Contacts of the helix formed by residues 20 - 25 (chain K) in PDB entry 4QOC
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 PRO 20 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLN 3.6 8.3 - - - +
19K ILE* 1.3 94.7 - - + +
21K ALA* 1.3 63.5 + - - +
22K SER* 3.0 24.0 + - - +
23K GLU* 3.2 24.3 + - + +
24K GLN* 4.7 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 5.8 2.2 - - + +
24C GLN* 4.8 7.9 - - - +
25C GLU* 4.0 9.2 - - + +
51C LYS* 3.8 26.5 - - - +
19K ILE 3.9 1.4 + - - -
20K PRO* 1.3 72.1 - - - +
22K SER* 1.3 61.8 + - - +
23K GLU 3.2 1.2 + - - -
24K GLN* 3.4 18.9 + - - +
25K GLU* 3.5 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 3.6 31.7 + - - +
20K PRO* 3.0 16.7 - - - +
21K ALA* 1.3 79.5 - - - +
23K GLU* 1.3 66.3 + - - +
25K GLU* 2.9 23.5 + - - +
26K THR* 3.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ILE* 4.3 9.6 - - + -
20K PRO* 3.2 20.9 + - + +
22K SER* 1.3 84.0 + - - +
24K GLN* 1.3 59.9 + - + +
26K THR* 2.8 33.9 + - - +
50K MET* 3.3 12.0 - - - +
100K TYR* 3.6 42.9 - - + +
104K TYR* 2.5 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA* 3.4 12.9 + - - +
22K SER 3.1 1.8 + - - -
23K GLU* 1.3 76.1 - - + +
25K GLU* 1.3 59.6 + - + +
26K THR 3.4 0.4 - - - -
49K THR* 4.0 2.9 - - - -
50K MET* 3.6 9.6 + - - -
51K LYS* 2.9 61.3 + - + +
54K LEU* 3.9 14.3 - - + +
100K TYR* 3.6 18.7 + - - +
201K 35T 3.9 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.7 16.1 - - + +
22C SER* 3.0 39.4 + - - +
25C GLU* 2.4 34.1 - - - +
45E LYS* 3.7 22.2 + - + +
52E GLU* 5.3 1.3 - - - +
21K ALA* 3.5 11.4 - - - +
22K SER* 2.9 11.5 + - - +
24K GLN* 1.3 79.8 - - + +
26K THR* 1.3 65.7 + - - +
27K LEU* 3.4 16.3 + - - +
49K THR* 4.7 6.6 - - - +
50K MET 4.7 0.2 - - - -
----------------------------------------------------------
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