Contacts of the strand formed by residues 1087 - 1094 (chain B) in PDB entry 3KQ4
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 ALA1087 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085B LEU 5.3 0.2 - - - +
1086B ILE* 1.3 76.6 - - - +
1088B VAL* 1.3 61.3 + - - +
1089B HIS* 3.3 22.5 - - + +
1131B THR* 4.6 1.1 - - + -
1132B ILE 3.1 5.2 - - - -
1133B ILE* 3.3 26.2 - - + -
1158B TRP* 3.4 1.2 - - - -
1159B ASP* 3.2 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B PHE* 4.2 13.2 - - + -
1086B ILE* 4.4 2.7 - - + -
1087B ALA* 1.3 72.7 - - - +
1089B HIS* 1.3 66.7 + - - +
1090B PHE* 3.6 26.6 - - + -
1109B ILE* 5.9 3.8 - - + -
1130B PRO 4.1 1.0 - - - +
1131B THR* 3.5 5.4 - - - -
1132B ILE* 2.8 55.0 + - + +
1139B LEU* 3.8 26.9 - - + -
1141B LEU* 6.0 4.0 - - + -
1156B ALA* 4.0 8.3 - - + -
1157B TYR 3.3 11.0 - - - +
1158B TRP* 4.3 8.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
1087B ALA* 3.3 21.8 + - + +
1088B VAL* 1.3 73.4 - - - +
1090B PHE* 1.3 64.5 + - - +
1130B PRO 5.4 0.2 - - - -
1131B THR* 3.6 33.6 + - + +
1156B ALA* 2.8 20.4 - - - +
1157B TYR* 2.9 63.4 + + + +
1159B ASP* 4.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B PHE* 5.0 4.0 - + - -
1088B VAL* 3.6 23.1 - - + -
1089B HIS* 1.3 80.2 - - - +
1091B THR* 1.3 60.1 + - - +
1092B ASN 4.2 8.1 - - - +
1093B PHE* 3.8 25.8 - + - -
1107B LEU* 4.1 24.0 - - + -
1109B ILE* 4.4 9.4 - - + -
1128B LEU* 3.2 36.6 - - + +
1129B PRO* 3.7 36.1 + - + +
1130B PRO 4.2 6.3 - - - -
1132B ILE* 4.2 12.3 - - + -
1141B LEU* 6.1 0.7 - - + -
1154B PHE* 4.3 8.7 - + + -
1155B SER 4.3 0.4 - - - +
1156B ALA* 3.5 15.7 - - + -
1157B TYR* 4.9 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B PHE* 1.3 75.8 - - - +
1092B ASN* 1.3 79.2 + - - +
1128B LEU* 3.9 12.9 - - - +
1155B SER* 2.9 21.8 + - - -
1156B ALA* 4.2 0.5 - - - -
1157B TYR* 4.0 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064B PHE* 3.5 38.2 - - + -
1090B PHE* 4.2 3.3 - - - -
1091B THR* 1.3 98.1 + - - +
1093B PHE* 1.3 63.1 + - - +
1128B LEU* 4.1 1.1 - - - -
1152B SER* 5.5 2.0 + - - +
1153B GLY 4.7 0.4 - - - +
1154B PHE* 3.1 7.0 - - - +
1155B SER* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B PHE* 3.8 18.4 - + + -
1092B ASN* 1.3 74.4 - - - +
1094B SER* 1.3 64.1 + - - +
1095B LEU* 3.7 20.4 - - + -
1107B LEU* 4.5 11.9 - - + -
1123B PHE* 3.7 35.2 - - + -
1124B TYR 3.6 19.5 - - - -
1125B GLY 3.6 10.5 - - - -
1126B SER 3.2 20.1 - - - +
1127B ASN 4.1 7.9 - - - +
1128B LEU* 3.3 23.4 - - + +
1129B PRO* 3.3 32.3 - - + -
1153B GLY 3.5 5.3 + - - -
1154B PHE* 4.0 10.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B PHE* 1.3 74.3 - - - +
1095B LEU* 1.3 60.4 + - - +
1125B GLY 3.8 2.9 - - - -
1126B SER* 4.4 12.2 + - - +
1151B ARG* 3.5 23.1 + - - +
1152B SER* 3.8 14.5 + - - -
1153B GLY* 3.0 30.2 + - - -
----------------------------------------------------------
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