Contacts of the helix formed by residues 76 - 88 (chain D) in PDB entry 2PK9
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 SER 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ASN 3.2 6.7 + - - -
75D ILE* 1.3 79.5 - - - +
77D ILE* 1.3 62.0 + - - +
78D PHE* 3.2 17.3 + - - +
79D ASN* 3.4 23.9 + - - +
80D TYR* 3.0 26.3 + - - +
238D SER* 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER* 4.1 8.5 + - - +
43D LEU* 4.0 36.3 - - + -
44D VAL* 3.1 31.2 - - + -
47D ILE* 5.0 4.5 - - + -
75D ILE 3.6 0.8 + - - -
76D SER* 1.3 75.2 - - - +
78D PHE* 1.3 65.6 + - + +
80D TYR* 3.7 3.3 + - + +
81D PHE* 3.2 22.9 + - - +
119D ALA* 4.1 27.4 - - + -
120D HIS* 4.3 18.4 + - + +
123D LEU* 4.3 13.8 - - + +
235D PRO* 5.4 3.6 - - + -
238D SER* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D THR* 4.8 3.1 - - + -
36D VAL* 3.2 28.0 - - + -
37D VAL* 3.8 22.0 - - + -
40D SER* 3.4 17.9 - - - +
76D SER* 3.2 4.2 + - - +
77D ILE* 1.3 78.4 - - + +
79D ASN* 1.3 81.2 + - - +
81D PHE* 3.3 1.7 + - - +
82D ILE* 3.0 52.6 + - + +
238D SER* 3.4 36.1 - - - +
239D ARG* 3.4 44.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ILE* 4.2 15.8 - - + +
76D SER* 3.3 24.2 + - - +
78D PHE* 1.3 95.8 - - - +
80D TYR* 1.3 66.5 + - - +
81D PHE 3.1 2.3 + - - -
82D ILE* 3.2 30.7 - - + +
83D ARG* 3.2 12.5 + - - +
239D ARG* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ILE* 3.9 13.4 - - + +
76D SER 3.0 17.0 + - - +
77D ILE* 4.1 4.3 - - + +
79D ASN* 1.3 76.7 - - - +
81D PHE* 1.3 58.5 + - - +
83D ARG* 3.6 11.7 - - - +
84D LEU* 3.2 50.6 + - + +
120D HIS* 3.8 45.3 - + + -
123D LEU* 4.6 9.2 - - + -
124D LEU* 3.5 16.0 - - + +
148D GLY* 2.6 42.6 + - - -
294D MES 3.4 39.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 3.8 23.6 - - + -
39D ILE* 3.7 30.7 - - + -
40D SER* 3.9 11.7 - - - +
43D LEU* 5.3 1.8 - - + -
77D ILE 3.2 17.9 + - - +
78D PHE 3.7 3.8 - - - +
79D ASN 3.1 0.8 - - - -
80D TYR* 1.3 75.8 - - - +
82D ILE* 1.3 64.4 + - - +
83D ARG 3.1 1.6 - - - -
84D LEU* 3.2 8.7 + - + -
85D THR* 2.8 29.9 + - - -
90D LEU* 4.4 2.0 - - + -
95D LEU* 3.6 39.5 - - + -
98D SER* 4.6 3.6 - - - -
123D LEU* 3.6 36.8 - - + -
127D THR* 3.9 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D THR* 5.2 11.0 - - + +
36D VAL* 3.7 18.1 - - + +
78D PHE* 3.0 40.4 + - + +
79D ASN* 3.2 35.9 - - + +
81D PHE* 1.3 74.6 - - - +
83D ARG* 1.3 60.9 + - + +
85D THR* 3.1 6.1 + - - -
86D LYS* 2.9 40.8 + - + +
239D ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 4.2 6.7 - - + -
184A ARG* 3.9 43.4 - - - +
240A PRO* 5.2 3.0 - - - +
75D ILE* 3.4 19.7 - - - +
79D ASN 3.2 17.4 + - - +
80D TYR* 3.6 13.2 - - - +
81D PHE 3.1 0.2 - - - -
82D ILE* 1.3 81.0 - - + +
84D LEU* 1.3 66.2 + - + +
85D THR 3.1 0.7 + - - -
86D LYS* 5.8 0.2 - - - -
87D PHE* 3.1 43.2 + - + -
146D LYS 5.1 0.4 + - - -
147D VAL* 3.0 35.5 + - + +
148D GLY 3.9 6.1 + - - -
149D GLY* 4.0 2.0 - - - +
294D MES 2.8 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TYR* 3.2 49.4 - - + +
81D PHE* 3.2 20.5 + - + +
83D ARG* 1.3 78.8 - - + +
85D THR* 1.3 61.0 + - - +
88D SER* 3.2 28.8 + - - +
90D LEU* 3.4 15.3 - - + +
123D LEU* 4.2 5.2 - - + +
124D LEU* 4.1 17.0 - - + +
127D THR* 3.8 24.2 - - + -
144D TYR 5.4 0.2 - - - +
147D VAL* 4.0 15.0 - - + +
148D GLY* 3.9 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG* 3.2 44.9 + - + +
36D VAL* 3.5 23.2 - - + +
81D PHE* 2.8 19.5 + - - -
82D ILE* 3.4 12.1 - - - -
84D LEU* 1.3 77.4 - - - +
86D LYS* 1.3 63.5 + - + +
89D SER* 3.2 4.5 + - - -
90D LEU* 3.0 34.5 + - - +
95D LEU* 3.6 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 4.6 6.7 - - - +
32B ARG* 4.1 28.8 + - - +
89B SER* 3.2 20.1 - - - -
92B HIS* 4.6 18.4 + - - -
32D ARG* 5.1 2.6 + - - +
82D ILE* 2.9 24.7 + - + +
85D THR* 1.3 77.6 - - + +
87D PHE* 1.3 99.2 + - + +
89D SER* 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 3.3 48.9 - - + -
165A PHE* 3.6 31.6 - + + -
184A ARG* 5.5 4.0 - - - -
89B SER* 3.8 16.3 + - - -
91B GLU* 4.3 17.3 - - + -
137B SER* 3.6 9.4 + - - +
83D ARG* 3.1 28.3 + - + +
86D LYS* 1.3 110.2 - - + +
88D SER* 1.3 52.4 + - - +
89D SER 3.5 0.4 - - - -
143D HIS* 2.8 32.1 + - - -
147D VAL* 3.9 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 4.2 1.1 - - - -
84D LEU* 3.2 17.9 + - - +
87D PHE* 1.3 74.7 - - - +
89D SER* 1.3 72.7 + - - +
90D LEU* 3.5 10.5 + - - +
127D THR* 6.3 0.2 - - - -
131D THR* 5.6 0.9 - - - +
139D SER* 4.6 5.5 + - - -
143D HIS* 3.8 10.2 + - - -
144D TYR* 3.6 39.0 + - - -
147D VAL* 3.6 28.2 - - - +
----------------------------------------------------------
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