Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 6MUO
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 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 1.3 90.4 - - + +
124A LYS* 1.3 63.0 + - - +
125A ASP 3.2 0.2 - - - -
126A VAL* 3.9 5.6 - - + +
127A GLN* 3.2 36.6 + - - +
47B SER* 5.1 1.3 - - - +
49B LEU* 3.6 41.1 - - + +
50B ILE* 3.7 17.9 - - + -
53B GLU* 3.9 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 5.1 9.0 - - - +
122A PHE* 3.1 14.3 - - + +
123A PRO* 1.3 76.9 - - - +
125A ASP* 1.3 60.2 + - - +
126A VAL 3.2 0.4 - - - -
127A GLN* 4.1 10.7 + - - +
128A LEU* 3.0 32.7 + - - +
115E HIS* 3.7 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 3.2 27.9 - - - +
112A LEU* 3.5 14.6 - - + +
113A THR* 3.0 36.0 - - + +
118A ARG* 4.0 11.8 + - - -
121A LEU* 4.6 4.3 - - + -
122A PHE* 2.8 23.1 + - - +
124A LYS* 1.3 77.3 - - - +
126A VAL* 1.3 61.3 + - - +
128A LEU* 4.4 3.6 - - - +
129A ALA* 3.4 8.9 - - - +
115E HIS* 2.4 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.3 23.1 - - + -
106A PHE* 5.1 15.5 - - + -
109A ALA* 4.5 10.3 - - + -
121A LEU* 5.2 4.3 - - + -
122A PHE 3.4 10.1 + - - +
123A PRO 3.7 2.0 + - - +
124A LYS 3.2 0.4 - - - -
125A ASP* 1.3 84.1 - - + +
127A GLN* 1.3 63.7 + - - +
128A LEU 3.2 1.6 - - - -
129A ALA* 3.1 13.2 + - - +
130A ARG* 3.2 18.5 + - - +
50B ILE* 4.4 14.8 - - + -
53B GLU* 4.1 28.7 - - + +
54B THR* 6.1 0.4 - - - +
57B VAL* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 3.2 25.7 + - - +
124A LYS* 4.2 12.1 + - - +
126A VAL* 1.3 78.2 - - - +
128A LEU* 1.3 57.8 + - - +
130A ARG* 3.9 1.9 + - - +
131A ARG* 3.7 9.9 + - - +
53B GLU* 4.3 21.7 + - - +
531L TRP* 3.1 41.4 - - + +
532L VAL* 3.4 46.2 - - - +
533L VAL* 4.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 9.0 - - + -
124A LYS 3.0 18.2 + - - +
127A GLN* 1.3 76.3 - - - +
129A ALA* 1.3 63.5 + - - +
130A ARG 3.2 1.1 - - - -
131A ARG* 3.9 7.4 - - + +
132A ILE* 3.3 35.3 + - + +
111E LEU* 3.8 34.5 - - + +
112E LEU* 3.8 12.6 - - + -
115E HIS* 3.6 42.8 - - + +
531L TRP* 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.4 13.0 - - + +
108A ASP 4.5 4.3 - - - +
109A ALA* 3.8 23.1 - - + +
112A LEU* 4.1 11.4 - - + +
125A ASP 3.4 21.2 + - - +
126A VAL* 3.1 7.9 + - - +
128A LEU* 1.3 78.1 - - - +
130A ARG* 1.3 60.7 + - - +
132A ILE* 4.5 2.9 - - - -
133A ARG* 3.3 24.5 + - - +
132E ILE* 4.6 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 6.3 1.3 - - + -
105A LEU* 4.6 15.5 - - + -
126A VAL* 3.2 19.1 + - - +
127A GLN* 4.4 3.7 - - - +
129A ALA* 1.3 82.5 - - - +
131A ARG* 1.3 63.6 + - - +
132A ILE 3.4 0.2 - - - -
133A ARG* 3.3 17.7 + - + +
134A GLY 3.6 5.7 + - - -
135A LEU 4.6 0.5 + - - -
137A GLU 6.0 0.4 - - - +
138A GLY* 3.8 20.3 + - - +
139A LEU* 2.4 38.9 + - - +
53B GLU* 5.3 2.2 + - - -
57B VAL* 4.1 37.5 - - - +
60B VAL* 4.3 5.3 - - - +
530L TRP* 3.8 27.7 + - + -
531L TRP* 2.2 40.5 + - + +
533L VAL* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN 3.7 8.5 + - - +
128A LEU* 3.5 10.2 + - + +
130A ARG* 1.3 77.7 - - - +
132A ILE* 1.3 66.4 + - - +
133A ARG 3.5 0.2 + - - -
134A GLY* 3.8 8.5 + - - -
110C ASN* 5.4 3.0 + - - -
104E HIS* 5.6 8.3 - - - -
107E GLU* 4.4 17.3 + - - -
108E ASP* 4.6 7.3 + - - +
111E LEU* 3.5 32.4 - - - +
530L TRP* 4.5 15.7 - - + +
531L TRP* 3.5 63.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 7.9 - - + -
128A LEU* 3.3 32.1 + - + +
129A ALA* 5.1 0.4 - - - -
131A ARG* 1.3 77.9 - - + +
133A ARG* 1.3 63.5 + - - +
134A GLY* 3.3 3.3 + - - -
108E ASP* 3.1 50.2 - - - +
111E LEU* 5.2 3.6 - - + -
112E LEU* 3.7 39.7 - - + -
129E ALA* 5.0 13.7 - - + +
132E ILE* 4.3 27.8 - - + -
133E ARG* 4.0 12.0 + - + +
----------------------------------------------------------
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