Contacts of the helix formed by residues 391 - 398 (chain E) in PDB entry 1ZMD
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 ASN 391 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E PHE* 4.1 9.8 - - + -
387E PRO 3.7 0.6 + - - -
388E PHE* 3.0 30.7 + - + +
390E ALA* 1.3 77.4 - - - +
392E SER* 1.3 67.2 + - - +
393E ARG* 3.1 7.0 + - - +
394E ALA* 2.8 25.7 + - + -
395E LYS* 2.9 25.3 + - - +
454E THR 2.9 23.0 + - - -
455E LEU* 3.4 17.3 + - - +
457E GLU* 3.8 7.3 + - - +
458E ALA* 3.5 22.3 - - + +
99F LEU* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E ALA 3.8 3.8 + - - -
391E ASN* 1.3 74.3 - - - +
393E ARG* 1.3 58.4 + - - +
395E LYS* 3.8 1.2 - - - +
396E THR* 2.7 33.9 + - - -
452E HIS* 3.6 32.4 - - - -
453E PRO* 3.9 8.3 - - - -
457E GLU* 4.9 2.6 + - - +
19F TYR* 5.7 0.7 + - - -
46F LEU* 5.4 3.6 - - - +
51F ILE* 4.0 12.2 - - - +
99F LEU* 4.2 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391E ASN* 3.1 10.5 + - - +
392E SER* 1.3 76.0 - - - +
394E ALA* 1.3 66.9 + - - +
396E THR* 3.2 6.4 + - - -
397E ASN* 2.9 47.3 + - - +
453E PRO* 3.5 29.2 + - + +
454E THR* 3.8 15.0 - - - +
455E LEU* 3.9 10.5 - - + +
54F LYS* 5.4 6.7 - - + +
359F TYR* 3.9 25.3 - - - -
363F GLU* 2.8 31.9 + - - -
424F GLY* 6.3 0.2 - - - -
427F GLU* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E PHE* 3.4 32.1 - - + +
391E ASN* 2.8 14.9 + - - +
393E ARG* 1.3 76.5 - - - +
395E LYS* 1.3 58.9 + - - +
397E ASN* 3.3 5.6 + - - +
398E ALA 2.9 22.2 + - - -
399E ASP 3.0 30.7 + - - +
400E THR* 3.5 3.3 - - + +
423E PRO* 4.4 0.9 - - + -
455E LEU* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389E ALA* 4.1 16.0 + - - +
391E ASN 2.9 17.0 + - - +
392E SER 3.9 3.1 - - - +
394E ALA* 1.3 78.3 - - - +
396E THR* 1.3 62.5 + - - +
398E ALA* 3.1 14.7 + - - +
400E THR* 3.7 21.8 + - + +
91F GLN* 4.7 0.3 + - - -
94F THR* 6.4 1.1 - - - -
95F ALA* 3.9 13.8 - - - +
98F ALA* 3.7 26.8 - - + +
99F LEU* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ARG* 5.0 0.5 + - - -
392E SER 2.7 23.0 + - - -
393E ARG* 3.2 7.3 + - - -
395E LYS* 1.3 78.4 - - - +
397E ASN* 1.3 58.1 + - - +
398E ALA 3.1 0.2 - - - -
453E PRO* 5.6 0.8 - - - +
51F ILE* 3.3 52.5 - - + +
54F LYS* 3.9 11.9 - - + -
55F ALA* 3.3 26.9 - - + +
58F ASN* 5.0 0.5 - - - +
91F GLN* 3.3 25.1 + - - +
95F ALA* 4.0 7.6 - - + -
99F LEU* 4.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ARG* 2.7 33.8 + - - -
393E ARG* 2.9 46.9 + - - +
394E ALA* 3.7 7.2 - - - +
396E THR* 1.3 76.0 - - - +
398E ALA* 1.3 61.3 + - - +
399E ASP* 4.3 12.3 - - + +
423E PRO* 6.1 1.8 - - - +
455E LEU* 4.9 8.7 - - - +
54F LYS* 5.1 1.9 - - - +
58F ASN* 3.4 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ASP* 4.7 4.2 - - - +
73E SER* 6.0 1.8 - - - +
74E ARG* 4.1 11.7 + - - +
394E ALA 2.9 5.6 + - - -
395E LYS* 3.1 15.2 + - - +
396E THR 3.1 0.2 - - - -
397E ASN* 1.3 82.3 - - - +
399E ASP* 1.3 59.6 + - - +
400E THR* 4.1 3.6 - - - -
91F GLN* 3.8 21.5 - - + +
----------------------------------------------------------
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