + +
734D GLU* 4.2 21.0 + - + +
735D ILE* 2.8 29.5 + - - +
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Residues in contact with ASN 732 (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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725D GLU* 5.4 3.3 - - - +
730D LYS 4.8 2.6 - - - +
731D ALA* 1.3 77.2 - - - +
733D LYS* 1.3 64.1 + - - +
734D GLU 3.4 0.2 - - - -
735D ILE* 4.2 8.5 - - - +
736D LEU* 3.2 27.9 + - - +
758D LEU* 3.4 49.3 + - + +
759D THR 4.7 6.9 + - - +
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Residues in contact with LYS 733 (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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731D ALA* 3.4 6.7 - - + +
732D ASN* 1.3 80.0 - - - +
734D GLU* 1.3 65.8 + - + +
736D LEU* 4.1 3.3 - - - +
737D ASP* 3.1 31.9 + - - +
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Residues in contact with GLU 734 (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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730D LYS* 4.2 21.1 - - + +
731D ALA* 4.1 21.0 + - + +
732D ASN 3.4 0.2 - - - -
733D LYS* 1.3 76.7 - - + +
735D ILE* 1.3 69.0 + - - +
737D ASP* 2.9 18.8 + - - +
738D GLU* 3.1 18.6 + - - +
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Residues in contact with ILE 735 (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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725D GLU* 6.1 0.7 - - - +
730D LYS* 4.0 32.9 - - + +
731D ALA 2.8 24.8 + - - +
732D ASN* 4.2 11.0 - - - +
733D LYS 3.6 0.4 - - - -
734D GLU* 1.3 76.6 - - - +
736D LEU* 1.3 53.8 + - - +
738D GLU* 2.5 35.0 + - + +
739D ALA* 2.6 16.2 + - + -
742D MET* 6.4 1.3 - - + -
756D ILE* 4.7 6.7 - - + -
758D LEU* 4.6 20.2 - - + -
762D VAL* 4.9 13.2 - - + -
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Residues in contact with LEU 736 (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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680D LEU* 4.7 1.1 - - + -
682D ILE* 3.7 30.1 - - + -
732D ASN 3.2 18.3 + - - +
733D LYS* 4.1 4.0 - - - +
735D ILE* 1.3 80.0 - - - +
737D ASP* 1.3 60.9 + - - +
739D ALA* 3.4 8.7 - - + +
740D TYR* 2.9 71.4 + - + +
756D ILE* 3.8 19.1 - - + -
758D LEU* 4.0 15.5 - - + -
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Residues in contact with ASP 737 (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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733D LYS* 3.1 17.5 + - - +
734D GLU* 2.9 14.8 + - - +
736D LEU* 1.3 80.0 - - - +
738D GLU* 1.3 66.8 + - - +
740D TYR* 3.8 22.9 - - - +
741D VAL* 3.5 16.8 - - - +
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Residues in contact with GLU 738 (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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734D GLU* 3.1 18.8 + - - +
735D ILE* 2.5 24.5 + - + +
737D ASP* 1.3 77.3 - - - +
739D ALA* 1.3 55.3 + - - +
740D TYR 3.1 1.6 - - - -
741D VAL* 2.7 35.6 + - - +
742D MET* 3.0 33.2 + - + +
833D GLY 5.8 1.6 - - - +
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Residues in contact with ALA 739 (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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680D LEU* 3.7 18.6 - - + +
735D ILE* 2.6 12.7 + - + +
736D LEU* 3.4 19.1 - - - +
738D GLU* 1.3 71.9 - - - +
740D TYR* 1.3 51.8 + - - +
742D MET* 3.0 18.7 + - - +
743D ALA* 2.8 35.9 + - - +
753D LEU* 4.6 7.0 - - + +
756D ILE* 3.9 20.9 - - + -
764D LEU* 5.9 0.7 - - + -
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Residues in contact with TYR 740 (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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679D LEU* 4.7 15.8 - - + +
680D LEU* 3.6 33.7 - - + -
682D ILE* 3.9 13.6 - - + +
736D LEU* 2.9 56.5 + - + +
737D ASP* 3.8 18.6 - - - +
739D ALA* 1.3 75.7 - - - +
741D VAL* 1.3 65.2 + - + +
743D ALA* 3.3 5.6 + - - +
744D SER* 3.3 18.7 + - - -
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Residues in contact with VAL 741 (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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737D ASP 3.5 17.3 - - - +
738D GLU* 2.7 25.9 + - - +
740D TYR* 1.3 69.6 - - + +
742D MET* 1.3 54.4 + - + +
743D ALA 2.9 3.8 - - - -
744D SER* 2.7 43.6 + - - +
745D VAL* 3.8 6.3 + - - +
807D ARG* 4.3 9.9 - - - +
809D LEU* 4.4 26.2 - - + -
832D PHE* 5.5 0.9 - - - -
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Residues in contact with MET 742 (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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1D ITI 3.2 41.9 - - + -
735D ILE* 6.4 1.6 - - + -
738D GLU* 3.0 36.7 + - + +
739D ALA* 3.0 15.5 + - - +
741D VAL* 1.3 75.3 - - + +
743D ALA* 1.3 55.7 + - - +
744D SER 3.4 0.2 - - - -
745D VAL* 3.4 16.1 - - - +
752D ARG* 4.2 0.2 - - - -
753D LEU* 3.2 33.7 + - + -
764D LEU* 5.9 1.6 - - - -
832D PHE* 4.2 18.7 - - + +
833D GLY* 3.8 28.7 - - - +
834D LEU* 4.3 5.4 - - + -
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Residues in contact with ALA 743 (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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679D LEU* 3.5 18.2 - - + +
680D LEU* 3.6 31.0 - - + -
739D ALA 2.8 14.4 + - - +
740D TYR 3.7 6.7 - - - +
741D VAL 2.9 0.6 - - - -
742D MET* 1.3 76.6 - - - +
744D SER* 1.3 58.8 + - - +
745D VAL 3.5 2.0 - - - -
752D ARG* 3.0 23.0 + - - +
753D LEU* 3.3 23.6 - - + +
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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