Contacts of the strand formed by residues 1102 - 1106 (chain F) in PDB entry 2BT4
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 VAL1102 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076F ILE* 3.4 18.2 - - + +
1078F ILE* 4.3 15.7 - - + -
1094F LEU* 4.4 27.4 - - + -
1097F CYS* 5.3 1.3 - - + -
1100F LEU* 3.8 6.7 - - + +
1101F PRO* 1.3 75.7 - - - +
1103F VAL* 1.3 69.3 + - - +
1125F ARG* 3.5 31.6 - - + +
1126F ALA* 3.8 20.4 - - + -
1127F ASP* 2.8 39.4 + - - +
1128F GLY 3.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076F ILE 2.9 9.7 + - - +
1077F VAL* 3.3 5.1 - - + +
1078F ILE* 2.9 27.0 + - - +
1102F VAL* 1.3 84.1 - - - +
1104F GLU* 1.3 70.4 + - - +
1105F VAL* 4.4 3.1 - - + -
1127F ASP* 5.6 1.1 - - + -
1128F GLY* 3.4 19.3 - - - +
1130F VAL* 4.3 14.6 - - + -
1140F PHE 5.3 0.2 - - - -
1141F GLY* 3.9 23.3 - - - +
1144F ARG* 3.7 35.7 - - + -
1145F ILE* 3.9 13.9 - - + -
1148F LEU* 5.8 1.1 - - + -
1533H CYS* 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078F ILE* 3.3 11.2 - - - +
1080F PRO* 4.1 4.9 - - + -
1084F SER* 4.1 1.9 + - - -
1103F VAL* 1.3 73.4 - - - +
1105F VAL* 1.3 59.3 - - - +
1106F HIS* 2.7 32.6 + - - +
1120F SER* 2.5 24.5 + - - -
1122F VAL* 3.7 18.4 - - + +
1123F SER* 2.5 35.9 + - - -
1126F ALA* 3.8 14.9 - - + +
1128F GLY 2.9 7.8 + - - +
1129F VAL* 3.2 9.4 - - + +
1130F VAL 2.7 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077F VAL* 3.8 25.6 - - + -
1078F ILE 2.9 10.2 + - - +
1079F ASN* 3.1 33.2 - - + +
1103F VAL* 4.4 7.2 - - + -
1104F GLU* 1.3 76.3 - - - +
1106F HIS* 1.3 81.2 + - - +
1130F VAL* 3.4 9.6 - - + +
1134F GLY 4.9 1.3 - - - +
1137F GLY* 3.5 39.7 - - - +
1138F TYR* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079F ASN* 4.0 0.4 + - - +
1080F PRO* 4.0 9.9 - - + -
1081F ALA 4.9 0.2 - - - -
1084F SER* 3.1 32.3 - - - -
1085F HIS* 5.3 1.1 - + - -
1104F GLU* 2.7 30.2 + - + -
1105F VAL* 1.3 80.2 + - - +
1107F ILE* 1.3 65.8 + - - +
1108F SER 3.5 14.1 - - - +
1110F ILE* 3.8 34.7 - - + +
1120F SER* 4.6 0.6 + - - -
1123F SER* 5.2 0.2 + - - -
1129F VAL* 4.5 6.1 - - + -
1130F VAL* 2.9 9.8 + - - +
1131F ALA* 3.4 13.7 - - + -
1132F GLY 3.0 16.5 + - - -
1133F CYS 4.3 1.9 + - - -
1134F GLY 4.7 0.3 - - - +
1137F GLY* 6.0 0.3 - - - -
1160F CA2 3.2 27.5 + - + +
----------------------------------------------------------
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