Contacts of the strand formed by residues 1085 - 1094 (chain B) in PDB entry 4OUL
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 THR1085 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A GLU* 5.8 0.2 - - - +
1085A THR* 5.0 7.1 + - - -
1050B HIS* 4.2 22.9 - - + -
1051B MET 3.3 17.3 - - - +
1052B LEU* 3.5 18.6 - - + +
1075B TYR 4.1 2.8 - - - +
1076B ALA* 3.4 11.0 - - - +
1084B GLU* 1.3 88.8 + - - +
1086B ALA* 1.3 69.0 + - - +
1087B SER* 4.0 4.9 + - - -
1116B TYR 5.6 1.6 - - - +
1074C ALA* 6.1 0.3 - - - +
1075C TYR 3.8 14.4 + - - -
1085C THR 5.0 7.3 + - - -
1087C SER* 4.7 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085A THR* 5.8 0.2 - - - -
1049B PHE* 4.0 3.6 - - - -
1050B HIS* 3.6 0.7 - - - -
1051B MET* 2.7 40.2 + - - +
1060B LEU* 3.8 25.6 - - + -
1062B VAL* 4.5 6.5 - - + -
1074B ALA* 3.6 21.8 - - + +
1075B TYR 3.9 12.3 - - - +
1076B ALA* 3.5 11.8 - - + +
1085B THR* 1.3 72.3 - - - +
1087B SER* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A HIS* 3.0 32.3 + - - +
1085A THR* 4.8 10.6 + - - +
1087A SER* 6.0 0.9 - - - -
1116A TYR 5.5 0.2 - - - +
1049B PHE* 3.0 18.6 + - - -
1050B HIS* 3.3 28.5 + - - -
1074B ALA* 3.3 13.6 - - - +
1075B TYR 5.2 0.2 + - - -
1085B THR* 4.0 6.6 + - - -
1086B ALA* 1.3 75.8 - - - +
1088B ASN* 1.3 67.6 + - - +
1087C SER* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A HIS* 3.5 16.8 + - - -
1115A LYS 3.6 10.3 + - - -
1116A TYR 3.1 19.9 + - - -
1118A THR* 2.7 25.1 + - - +
1048B ILE* 3.6 3.5 - - - +
1049B PHE* 3.1 53.3 + - + +
1072B VAL* 3.8 11.8 - - + +
1073B SER 2.7 25.2 + - - +
1087B SER* 1.3 78.2 + - - +
1089B HIS* 1.3 77.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A SER* 4.5 0.4 + - - -
1048A ILE* 3.4 51.0 - - + +
1050A HIS* 3.0 24.0 + - - -
1118A THR* 3.1 34.1 + - - +
1119A PHE 4.0 1.0 + - - -
1120A SER* 2.5 37.0 + - - -
1046B VAL* 5.8 2.5 - - + -
1047B PHE 3.1 14.8 - - - +
1048B ILE* 4.3 5.2 - - + -
1049B PHE* 5.3 1.1 - - - -
1064B LEU* 5.2 1.1 - - - -
1072B VAL* 3.7 15.0 - - - +
1088B ASN* 1.3 88.3 + - - +
1090B ALA* 1.3 70.5 + - - +
1091B ILE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A SER* 4.1 5.8 - - - +
1023A LEU* 5.1 2.9 - - + -
1045B TYR 3.8 0.6 - - - +
1046B VAL* 3.4 4.9 - - - +
1047B PHE* 2.9 33.0 + - + +
1064B LEU* 3.7 25.4 - - + -
1071B LEU* 5.2 0.7 - - + -
1072B VAL* 4.3 12.8 - - + -
1089B HIS* 1.3 82.8 - - - +
1091B ILE* 1.3 66.6 + - - +
1092B LEU* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A ALA* 4.1 11.0 - - + -
1000A PHE 4.0 6.5 - - - +
1001A SER* 3.3 28.0 + - - -
1023A LEU* 4.0 4.0 - - - +
1024A ASN* 3.3 14.6 - - - +
1048A ILE* 5.6 2.5 - - + -
1120A SER* 3.6 26.9 - - - -
1121A GLY 4.1 4.9 - - - +
1122A TYR* 3.5 33.0 - - + -
1044B THR* 3.7 21.5 - - + -
1045B TYR 3.2 10.1 - - - +
1046B VAL* 3.9 19.3 - - + -
1089B HIS* 4.8 1.8 - - + -
1090B ALA* 1.3 78.9 - - - +
1092B LEU* 1.3 66.6 + - - +
1124B LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LEU* 4.5 13.0 - - + +
1024A ASN* 3.7 11.0 - - - +
1044B THR* 4.3 0.2 - - - -
1045B TYR* 2.9 29.5 + - - +
1047B PHE* 3.4 25.8 - - + -
1066B LYS* 6.1 0.9 - - + -
1071B LEU* 3.5 38.4 - - + -
1090B ALA* 3.8 24.0 - - + -
1091B ILE* 1.3 75.9 - - - +
1093B GLN* 1.3 66.1 + - - +
1094B LEU* 3.4 33.7 + - + -
1100B ILE* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LEU 5.0 1.8 + - - -
1024A ASN* 3.7 13.5 - - - +
1043B GLY 3.5 8.1 - - - +
1044B THR* 4.3 7.9 - - - +
1066B LYS* 4.4 7.3 + - - +
1092B LEU* 1.3 73.7 - - - +
1094B LEU* 1.3 69.2 + - - +
1095B PHE* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B PHE* 3.9 13.2 - - + -
1039B CYS* 3.9 11.4 - - + -
1042B ASN* 3.3 3.5 - - - +
1043B GLY 2.8 30.9 + - - -
1045B TYR* 3.8 18.6 - - + -
1047B PHE* 3.8 11.0 - - + -
1066B LYS* 3.9 20.6 - - + +
1092B LEU* 3.4 31.2 - - + -
1093B GLN* 1.3 78.3 - - - +
1095B PHE* 1.3 70.1 + - - +
1098B ASP* 3.8 16.2 - - + +
1100B ILE* 3.7 30.7 - - + -
----------------------------------------------------------
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