Contacts of the helix formed by residues 3089 - 3097 (chain H) in PDB entry 2ZLE
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 ASN3089 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2933H GLU 4.1 3.4 + - - -
2934H TYR* 3.8 27.2 - - + +
3050H ASN* 3.4 14.6 - - - +
3054H ASP* 3.7 20.1 + - - +
3057H VAL* 3.2 13.9 - - - -
3087H VAL* 3.0 2.1 - - - +
3088H LYS* 1.3 89.3 - - - +
3090H ILE* 1.3 53.0 + - - +
3091H ALA* 3.2 11.0 + - - +
3092H GLU* 2.8 29.3 + - - +
3093H LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3090 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2934H TYR 3.6 7.2 - - - +
2935H GLY* 3.9 9.0 - - - -
2936H GLN* 4.9 0.4 - - - -
3037H ASN* 2.8 40.6 - - + +
3041H SER* 3.6 25.4 - - - +
3048H MET* 4.5 2.5 - - + -
3049H SER* 3.4 27.4 - - - +
3050H ASN* 3.3 13.9 + - - +
3057H VAL* 3.2 24.9 - - + +
3089H ASN* 1.3 70.8 - - - +
3091H ALA* 1.3 65.9 + - - +
3093H LEU* 3.9 7.6 - - + -
3094H ARG* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3091 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2932H VAL 3.3 15.0 - - - +
2933H GLU* 3.5 7.2 - - - +
2934H TYR 3.3 34.9 + - - +
2935H GLY 4.3 1.1 - - - +
3089H ASN* 3.2 8.4 + - - +
3090H ILE* 1.3 77.8 - - - +
3092H GLU* 1.3 59.6 + - + +
3094H ARG* 3.8 8.4 + - - +
3095H LYS* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3092 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3086H ALA* 2.9 27.7 - - - +
3087H VAL* 4.5 0.9 - - - -
3088H LYS* 3.0 47.5 + - - +
3089H ASN* 2.8 19.7 + - - +
3091H ALA* 1.3 74.0 - - + +
3093H LEU* 1.3 60.3 + - - +
3095H LYS* 2.7 37.3 + - + +
3096H VAL* 3.1 11.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3093 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3041H SER* 4.0 19.7 - - - +
3048H MET* 4.8 9.4 - - + -
3057H VAL* 4.6 5.4 - - + -
3079H ILE* 4.3 18.4 - - + -
3082H ALA* 5.0 4.3 - - - -
3087H VAL* 3.3 43.8 - - + +
3089H ASN 2.8 14.3 + - - +
3090H ILE* 4.0 9.9 - - + +
3092H GLU* 1.3 71.2 - - - +
3094H ARG* 1.3 64.0 + - + +
3096H VAL* 2.9 21.6 + - - +
3097H LEU* 3.1 48.8 + - + +
3106H LEU* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3094 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812H MET 4.1 0.6 + - - -
2813H VAL* 3.2 40.2 + - - +
2931H MET 3.8 5.9 + - - -
2932H VAL 4.7 1.8 + - - -
2935H GLY* 3.4 25.9 - - - -
3037H ASN* 4.4 6.3 + - - -
3040H ASP* 2.3 56.1 + - - +
3041H SER* 3.4 28.3 - - - +
3090H ILE* 3.0 26.1 + - + +
3091H ALA* 3.8 7.6 - - - +
3093H LEU* 1.3 77.2 - - + +
3095H LYS* 1.3 60.1 + - - +
3096H VAL 3.1 0.6 + - - -
3097H LEU 3.6 1.8 + - - +
3098H ASP* 3.3 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3095 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2782H LYS* 5.6 5.5 - - - +
3091H ALA 2.9 15.4 + - - +
3092H GLU* 2.7 24.5 + - + +
3094H ARG* 1.3 72.1 - - - +
3096H VAL* 1.3 59.8 + - + +
3098H ASP* 4.3 6.9 - - - +
3099H SER* 3.5 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3096 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3082H ALA* 3.7 43.3 - - + +
3083H ASN* 4.5 5.4 - - + -
3084H GLN* 4.5 3.1 - - - +
3085H GLN* 5.7 2.0 - - + +
3086H ALA 5.6 0.7 - - - +
3092H GLU* 3.5 13.9 - - + +
3093H LEU 2.9 6.6 + - - +
3095H LYS* 1.3 81.1 - - + +
3097H LEU* 1.3 60.7 + - + +
3098H ASP 2.8 11.4 + - - -
3099H SER* 3.1 17.8 + - - +
3100H LYS* 3.2 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3097 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3041H SER 3.7 11.7 - - - +
3042H SER* 3.0 37.9 - - - +
3043H SER* 2.8 27.0 + - - -
3083H ASN* 4.7 4.5 - - + -
3093H LEU* 3.1 44.1 + - + +
3094H ARG 3.6 2.1 + - - +
3096H VAL* 1.3 80.1 - - + +
3098H ASP* 1.3 57.7 + - - +
3100H LYS* 5.3 3.1 - - + +
3101H PRO* 4.6 8.5 - - - +
3104H LEU* 3.3 40.2 - - + -
3106H LEU* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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