Contacts of the helix formed by residues 1082 - 1094 (chain B) in PDB entry 5NPK
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 GLY1082 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081B HIS* 1.3 76.9 - - - +
1083B ASP* 1.4 64.3 + - - -
1084B SER* 3.1 5.8 - - - -
1085B SER* 3.2 22.0 + - - -
1086B ILE* 3.6 7.3 + - - +
1122D ARG* 4.2 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1083 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071B VAL* 3.8 18.8 - - + +
1075B MET* 3.7 24.1 - - + +
1081B HIS 3.4 2.0 + - - -
1082B GLY* 1.4 68.6 - - - -
1084B SER* 1.3 73.1 + - - +
1086B ILE* 3.2 5.1 + - - +
1087B TYR* 2.8 31.9 + - - +
1121B MET* 3.9 21.6 - - + +
1122D ARG* 3.7 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1084 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B GLY* 3.1 3.5 - - - -
1083B ASP* 1.3 86.9 + - - +
1085B SER* 1.3 64.4 + - - +
1087B TYR* 4.4 5.8 - - - +
1088B GLU* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1085 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B VAL* 4.2 5.6 - - - +
1079B HIS* 4.5 13.2 + - - -
1081B HIS* 5.0 5.2 - - - +
1082B GLY* 3.2 16.0 + - - -
1084B SER* 1.3 83.5 + - - +
1086B ILE* 1.3 61.0 + - - +
1088B GLU* 4.5 3.9 - - - +
1089B ALA* 3.4 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B VAL* 4.0 7.0 - - + -
1049B ILE* 3.5 27.5 - - + +
1071B VAL* 4.0 19.1 - - + +
1074B VAL* 4.1 13.2 - - + -
1075B MET* 3.6 38.6 - - + +
1079B HIS* 3.5 42.0 - - + +
1081B HIS 4.1 0.4 - - - +
1082B GLY 3.6 11.2 + - - +
1083B ASP* 3.2 8.8 + - - +
1085B SER* 1.3 73.2 - - - +
1087B TYR* 1.3 67.1 - - - +
1089B ALA 3.3 2.1 + - - -
1090B MET* 3.0 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B SER* 3.7 7.6 - - - -
1071B VAL* 3.9 16.6 - - + +
1083B ASP* 2.8 21.2 + - - +
1084B SER* 4.2 4.3 - - - +
1086B ILE* 1.3 76.0 - - - +
1088B GLU* 1.3 63.5 + - + +
1090B MET* 3.1 18.2 + - + +
1091B VAL* 2.8 53.5 + - + +
1110B PHE* 4.9 1.4 - + - -
1118B ALA* 3.6 10.9 - - + +
1119B ALA 2.7 28.8 + - - -
1120B ALA* 4.5 1.8 - - - -
1121B MET* 3.6 38.8 - - + -
1124B THR* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B SER* 2.9 36.2 + - - +
1085B SER* 4.5 2.9 - - - +
1087B TYR* 1.3 83.7 - - + +
1089B ALA* 1.3 62.8 + - - +
1091B VAL* 3.4 10.5 + - + +
1092B ARG* 3.2 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B VAL* 4.1 12.3 - - + -
1046B HIS* 3.7 23.5 - - + +
1049B ILE* 3.9 13.2 - - + -
1085B SER 3.4 17.4 + - - +
1086B ILE 3.3 4.8 + - - +
1087B TYR 3.2 0.4 - - - -
1088B GLU* 1.3 77.8 - - - +
1090B MET* 1.3 63.4 + - - +
1092B ARG* 3.6 8.8 + - - +
1093B MET* 3.3 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B ILE* 3.8 22.1 - - + +
1053B LEU* 5.4 2.2 - - - -
1067B SER* 3.5 33.9 - - - +
1070B ILE* 4.0 27.1 - - - -
1071B VAL* 4.7 6.3 - - + -
1086B ILE 3.0 13.5 + - - +
1087B TYR* 3.1 23.1 + - + +
1089B ALA* 1.3 73.6 - - - +
1091B VAL* 1.3 67.9 + - - +
1093B MET* 3.1 20.7 + - - +
1094B ALA* 3.4 11.4 + - - +
1104B VAL* 4.0 15.9 - - + +
1110B PHE* 4.5 9.0 - - + -
1126B ALA* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087B TYR* 2.8 54.0 + - + +
1088B GLU* 3.7 11.7 - - + +
1089B ALA 3.4 0.2 - - - -
1090B MET* 1.3 76.1 - - - +
1092B ARG* 1.3 62.9 + - + +
1094B ALA* 3.0 14.2 + - - +
1095B GLN* 3.4 21.6 + - - +
1110B PHE* 3.5 41.2 - - + +
1118B ALA* 3.6 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B HIS* 5.4 5.1 + - - +
1088B GLU 3.2 16.8 + - - +
1089B ALA* 3.8 9.0 - - - +
1090B MET 3.3 0.4 - - - -
1091B VAL* 1.3 76.2 - - + +
1093B MET* 1.3 62.3 + - - +
1094B ALA 3.1 1.2 + - - -
1095B GLN* 3.2 32.2 + - - +
1098B SER* 3.7 23.5 + - - +
1099B TYR* 3.2 44.3 + - + +
1170B ASN 5.9 1.4 + - - -
1172B ALA* 6.2 1.0 - - - +
1173B SER* 4.8 13.3 + - - +
1266B PHE* 5.8 3.4 - - - -
1267B GLN* 4.8 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042B LEU* 5.3 0.2 - - - -
1046B HIS* 3.6 24.2 - - + -
1049B ILE* 3.7 43.7 - - + -
1050B LEU* 4.1 12.1 - - + -
1089B ALA 3.3 18.1 + - - +
1090B MET* 3.1 10.6 + - - +
1092B ARG* 1.3 75.6 - - - +
1094B ALA* 1.3 55.6 + - - +
1095B GLN 3.5 0.4 - - - -
1099B TYR* 3.5 32.1 - - + +
1102B PRO* 3.4 8.1 - - - +
1103B LEU* 2.9 50.0 + - + -
1104B VAL* 3.1 15.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B MET 3.4 3.0 + - - +
1091B VAL 3.0 10.8 + - - +
1093B MET* 1.3 76.1 - - - +
1095B GLN* 1.3 61.2 + - - +
1096B ASP 3.8 1.7 + - - -
1102B PRO* 4.6 5.1 - - - +
1104B VAL* 3.2 39.2 - - + +
1106B GLY* 4.2 8.6 + - - +
1110B PHE* 3.9 24.8 - - + +
----------------------------------------------------------
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