Contacts of the strand formed by residues 1087 - 1094 (chain A) in PDB entry 5XRA
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 LYS1087 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A ASP 3.7 18.7 + - - +
1052A LEU* 3.3 10.0 - - + +
1053A VAL* 3.2 23.6 + - - +
1085A GLY 4.2 0.8 + - - -
1086A ARG* 1.3 73.1 - - - +
1088A VAL* 1.3 60.6 + - - +
1118A GLU* 3.3 15.5 - - + +
1120A VAL* 3.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A PHE* 6.0 4.0 - - + -
1052A LEU* 4.3 1.6 - - - -
1053A VAL* 3.2 25.8 - - + +
1055A LEU* 4.4 18.6 - - + -
1083A ALA* 5.1 1.6 - - + +
1086A ARG* 3.3 20.0 - - + +
1087A LYS* 1.3 79.7 - - - +
1089A ALA* 1.3 72.5 + - - +
1090A CYS* 5.0 0.2 - - - -
1112A LEU* 2.9 39.5 - - + -
1117A ALA* 3.5 7.9 - - + -
1118A GLU 3.0 5.6 + - - +
1119A ILE* 3.3 7.8 - - - -
1120A VAL* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A LEU* 5.3 0.2 - - + -
1053A VAL 3.3 5.1 + - - +
1054A LEU* 3.4 18.4 - - + +
1055A LEU 3.1 21.8 + - - -
1088A VAL* 1.3 77.0 - - - +
1090A CYS* 1.3 66.1 + - - +
1109A GLU* 5.4 0.2 - - - -
1112A LEU* 5.6 0.2 - - - -
1119A ILE* 5.9 1.1 - - - -
1120A VAL* 4.9 0.9 - - + -
1121A GLN 4.3 15.5 - - - +
1140A TRP* 3.6 26.7 - - + -
1144A VAL* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A LEU* 3.3 14.8 - - - +
1088A VAL* 5.0 0.2 - - - -
1089A ALA* 1.3 80.3 - - - +
1091A PHE* 1.3 62.0 + - - +
1105A VAL* 3.7 22.9 - - + -
1108A ILE* 3.6 30.7 - - + -
1109A GLU* 3.5 31.4 + - + +
1112A LEU* 4.9 10.5 - - - -
1123A GLY* 3.1 6.1 - - - -
1124A LEU 2.9 21.1 + - - -
1140A TRP* 3.3 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A ILE* 3.7 29.2 - - + -
1008A TYR* 4.6 1.1 - - + -
1015A THR* 3.9 14.6 - - + -
1018A THR* 3.5 18.8 - - + -
1019A ALA* 3.8 29.6 - - + -
1022A ILE* 3.8 14.8 - - + -
1054A LEU* 4.0 13.0 - - + -
1055A LEU 3.0 10.1 + - - +
1056A GLY* 3.1 31.6 - - - -
1057A CYS 3.1 21.0 + - - +
1090A CYS* 1.3 76.5 - - - +
1092A GLY* 1.3 60.8 + - - +
1105A VAL* 3.6 11.3 - - - +
1108A ILE* 5.7 0.5 - - - +
1124A LEU* 3.2 32.3 - - + -
1140A TRP* 4.1 9.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A THR* 4.5 2.7 - - - -
1018A THR* 5.7 0.4 - - - +
1057A CYS 3.1 17.5 - - - -
1091A PHE* 1.3 84.2 - - - +
1093A CYS* 1.3 67.0 + - - -
1102A CYS* 3.8 3.6 - - - -
1105A VAL* 3.8 6.7 - - - +
1124A LEU* 3.0 11.2 + - - +
1125A ARG* 3.7 1.9 - - - -
1126A ILE* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A FMN 3.4 22.2 + - - +
1014A ASN* 3.6 1.3 - - + -
1015A THR* 3.6 32.4 + - - +
1018A THR* 3.5 15.5 - - - -
1057A CYS 3.9 3.2 + - - -
1058A SER* 4.0 1.2 + - - +
1059A THR* 3.6 23.4 + - - -
1092A GLY* 1.3 76.4 - - - -
1094A GLY* 1.3 60.3 + - - +
1102A CYS* 3.7 7.2 - - - -
1126A ILE* 3.5 13.2 - - + +
1128A GLY 5.2 1.3 - - - +
1130A PRO* 3.5 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A FMN 3.4 34.6 + - - -
1093A CYS* 1.3 77.9 - - - +
1095A ASP* 1.3 61.2 + - - +
1101A PHE* 4.2 1.1 - - - -
1102A CYS* 3.9 3.6 - - - -
1126A ILE 2.8 14.5 + - - +
1127A ASP* 4.0 0.4 - - - -
1128A GLY* 2.9 25.5 + - - +
----------------------------------------------------------
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