Contacts of the helix formed by residues 1125 - 1134 (chain A) in PDB entry 3UON
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 ARG1125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120A MET* 3.2 22.7 + - + +
1123A GLN* 3.1 48.3 + - + +
1124A LYS* 1.3 74.5 - - - +
1126A TRP* 1.3 60.0 + - - +
1127A ASP 3.6 1.8 - - - -
1128A GLU* 2.8 49.5 + - + +
1129A ALA* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091A LEU* 4.2 4.9 - - + -
1092A ASP* 5.1 1.1 - - - -
1095A ARG* 3.4 50.9 - - - +
1121A LEU* 3.8 31.4 - - + -
1124A LYS* 3.3 60.0 + - + +
1125A ARG* 1.3 70.3 - - - +
1127A ASP* 1.3 64.7 + - - +
1129A ALA* 3.2 5.5 + - - +
1130A ALA* 2.9 28.2 + - - +
1153A PHE* 3.4 13.9 - - - +
1154A ARG* 3.3 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125A ARG 3.6 0.2 - - - -
1126A TRP* 1.3 79.1 - - - +
1128A GLU* 1.3 61.6 + - + +
1130A ALA* 3.4 3.3 + - - +
1131A VAL* 3.0 33.6 + - + +
1154A ARG* 3.5 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120A MET* 3.3 17.1 - - + +
1125A ARG* 2.8 55.7 + - + +
1126A TRP 3.3 0.4 - - - -
1127A ASP* 1.3 77.2 - - + +
1129A ALA* 1.3 62.4 + - - +
1130A ALA 3.2 0.2 - - - -
1131A VAL* 3.4 8.9 + - - +
1132A ASN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117A SER* 4.1 3.2 + - - +
1120A MET* 3.9 23.5 - - + +
1121A LEU* 3.8 31.6 - - + -
1125A ARG 3.1 20.5 + - - +
1126A TRP 3.4 5.8 - - - +
1128A GLU* 1.3 77.0 - - - +
1130A ALA* 1.3 57.2 + - - +
1132A ASN* 3.4 2.5 + - - +
1133A LEU* 2.9 37.8 + - + +
1153A PHE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126A TRP 2.9 11.7 + - - +
1127A ASP 3.4 2.2 - - - +
1128A GLU 3.2 0.2 - - - -
1129A ALA* 1.3 74.1 - - - +
1131A VAL* 1.3 66.5 + - - +
1133A LEU* 3.0 13.8 + - - +
1134A ALA* 3.1 14.8 + - - +
1150A ILE* 3.5 30.9 - - + +
1153A PHE* 6.3 1.7 - - + +
1154A ARG* 3.3 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A ASP* 3.0 19.0 + - + +
1128A GLU* 3.7 10.3 - - - +
1130A ALA* 1.3 75.4 - - - +
1132A ASN* 1.3 62.7 + - - +
1134A ALA* 3.4 13.9 + - - +
1135A LYS* 3.5 33.6 + - - +
1154A ARG* 4.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114A PHE* 6.0 0.3 - - - -
1116A ASN* 4.0 10.6 - - - +
1117A SER* 2.5 35.4 + - - +
1120A MET* 3.6 19.5 - - - +
1128A GLU 2.9 17.8 + - - +
1129A ALA 3.7 2.0 - - - +
1131A VAL* 1.3 78.2 - - + +
1133A LEU* 1.3 62.0 + - - +
1135A LYS* 3.3 37.2 + - - +
1136A SER* 4.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A MET* 4.7 6.5 - - + -
1114A PHE* 3.6 28.0 - - + -
1117A SER* 3.5 24.2 - - - +
1118A LEU* 6.1 2.0 - - + -
1121A LEU* 5.3 5.2 - - + -
1129A ALA* 2.9 30.5 + - + +
1130A ALA* 3.0 5.3 + - - +
1132A ASN* 1.3 71.2 - - - +
1134A ALA* 1.3 58.1 + - - +
1135A LYS 3.1 5.7 + - - -
1136A SER* 2.7 28.6 + - - -
1138A TRP* 4.4 11.0 - - + -
1139A TYR* 4.0 2.9 - - - +
1150A ILE* 3.6 29.5 - - + +
1153A PHE* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130A ALA 3.1 11.3 + - - +
1131A VAL* 3.7 11.9 - - - +
1132A ASN 3.3 0.4 - - - -
1133A LEU* 1.3 76.8 - - - +
1135A LYS* 1.3 60.2 + - - +
1136A SER 3.2 8.7 + - - +
1139A TYR* 3.6 45.1 - - + -
1140A ASN* 4.2 3.5 + - - +
1150A ILE* 4.0 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