Contacts of the helix formed by residues 3485 - 3493 (chain I) 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 ASN3485 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3329I GLU 4.1 3.8 + - - -
3330I TYR* 3.8 26.8 - - + +
3334I LYS* 6.5 0.2 - - - -
3446I ASN* 3.4 13.7 - - - +
3450I ASP* 3.7 20.1 + - - +
3453I VAL* 3.2 13.5 - - - -
3483I VAL* 3.0 2.3 - - - +
3484I LYS* 1.3 89.5 - - - +
3486I ILE* 1.3 53.2 + - - +
3487I ALA* 3.2 11.1 + - - +
3488I GLU* 2.8 28.5 + - - +
3489I LEU* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3486 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3330I TYR 3.5 7.4 + - - +
3331I GLY* 3.9 10.5 - - - -
3332I GLN* 4.9 0.7 - - - -
3433I ASN* 2.8 40.4 - - + +
3437I SER* 3.6 25.6 - - - +
3444I MET* 4.5 1.8 - - + -
3445I SER* 3.4 26.2 - - - +
3446I ASN* 3.3 13.8 + - - +
3453I VAL* 3.2 26.7 - - + -
3485I ASN* 1.3 71.1 - - - +
3487I ALA* 1.3 66.0 + - - +
3489I LEU* 3.9 7.2 - - + -
3490I ARG* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3487 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3328I VAL 3.3 15.7 - - - +
3329I GLU* 3.5 6.7 - - - -
3330I TYR 3.3 34.7 + - - +
3331I GLY 4.3 0.9 - - - +
3485I ASN* 3.2 8.4 - - - +
3486I ILE* 1.3 77.7 - - - +
3488I GLU* 1.3 58.1 + - + +
3490I ARG* 3.8 8.5 + - - +
3491I LYS* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3488 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3482I ALA* 2.9 27.8 - - - +
3483I VAL* 4.5 0.9 - - - -
3484I LYS* 3.0 46.8 + - - +
3485I ASN* 2.8 21.7 + - - +
3487I ALA* 1.3 73.1 - - + +
3489I LEU* 1.3 60.3 + - - +
3491I LYS* 2.6 35.7 + - + +
3492I VAL* 3.1 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3489 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3437I SER* 4.0 19.5 - - - +
3444I MET* 4.8 9.4 - - + -
3453I VAL* 4.6 5.2 - - + -
3475I ILE* 4.3 18.4 - - + -
3478I ALA* 5.0 4.5 - - - -
3483I VAL* 3.3 42.1 - - + +
3485I ASN 2.8 13.2 + - - +
3486I ILE* 4.0 10.5 - - + +
3488I GLU* 1.3 71.1 - - - +
3490I ARG* 1.3 63.7 + - + +
3492I VAL* 2.9 22.6 + - - +
3493I LEU* 3.1 48.8 + - + +
3502I LEU* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3490 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3208I MET 5.5 0.7 - - - -
3209I VAL* 3.2 40.0 + - - +
3327I MET 3.8 6.1 + - - -
3328I VAL 4.7 2.0 + - - -
3331I GLY* 3.4 25.1 - - - -
3433I ASN* 4.4 6.3 + - - -
3436I ASP* 2.3 56.9 + - - +
3437I SER* 3.4 28.7 - - - +
3486I ILE* 3.0 25.6 + - - +
3487I ALA* 3.9 8.2 - - - +
3489I LEU* 1.3 76.8 - - + +
3491I LYS* 1.3 59.1 + - - +
3492I VAL 3.1 0.6 + - - -
3493I LEU 3.6 2.3 + - - +
3494I ASP* 3.3 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3491 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3178I LYS* 5.6 5.3 - - - +
3487I ALA 2.9 15.1 + - - +
3488I GLU* 2.6 27.5 + - + +
3490I ARG* 1.3 72.7 - - - +
3492I VAL* 1.3 57.7 + - + -
3494I ASP* 4.3 6.7 - - - +
3495I SER* 3.5 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3492 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3478I ALA* 3.7 43.1 - - + +
3479I ASN* 4.5 6.1 - - + -
3480I GLN* 4.5 3.6 - - - +
3481I GLN* 5.7 2.5 - - + +
3482I ALA 5.6 0.9 - - - +
3488I GLU* 3.5 13.7 - - + +
3489I LEU 2.9 6.6 + - - +
3491I LYS* 1.3 82.0 - - + +
3493I LEU* 1.3 60.3 + - + +
3494I ASP 2.8 10.8 + - - -
3495I SER* 3.1 17.3 + - - +
3496I LYS* 3.2 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3493 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3437I SER 3.7 12.1 - - - +
3438I SER* 3.0 38.6 - - - +
3439I SER* 2.8 27.5 + - - +
3479I ASN* 4.7 4.3 - - + -
3489I LEU* 3.1 44.0 + - + +
3490I ARG 3.6 1.9 + - - +
3492I VAL* 1.3 79.9 - - + +
3494I ASP* 1.3 56.8 + - - +
3496I LYS 5.3 3.6 - - - +
3497I PRO* 4.6 9.1 - - - +
3500I LEU* 3.3 39.7 - - + -
3502I LEU* 4.5 6.1 - - + -
----------------------------------------------------------
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