Contacts of the helix formed by residues 1165 - 1171 (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 PRO1165 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164B PHE* 1.3 83.1 - - + +
1166B ASN* 1.3 60.3 + - - +
1167B LEU 3.5 2.2 + - - -
1168B LEU* 3.7 6.5 + - + +
1169B ALA* 3.1 27.4 + - - +
1188B LEU* 4.2 3.4 - - + -
1191B LEU* 3.7 30.1 - - + +
1192B ILE* 4.0 22.7 - - + +
1195B VAL* 4.7 8.3 - - + -
1352B LEU* 5.3 4.7 - - + -
1355B TYR* 3.3 41.3 - - + +
1473B LEU* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B ARG 5.3 1.2 + - - -
1040B ASP* 2.9 28.3 + - - +
1041B GLY 4.0 6.7 + - - -
1042B LEU* 3.7 21.0 - - - +
1099B TYR* 6.0 0.6 - - - -
1103B LEU* 4.2 5.4 - - - +
1135B LEU* 3.8 26.8 - - + +
1164B PHE* 2.8 24.0 + - + +
1165B PRO* 1.3 70.7 - - - +
1167B LEU* 1.3 68.0 + - - +
1169B ALA* 4.1 0.9 - - - -
1170B ASN* 2.9 53.7 + - - +
1171B GLY 4.0 0.7 + - - +
1355B TYR* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B PRO* 3.7 27.6 - - + -
1037B ASP 4.1 2.0 - - - +
1038B VAL* 4.0 37.7 - - + +
1039B ARG 5.6 0.6 + - - -
1040B ASP 4.4 0.2 - - - -
1041B GLY* 3.5 34.0 - - - +
1165B PRO 3.5 0.6 - - - -
1166B ASN* 1.3 75.8 - - - +
1168B LEU* 1.3 61.7 + - + +
1171B GLY* 3.0 30.3 + - - -
1172B ALA* 4.6 4.7 - - + -
1183B ILE* 3.9 23.2 - - + +
1337B ALA* 4.2 8.7 - - + -
1346B ILE* 4.5 7.9 - - + -
1351B ALA* 4.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B PRO* 3.7 6.9 + - + +
1166B ASN 3.3 0.2 - - - -
1167B LEU* 1.3 82.2 - - + +
1169B ALA* 1.3 63.5 + - - +
1183B ILE* 4.2 15.5 - - + -
1184B PRO 3.5 1.5 - - - +
1185B PRO* 3.4 3.8 - - - +
1186B HIS* 2.8 50.7 + - + +
1191B LEU* 3.7 22.7 - - + -
1335B MET* 4.4 11.7 - - - -
1348B LEU* 3.8 22.7 - - + -
1351B ALA* 4.0 22.4 - - + +
1352B LEU* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100B ARG* 3.5 7.1 - - - +
1101B TYR* 4.0 20.9 - - + -
1164B PHE* 4.2 13.0 - - + -
1165B PRO 3.1 20.9 + - - +
1166B ASN* 3.2 7.6 + - - +
1168B LEU* 1.3 77.0 - - - +
1170B ASN* 1.3 61.4 + - - +
1185B PRO* 3.2 6.9 - - - +
1186B HIS 3.0 27.1 + - - +
1188B LEU* 4.5 3.8 - - + -
1191B LEU* 3.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092B ARG* 5.9 1.2 + - - -
1098B SER 4.9 8.0 - - - +
1099B TYR* 3.5 32.2 - - + -
1100B ARG* 3.2 9.5 + - - +
1101B TYR* 2.7 50.9 + - - +
1103B LEU* 3.8 8.1 - - - +
1164B PHE* 4.8 1.6 - - - -
1166B ASN* 2.9 34.5 + - - +
1169B ALA* 1.3 77.5 - - - +
1171B GLY* 1.3 66.3 + - - +
1185B PRO* 3.9 14.4 - - - +
1266B PHE* 5.5 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B GLY 4.7 7.3 - - - +
1099B TYR* 5.8 1.6 + - - -
1166B ASN 4.9 0.7 - - - +
1167B LEU* 3.0 24.4 + - - +
1168B LEU 3.8 1.2 + - - -
1169B ALA 3.5 1.8 - - - -
1170B ASN* 1.3 85.5 - - - +
1172B ALA* 1.3 65.8 + - - +
1183B ILE* 3.2 16.8 - - - -
1184B PRO 3.9 11.0 - - - -
1185B PRO* 4.0 0.7 - - - -
----------------------------------------------------------
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