Contacts of the helix formed by residues 125 - 133 (chain A) in PDB entry 1FQV
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 CYS 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A CYS 4.1 1.6 + - - -
124A LEU* 1.3 73.7 - - - +
126A LEU* 1.3 67.6 + - - +
127A PRO* 3.2 20.4 - - + -
128A GLU* 2.9 43.8 + - - +
129A LEU* 2.9 9.7 + - - +
427A ARG 5.5 3.6 - - - -
428A LEU* 4.5 2.9 - - - -
429A THR 5.8 0.4 - - - +
128B LYS* 4.1 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A CYS* 1.3 71.1 - - - +
127A PRO* 1.3 65.3 - - + +
129A LEU* 3.1 5.4 + - + +
130A LEU* 3.1 24.8 + - + +
149A TRP* 3.6 36.3 - - + -
152A LEU* 4.2 4.5 - - + -
154A LEU* 3.7 18.8 - - + -
427A ARG 5.5 0.2 + - - -
428A LEU* 3.9 25.4 - - + +
429A THR 3.1 37.0 + - - +
430A LEU* 3.5 24.2 - - + -
159B TRP* 3.8 14.1 - - + -
160B CYS* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A CYS* 3.2 25.4 - - + -
126A LEU* 1.3 96.5 - - + +
128A GLU* 1.3 64.1 + - - +
130A LEU* 3.5 3.9 + - + +
131A LYS* 3.2 20.0 + - - +
429A THR 4.3 5.6 - - - +
430A LEU* 4.4 9.6 - - + -
160B CYS* 3.9 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.6 21.5 - - + -
125A CYS* 2.9 37.0 + - - +
127A PRO* 1.3 83.0 - - - +
129A LEU* 1.3 67.7 + - - +
131A LYS* 3.0 45.9 + - - +
132A VAL* 3.1 19.8 + - - +
127B ILE* 5.3 0.9 - - + -
128B LYS* 3.7 37.8 + - + +
129B GLY 4.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.1 15.9 - - + +
124A LEU* 4.0 7.3 - - + +
125A CYS 2.9 11.3 + - - +
126A LEU* 3.1 10.5 + - + +
128A GLU* 1.3 78.6 - - - +
130A LEU* 1.3 60.0 + - + +
132A VAL* 2.9 28.8 - - + +
133A SER* 3.2 8.8 + - - -
143A ALA* 3.6 34.8 - - + +
148A LEU* 3.8 23.3 - - + -
149A TRP* 3.6 27.8 - - + +
427A ARG* 5.0 3.1 - - - +
428A LEU* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.1 14.8 + - + +
127A PRO* 4.0 5.6 - - + +
128A GLU 3.2 0.4 - - - -
129A LEU* 1.3 76.3 - - + +
131A LYS* 1.3 61.9 + - - +
133A SER* 2.7 23.0 + - - +
134A GLY 4.2 0.5 + - - -
143A ALA 5.7 0.4 - - - +
149A TRP* 3.9 30.3 - - + -
167A LEU* 5.8 1.3 - - + -
153B VAL* 5.1 0.5 - - - +
157B ASN* 3.2 41.6 + - + +
159B TRP* 3.5 21.8 - - + +
160B CYS* 3.4 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO 3.2 11.4 + - - +
128A GLU* 3.0 38.7 + - - +
130A LEU* 1.3 77.5 - - - +
132A VAL* 1.3 63.3 + - - +
134A GLY* 3.0 15.8 + - - -
127B ILE* 3.1 26.8 + - + +
128B LYS* 3.6 2.4 - - - +
129B GLY* 3.2 12.5 - - - +
130B LYS 3.2 21.9 + - - +
131B THR* 4.8 1.6 - - - -
132B PRO* 3.9 27.7 - - + +
135B ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.2 13.2 - - + -
124A LEU* 3.4 17.3 - - + -
128A GLU 3.3 12.8 - - - +
129A LEU* 2.9 35.4 - - + +
131A LYS* 1.3 71.9 - - + +
133A SER* 1.3 53.5 + - - +
134A GLY 2.8 15.7 + - - -
135A VAL* 2.8 30.3 + - - +
139A TRP* 3.5 26.8 - - + +
143A ALA* 4.3 1.3 - - + -
127B ILE* 3.4 33.4 - - + -
135B ILE* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.2 5.1 + - - -
130A LEU* 2.7 28.0 + - - -
132A VAL* 1.3 79.5 - - - +
134A GLY* 1.3 56.8 + - - +
135A VAL 3.4 0.2 - - - -
139A TRP 4.1 0.2 - - - -
140A TYR* 2.9 49.8 + - - +
143A ALA* 3.4 29.8 - - - -
144A SER* 5.6 1.8 - - - -
145B PHE* 3.6 2.3 - - - -
153B VAL* 3.9 2.1 - - - +
157B ASN* 3.3 14.7 + - - -
----------------------------------------------------------
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