Contacts of the helix formed by residues 3020 - 3023 (chain B) in PDB entry 1DJO
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 THR3020 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3019B GLY* 1.3 68.1 - - - -
3021B ILE* 1.3 56.2 + - - +
3022B ALA 2.9 5.8 - - - -
3023B GLY* 2.6 21.9 + - - +
3034B TYR* 2.5 21.5 + - + -
3099B GLY* 4.3 3.2 - - - -
3100B THR* 5.3 0.6 - - - +
3125B SER 3.4 12.3 - - - +
3126B MET 4.0 0.9 - - - +
3127B ARG 3.7 3.1 - - - -
3128B PRO* 3.6 33.6 - - + +
4000B CAB 1.5 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3021 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3018B GLY 3.5 17.7 - - - +
3019B GLY* 4.6 0.9 - - - -
3020B THR* 1.3 79.2 - - - +
3022B ALA* 1.3 61.7 + - + +
3023B GLY 3.4 0.8 + - - +
3039B VAL* 5.5 0.2 - - - +
3044B LEU* 3.3 26.5 - - + +
3097B THR* 4.0 33.0 - - + -
3098B HIS 4.9 2.0 - - - +
3123B VAL* 4.7 5.6 - - + -
3124B GLY* 4.1 25.1 - - - +
3125B SER* 3.1 29.2 + - - +
3127B ARG 4.9 0.4 - - - -
3129B GLY* 4.6 11.3 + - - +
3136B GLY* 4.1 24.7 - - - +
3140B LEU* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3022 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3018B GLY* 3.8 23.3 - - - +
3019B GLY 3.3 6.7 + - - +
3020B THR 2.9 0.4 - - - -
3021B ILE* 1.3 78.7 - - - +
3023B GLY* 1.3 60.0 + - - +
3037B ALA* 4.4 3.8 - - - -
3038B LYS* 2.8 5.9 + - - -
3039B VAL* 2.6 66.1 + - + +
3044B LEU* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3023 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3019B GLY 3.3 6.2 + - - -
3020B THR* 2.6 15.8 + - - -
3021B ILE 4.9 0.2 - - - +
3022B ALA* 1.3 82.2 - - - +
3024B ALA* 1.3 62.5 + - - +
3034B TYR* 4.8 0.7 - - - -
3035B GLN 3.0 15.0 - - - -
3036B ALA* 3.9 4.7 - - - -
3037B ALA 4.1 0.4 - - - -
3038B LYS* 4.3 1.3 - - - -
3039B VAL* 4.5 5.9 - - - +
3128B PRO* 3.9 7.0 - - - -
3129B GLY* 3.6 19.8 + - - -
3130B THR* 4.5 1.9 + - - +
----------------------------------------------------------
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