Contacts of the strand formed by residues 1029 - 1035 (chain F) in PDB entry 3F5P
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 ARG1029 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015F GLU* 2.9 35.1 + - + +
1016F GLY 3.5 7.0 - - - +
1017F VAL* 5.8 5.4 - - + -
1028F THR* 1.3 84.4 - - - +
1030F VAL* 1.3 66.1 + - - +
1066F LEU* 5.2 0.2 - - - +
1080F GLU* 4.9 0.9 - - - +
1081F LEU* 3.3 25.5 + - + +
1083F THR* 3.4 32.4 - - - +
1145F GLU* 4.6 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1030 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015F GLU* 3.7 1.4 - - - -
1016F GLY 3.1 36.2 + - - +
1017F VAL 4.2 0.2 - - - -
1018F ALA* 3.8 27.8 - - + +
1028F THR* 4.5 4.3 - - + +
1029F ARG* 1.3 81.4 - - - +
1031F ALA* 1.3 58.6 + - - +
1032F ILE* 3.5 25.8 - - + -
1066F LEU* 3.3 33.2 - - + -
1078F ILE* 3.5 12.1 - - + -
1079F MET 3.3 7.6 - - - +
1081F LEU* 3.4 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1031 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 3.5 56.3 - - + +
1005F LEU* 4.5 0.4 - - + -
1013F VAL* 4.0 5.6 - - + -
1014F TYR 3.4 5.4 - - - +
1030F VAL* 1.3 75.1 - - - +
1032F ILE* 1.3 67.0 + - - +
1077F VAL 3.5 0.5 - - - +
1079F MET 2.9 31.3 + - - +
1081F LEU* 3.7 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1032 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 3.9 1.6 - - - -
999F ILE* 3.8 19.7 - - + -
1000F THR 5.4 0.2 - - - +
1001F MET* 3.6 30.7 - - + -
1012F MET 3.5 2.4 - - - +
1013F VAL* 3.3 1.8 - - - -
1014F TYR* 2.6 49.0 + - + +
1015F GLU 4.9 0.9 - - - +
1016F GLY* 4.9 7.4 - - - +
1030F VAL* 3.5 21.8 - - + +
1031F ALA* 1.3 81.6 - - - +
1033F LYS* 1.3 62.2 + - - +
1076F LEU* 3.7 24.0 - - + -
1077F VAL 3.3 5.4 - - - +
1078F ILE* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1033 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 2.9 55.3 + - + +
1008F GLY* 3.1 6.0 - - - -
1009F SER* 2.6 45.6 + - - +
1010F PHE* 3.3 20.9 - - - +
1011F GLY* 3.4 12.6 - - - +
1012F MET 3.7 11.0 - - - +
1013F VAL* 4.2 11.9 - - + +
1032F ILE* 1.3 74.4 - - - +
1034F THR* 1.3 68.6 + - - +
1047F PHE* 4.2 8.5 - - + -
1075F THR 3.4 5.2 - - - +
1076F LEU* 3.4 5.9 - - - +
1077F VAL* 3.1 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1034 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001F MET* 3.7 21.3 - - + -
1011F GLY* 3.5 5.9 - - - -
1012F MET* 3.3 35.2 + - - +
1014F TYR* 3.5 12.5 + - + -
1033F LYS* 1.3 73.3 - - - +
1035F VAL* 1.3 63.3 + - - +
1036F ASN* 3.7 4.5 + - - +
1074F PRO* 4.3 18.6 - - + -
1075F THR 3.6 2.7 - - - -
1076F LEU* 3.4 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1035 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010F PHE* 3.6 22.0 - - + +
1033F LYS* 5.1 0.4 - - + +
1034F THR* 1.3 73.0 - - - +
1036F ASN* 1.3 70.7 + - - +
1039F ALA* 4.5 13.5 - - + -
1043F GLU* 5.5 1.1 - - + -
1044F ARG* 4.5 23.3 + - + +
1047F PHE* 3.4 40.4 - - + -
1048F LEU* 5.5 0.7 - - + -
1074F PRO* 3.3 22.0 - - - +
1075F THR* 3.2 33.2 + - + +
1077F VAL* 4.9 2.5 - - + -
----------------------------------------------------------
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