Contacts of the helix formed by residues 82 - 92 (chain B) in PDB entry 4GDK
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 PRO 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG 4.1 2.2 - - - +
42B VAL 4.5 4.0 - - - +
43B SER 3.5 9.6 - - - +
44B TYR* 4.0 13.2 - - + +
80B HIS 3.9 5.8 - - - +
81B TYR* 1.3 87.9 - - + +
83B ILE* 1.3 66.0 + - - +
84B GLY 3.3 0.2 - - - -
85B LEU* 3.1 21.9 + - + +
86B LEU* 3.2 10.7 + - - +
260B TYR* 3.5 38.6 - - + -
262B ASP* 4.0 18.2 - - - +
266B HIS* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.3 9.0 - - + -
39B LEU* 3.8 23.6 - - + -
40B PRO* 3.4 25.4 - - + +
41B ARG 3.5 0.4 + - - -
43B SER 2.9 18.2 + - - +
44B TYR 3.7 17.7 - - - +
45B LEU* 3.6 26.2 - - + +
48B VAL* 3.7 21.3 - - + -
81B TYR 3.5 1.3 + - - +
82B PRO* 1.3 73.0 - - - +
84B GLY* 1.3 64.4 + - - +
86B LEU* 3.2 10.6 + - - +
87B PHE* 3.1 21.3 + - - +
98B TRP* 3.8 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.0 4.0 - - - -
41B ARG* 2.8 48.1 + - - -
83B ILE* 1.3 74.2 - - - +
85B LEU* 1.3 57.6 + - - +
87B PHE* 3.6 0.5 + - - +
88B ASP* 3.0 35.5 + - - +
260B TYR* 3.6 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.6 28.9 - - + -
82B PRO* 3.1 19.1 + - + +
84B GLY* 1.3 75.1 - - - +
86B LEU* 1.3 61.2 + - - +
88B ASP* 3.4 3.4 + - - +
89B LEU* 2.9 40.5 + - + +
190B TYR* 3.6 48.7 - - + +
260B TYR* 3.3 16.4 + - + +
266B HIS* 4.1 19.7 - - + +
268B SER* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.0 26.5 - - + -
77B LEU* 4.1 11.7 - - + -
78B LYS* 3.4 31.0 - - + +
81B TYR* 3.7 37.9 - - + +
82B PRO 3.2 8.3 + - - +
83B ILE* 3.2 9.1 + - - +
85B LEU* 1.3 79.4 - - + +
87B PHE* 1.3 57.4 + - - +
89B LEU* 4.7 5.4 - - + -
90B LEU* 2.8 51.4 + - + +
98B TRP* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.5 40.2 - - + -
41B ARG* 4.0 4.3 - - - -
83B ILE 3.1 8.9 + - - +
84B GLY 3.9 0.4 - - - +
86B LEU* 1.3 74.5 - - - +
88B ASP* 1.3 73.2 + - - +
91B ALA* 2.7 57.4 + - + +
92B SER* 3.0 24.9 + - - -
94B SER 5.6 0.2 - - - -
95B ALA 6.0 0.9 - - - -
96B LEU* 3.7 26.9 - - + -
98B TRP* 3.6 48.3 - + + -
28C GLN* 4.0 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 2.9 28.5 + - - -
84B GLY 3.0 21.6 + - - +
85B LEU* 3.7 4.8 - - - +
87B PHE* 1.3 76.1 - - - +
89B LEU* 1.3 63.1 + - - +
92B SER* 2.7 30.0 + - - -
239B MET* 3.6 20.9 - - + +
240B ILE 4.1 0.2 - - - -
241B HIS* 3.5 10.9 + - - -
242B GLY* 2.7 27.8 + - - -
260B TYR* 4.7 1.2 + - - -
268B SER* 4.1 12.1 - - - +
270B ILE* 4.0 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 5.5 6.1 - - + -
85B LEU* 2.9 24.6 + - + +
86B LEU* 3.9 5.8 - - + +
88B ASP* 1.3 80.3 - - - +
90B LEU* 1.3 66.0 + - + +
190B TYR* 3.6 46.9 - - + +
191B GLN* 4.3 3.4 - - - +
192B THR* 3.9 32.3 - - + +
268B SER* 3.7 23.1 - - - +
269B ILE 4.7 0.2 - - - +
270B ILE* 4.2 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.4 30.2 + - + -
75B THR* 4.4 25.8 - - + +
77B LEU* 3.6 32.1 - - + -
86B LEU* 2.8 34.7 + - + +
88B ASP 4.8 0.2 - - - -
89B LEU* 1.3 86.9 - - + +
91B ALA* 1.3 58.1 + - + +
92B SER 3.8 0.9 - - - -
94B SER* 5.2 0.7 + - - -
98B TRP* 5.5 1.1 - - + -
192B THR* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.4 29.2 - - + +
87B PHE* 2.7 31.3 + - + -
90B LEU* 1.3 74.6 - - + +
92B SER* 1.3 62.6 + - - +
93B SER 3.3 2.9 - - - -
94B SER* 3.2 21.4 + - - +
98B TRP* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.0 21.8 + - - -
88B ASP* 2.7 35.4 + - - -
90B LEU 3.8 1.0 - - - -
91B ALA* 1.3 78.7 - - - +
93B SER* 1.3 62.9 + - - +
94B SER 3.6 5.5 + - - +
239B MET* 4.0 17.3 - - - -
270B ILE* 3.4 17.7 - - - +
28C GLN* 5.9 0.5 + - - -
26F ARG* 5.7 1.0 + - - -
----------------------------------------------------------
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