Contacts of the strand formed by residues 122 - 126 (chain D) in PDB entry 6F0X
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 ALA 122 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D SER* 3.0 23.0 + - - +
110D GLU* 3.1 30.9 + - + +
112D LEU* 3.5 19.3 - - + -
120D ILE 2.8 4.2 + - - -
121D ALA* 1.3 74.8 - - - +
123D ASN* 1.3 67.0 + - - +
210D ILE* 5.4 4.9 - - + -
211D GLU 3.6 7.2 - - - +
212D ILE* 5.0 0.2 - - - +
232D MET* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D SER* 2.3 33.7 + - - +
121D ALA* 4.1 1.4 - - - -
122D ALA* 1.3 75.7 + - - +
124D HIS* 1.3 60.7 + - - +
125D TRP* 4.0 12.8 - - + -
210D ILE* 3.5 7.3 - - - +
211D GLU* 2.9 74.3 + - + +
213D ASN* 5.6 1.8 - - - +
286E GLN* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D PRO* 3.6 21.4 - - + +
108D SER* 3.6 13.2 + - - +
109D SER 4.6 3.6 - - - +
110D GLU* 3.5 31.4 - - + +
122D ALA 4.4 0.4 - - - +
123D ASN* 1.3 75.2 - - - +
125D TRP* 1.3 60.9 + - - +
126D VAL* 3.7 3.1 + - + +
208D GLN* 2.8 27.1 + - - -
209D LEU 3.5 3.1 - - - -
210D ILE* 3.2 25.1 - - + -
239D LEU* 3.5 18.1 - - + +
156P GLY* 4.6 5.1 + - - -
157P ASN* 3.0 41.8 + - + +
160P SER* 5.5 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLY* 3.3 30.4 + - - -
108D SER* 4.5 6.0 + - - -
123D ASN* 4.0 8.3 - - + -
124D HIS* 1.3 77.8 - - - +
126D VAL* 1.3 68.8 + - - +
127D LEU* 3.4 1.6 + - + -
131D GLU* 2.5 40.1 + - + +
132D PHE* 3.2 25.1 - + + -
190D LYS* 3.9 23.8 - - + -
208D GLN* 3.9 2.8 - - - -
209D LEU* 2.9 67.8 + - + +
211D GLU* 3.6 24.9 - - + -
286E GLN* 6.2 4.3 - - + -
289E ARG* 4.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 3.7 21.8 - - + +
105D ASP 5.2 12.1 + - - +
107D PRO* 6.0 1.1 - - + -
124D HIS* 3.7 3.6 + - + +
125D TRP* 1.3 75.2 - - - +
127D LEU* 1.3 76.6 + - - +
129D ALA* 4.0 13.9 - - - +
131D GLU* 5.2 1.7 - - - +
206D TYR* 5.5 2.2 - - + -
207D GLY 4.4 6.7 - - - +
208D GLN* 4.5 2.5 - - - +
157P ASN* 3.3 42.4 - - + +
158P ALA* 4.7 7.9 - - + +
159P LEU* 4.3 20.6 - - + +
229P LYS* 5.2 2.2 - - - +
----------------------------------------------------------
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