Contacts of the helix formed by residues 1112 - 1122 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B GLY 3.1 10.8 + - - +
1068B ILE* 2.9 30.6 + - + +
1070B SER* 3.9 9.2 + - - +
1110B VAL* 3.1 5.7 - - - +
1111B ALA* 1.3 78.6 - - - +
1113B PRO* 1.4 57.5 - - - +
1114B ASP* 4.1 2.9 + - - +
1115B GLY* 3.4 12.5 + - - -
1116B TYR* 3.1 21.1 + - - +
1127B ARG 3.4 9.7 + - - -
1128B LYS 2.9 30.1 + - - +
1129B THR* 3.9 13.2 - - - +
1143B PRO* 4.0 7.1 - - + +
1175B GLU* 4.9 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015B LEU* 4.1 12.3 - - + +
1019B TYR* 3.7 24.7 - - - +
1041B SER* 4.2 12.3 - - - -
1045B ARG* 4.1 11.2 - - + -
1046B PRO 4.4 2.2 - - - +
1047B MET* 4.0 19.7 - - - -
1110B VAL* 3.7 22.2 - - + +
1111B ALA 3.7 7.4 - - - +
1112B ASN* 1.4 84.4 - - - +
1114B ASP* 1.3 67.0 + - - +
1116B TYR* 3.7 1.2 - - + +
1117B VAL* 3.2 29.3 + - - +
1175B GLU* 4.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A GLU 5.6 0.2 - - - +
1044A ASN* 5.5 1.0 + - - -
1041B SER* 2.6 24.1 + - - -
1042B PHE* 3.1 15.9 + - - +
1043B GLU* 2.7 51.8 + - - +
1045B ARG* 2.9 21.4 + - - +
1112B ASN* 3.4 2.4 - - - +
1113B PRO* 1.3 78.7 - - - +
1115B GLY* 1.3 53.1 + - - +
1117B VAL* 3.6 2.9 + - - +
1118B TYR* 2.8 33.3 + - - +
1130B ARG* 4.0 17.8 - - + +
1175B GLU* 3.9 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B SER* 3.2 20.9 - - - -
1112B ASN* 3.4 12.9 + - - -
1113B PRO 3.3 0.2 - - - -
1114B ASP* 1.3 75.7 - - - +
1116B TYR* 1.3 52.9 + - - +
1118B TYR* 3.2 8.6 + - - +
1119B THR* 2.6 40.4 + - - +
1126B TRP* 4.2 5.1 - - - -
1128B LYS 4.1 7.9 - - - -
1130B ARG* 4.1 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B TYR* 4.6 5.4 - - - +
1013B HIS 2.7 34.6 + - - -
1015B LEU* 3.7 22.7 - - + -
1018B ILE* 3.5 20.4 - - + +
1070B SER* 3.3 8.1 - - - -
1073B TRP* 3.7 31.7 - + - +
1076B GLN* 3.4 31.5 - - + +
1110B VAL* 3.8 19.3 - - + -
1112B ASN 3.1 14.0 + - - +
1113B PRO* 3.7 8.1 - - + +
1114B ASP 3.3 0.2 - - - -
1115B GLY* 1.3 74.8 - - - +
1117B VAL* 1.3 65.7 + - - +
1119B THR* 2.6 27.8 + - - -
1120B GLN* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A GLU 4.4 0.2 - - - +
1044A ASN* 3.2 41.7 - - + +
1045A ARG* 5.4 0.2 - - - -
1015B LEU* 3.7 28.7 - - + +
1045B ARG* 3.7 23.3 - - - +
1113B PRO 3.2 16.3 + - - +
1114B ASP 3.8 2.9 - - - +
1116B TYR* 1.3 77.8 - - - +
1118B TYR* 1.3 64.3 + - - +
1120B GLN* 2.8 18.7 + - - +
1121B THR* 3.0 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A ASN* 3.7 19.5 - - - +
1114B ASP 2.8 22.0 + - - +
1115B GLY* 3.3 8.7 - - - +
1117B VAL* 1.3 73.4 - - - +
1119B THR* 1.3 56.6 + - - +
1121B THR* 3.7 5.4 - - - -
1122B GLN* 2.8 51.0 + - + +
1123B ASN* 3.1 31.8 + - + +
1126B TRP* 3.5 38.1 - + + -
1130B ARG* 3.3 50.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 4.9 3.5 + - - -
1070B SER* 3.4 22.9 - - - +
1071B ARG 3.7 6.5 - - - +
1073B TRP* 2.9 28.4 + - - -
1115B GLY 2.6 27.4 + - - +
1116B TYR* 2.6 21.3 + - - -
1118B TYR* 1.3 70.3 - - - +
1120B GLN* 1.3 58.7 + - - +
1121B THR 3.5 0.2 - - - -
1122B GLN 4.6 0.2 + - - -
1123B ASN 3.1 16.6 + - - +
1124B ARG* 3.2 35.6 + - - +
1126B TRP* 3.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 3.1 24.7 + - - +
93B MET* 3.5 19.1 - - + +
1014B SER* 3.2 35.0 - - - +
1015B LEU 4.2 2.4 - - - +
1073B TRP* 3.4 31.7 - - + -
1116B TYR* 3.3 41.0 + - + +
1117B VAL* 2.8 10.6 + - - +
1119B THR* 1.3 78.7 - - - +
1121B THR* 1.3 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A HIS* 4.0 33.7 - - + +
1044A ASN* 3.4 21.9 - - - +
4B ARG* 3.8 23.0 - - - +
1117B VAL* 3.0 30.5 + - + +
1118B TYR* 3.7 1.2 + - - -
1120B GLN* 1.3 83.7 - - + +
1122B GLN* 1.3 85.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A HIS* 5.8 2.6 - - - +
1042A PHE 5.6 0.2 + - - -
1044A ASN* 2.9 23.6 + - - +
4B ARG* 3.7 20.0 + - - +
5B GLU* 2.7 34.5 + - - +
1118B TYR* 2.8 40.7 + - + +
1119B THR 4.6 0.4 + - - -
1120B GLN 3.8 0.6 - - - -
1121B THR* 1.3 105.5 + - - +
1123B ASN* 1.3 56.3 + - - +
1124B ARG 4.2 0.7 - - - -
----------------------------------------------------------
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