Contacts of the helix formed by residues 1112 - 1122 (chain A) in PDB entry 2BOA
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 ASN1112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A GLY 3.1 10.6 + - - +
1068A ILE* 3.1 30.6 + - + +
1070A SER* 3.8 10.1 + - - +
1110A VAL* 3.2 3.7 - - - +
1111A ALA* 1.3 78.2 - - - +
1113A PRO* 1.3 60.0 - - - +
1114A ASP* 3.9 2.8 + - - +
1115A GLY* 3.2 14.3 + - - -
1116A TYR* 3.1 21.3 + - - +
1127A ARG 3.5 5.1 + - - -
1128A LYS 2.8 29.9 + - - -
1129A THR* 3.8 16.9 - - + +
1143A PRO* 3.9 5.7 - - + +
1175A GLU* 4.8 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A LEU* 3.8 13.3 - - + +
1019A TYR* 3.6 25.1 - - - +
1041A SER* 4.2 6.5 - - - -
1045A ARG* 4.0 9.7 - - + -
1046A PRO 4.5 0.7 - - - +
1047A MET* 3.6 31.9 - - - -
1110A VAL* 3.6 23.3 - - + +
1111A ALA 3.8 0.4 - - - +
1112A ASN* 1.3 83.5 - - - +
1114A ASP* 1.3 66.8 + - - +
1116A TYR* 3.8 1.4 - - + +
1117A VAL* 3.2 28.9 + - - +
1175A GLU* 4.1 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041A SER* 2.4 26.5 + - - -
1042A PHE* 3.3 12.2 + - - +
1043A GLU* 2.7 51.5 + - - +
1045A ARG* 3.1 20.8 + - - +
1112A ASN* 3.4 3.2 + - - +
1113A PRO* 1.3 74.9 - - - +
1115A GLY* 1.3 60.8 + - - +
1117A VAL* 3.6 2.1 + - - +
1118A TYR* 2.9 29.3 + - - +
1130A ARG* 3.7 20.6 - - + +
1175A GLU* 4.0 2.9 - - - +
1403A GOL 5.3 0.3 + - - -
1044B ASN* 5.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A SER* 3.1 20.0 - - - -
1112A ASN* 3.2 14.3 + - - -
1114A ASP* 1.3 76.7 - - - +
1116A TYR* 1.3 58.4 + - - +
1118A TYR* 3.4 3.4 + - - +
1119A THR* 2.8 34.0 + - - +
1126A TRP* 4.1 8.9 - - - -
1128A LYS 4.0 8.7 - - - -
1130A ARG* 4.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A TYR* 5.0 3.1 - - - +
1013A HIS 2.5 35.5 + - - -
1015A LEU* 3.9 22.7 - - + -
1018A ILE* 3.6 20.7 - - + +
1070A SER* 3.3 10.3 - - - -
1073A TRP* 3.6 32.6 + + - +
1076A GLN* 3.3 32.6 - - + +
1110A VAL* 3.9 15.7 - - + -
1112A ASN 3.1 16.7 + - - +
1113A PRO 3.8 4.9 - - - +
1114A ASP 3.3 0.2 - - - -
1115A GLY* 1.3 76.7 - - - +
1117A VAL* 1.3 62.3 + - - +
1119A THR* 2.7 22.7 + - - -
1120A GLN* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A LEU* 3.9 27.1 - - + +
1045A ARG* 3.9 23.8 - - - +
1113A PRO 3.2 16.6 + - - +
1114A ASP 4.0 3.1 - - - +
1116A TYR* 1.3 77.8 - - - +
1118A TYR* 1.3 62.2 + - - +
1120A GLN* 2.9 16.9 + - + +
1121A THR* 2.8 22.6 + - + +
1044B ASN* 3.3 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 5.0 4.7 + - - -
1114A ASP 2.9 21.8 + - - +
1115A GLY 3.6 4.9 - - - +
1116A TYR 3.3 0.2 - - - -
1117A VAL* 1.3 72.8 - - - +
1119A THR* 1.3 56.9 + - - +
1121A THR* 3.7 5.2 - - - -
1122A GLN* 2.8 58.0 + - + +
1123A ASN* 3.0 30.2 + - + +
1126A TRP* 3.4 37.2 - + + -
1130A ARG* 3.4 51.7 + - + -
1403A GOL 3.5 7.6 + - - -
1044B ASN* 3.6 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 5.5 2.1 + - - -
1070A SER* 3.5 9.6 - - - +
1071A ARG 3.8 6.3 - - - +
1073A TRP* 2.9 32.1 + - - -
1115A GLY 2.8 27.7 + - - +
1116A TYR* 2.7 20.1 + - - -
1118A TYR* 1.3 74.2 - - - +
1120A GLN* 1.3 59.9 + - - +
1121A THR 3.6 0.3 + - - -
1122A GLN 4.6 0.2 + - - -
1123A ASN 3.1 16.3 + - - +
1124A ARG* 3.3 30.5 + - - +
1126A TRP* 3.4 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 4.0 20.6 + - - +
93A MET* 4.0 13.5 - - - +
1013A HIS 3.2 11.0 + - - +
1014A SER* 3.0 30.7 + - - -
1015A LEU 4.3 0.5 + - - -
1073A TRP* 3.5 34.7 - - + -
1116A TYR* 3.2 44.6 + - + +
1117A VAL* 2.9 9.3 + - + +
1119A THR* 1.3 78.1 - - - +
1121A THR* 1.3 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.3 25.3 + - - +
1117A VAL* 2.8 32.2 + - + +
1118A TYR* 3.7 1.2 - - - -
1120A GLN* 1.3 86.4 - - + +
1122A GLN* 1.3 72.9 + - - +
1037B LYS* 5.4 0.4 - - - +
1040B HIS* 3.8 37.7 - - + +
1044B ASN* 3.5 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.9 24.4 + - - +
5A GLU* 2.9 30.0 + - - +
1118A TYR* 2.8 52.6 + - + +
1119A THR 4.6 0.6 + - - -
1121A THR* 1.3 91.2 + - - +
1123A ASN* 1.3 60.0 + - - +
1403A GOL 5.0 3.5 - - - -
1040B HIS* 6.1 1.4 + - - +
1044B ASN* 3.3 21.4 + - - +
----------------------------------------------------------
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