Contacts of the helix formed by residues 81 - 93 (chain D) in PDB entry 3P3W
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 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D SER* 4.1 21.9 - - - -
55D SER* 4.8 4.3 - - - -
58D VAL* 4.3 22.2 - - - -
76D PHE 4.5 1.4 + - - -
77D TYR* 3.4 16.7 - - - +
78D ASP* 3.0 27.7 + - - -
80D MET* 1.3 76.5 - - - +
82D MET* 1.3 63.3 + - - +
83D ASN 3.6 0.4 - - - -
84D THR* 3.8 11.5 + - - -
85D LEU* 3.8 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 3.5 24.3 - - + -
78D ASP 2.9 16.3 + - - +
79D GLN* 4.1 8.3 - - - +
80D MET 3.2 1.4 - - - -
81D SER* 1.3 79.8 - - - +
83D ASN* 1.3 76.7 + - + +
84D THR 3.4 0.2 + - - -
85D LEU* 3.6 2.4 + - - +
86D THR* 3.3 31.2 + - - +
101D PHE* 3.5 28.3 - - + -
103D THR* 3.8 24.2 - - + -
104D ASP* 4.7 20.0 - - + +
105D ALA 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER 5.6 0.2 + - - -
55B SER* 4.8 4.4 - - - -
79B GLN 5.0 2.2 - - - +
80B MET* 2.6 68.7 + - - +
83B ASN* 5.5 5.8 - - + -
84B THR* 4.8 3.6 + - - +
79D GLN 5.2 0.6 + - - +
80D MET 4.3 5.8 + - - +
82D MET* 1.3 89.3 - - + +
84D THR* 1.3 60.9 + - - +
86D THR* 2.8 16.5 + - - -
87D SER* 2.7 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 4.8 0.7 - - - -
83B ASN* 4.8 3.1 + - - +
84B THR* 3.8 23.3 + - + +
55D SER* 3.2 23.9 + - - +
58D VAL* 4.6 10.3 - - + -
59D THR* 3.7 30.1 - - + -
80D MET 4.4 3.8 + - - -
81D SER* 3.8 15.0 + - - -
82D MET 3.3 0.8 - - - -
83D ASN* 1.3 80.2 - - - +
85D LEU* 1.3 64.2 + - + +
87D SER* 3.9 2.0 + - - -
88D PHE* 3.2 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.2 18.6 - - + -
58D VAL* 4.2 24.7 - - + -
62D PHE* 4.0 31.2 - - + -
76D PHE 4.6 6.3 - - - +
77D TYR* 3.9 28.3 - - + -
81D SER* 3.8 18.5 + - - +
82D MET 3.6 3.2 + - - +
83D ASN 3.4 0.4 - - - -
84D THR* 1.3 79.9 - - + +
86D THR* 1.3 64.2 + - - +
88D PHE* 3.9 3.5 - - + +
89D CYS* 3.1 30.8 + - - -
96D PHE* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 5.6 1.7 - - - +
77D TYR* 5.0 6.7 - - + +
82D MET* 3.3 20.4 + - + +
83D ASN* 2.8 28.8 + - - -
85D LEU* 1.3 77.4 - - - +
87D SER* 1.3 57.7 + - - +
89D CYS* 3.6 3.3 + - - +
90D GLY* 3.2 20.6 + - - -
96D PHE* 6.4 0.2 - - + -
103D THR* 3.8 28.5 - - + -
107D VAL* 4.3 18.7 - - + +
108D GLN 4.2 8.3 - - - +
110D VAL* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER 3.8 17.3 - - - -
54B ASN* 4.1 5.8 - - - +
55B SER* 3.1 31.9 + - - -
56B PHE 4.7 0.5 + - - -
80B MET* 4.4 10.8 - - - -
83D ASN* 2.7 24.2 + - - -
84D THR 3.9 0.2 + - - -
86D THR* 1.3 75.3 + - - +
88D PHE* 1.3 62.2 + - - +
89D CYS 3.4 0.2 - - - -
90D GLY* 3.9 2.6 - - - +
91D ALA* 3.4 23.0 + - - +
107D VAL* 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.9 18.2 - - - -
56B PHE* 4.4 23.1 - + - +
59B THR* 3.7 40.6 - - + -
84B THR* 5.1 0.2 - - + -
88B PHE* 5.6 0.2 - + - -
59D THR* 4.1 21.3 - - + -
62D PHE* 3.4 38.8 - + + -
63D CYS* 5.0 11.0 - - - -
84D THR* 3.2 35.7 + - + +
85D LEU* 3.9 5.4 - - + +
86D THR 3.4 0.2 - - - -
87D SER* 1.3 76.1 + - - +
89D CYS* 1.3 59.5 + - - +
91D ALA* 3.6 3.4 + - - +
92D LEU* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PHE* 4.2 21.5 - - - -
73D ILE* 5.6 0.9 - - - -
85D LEU* 3.1 24.7 + - - +
86D THR* 3.8 5.2 - - - +
87D SER 3.4 0.2 - - - -
88D PHE* 1.3 75.6 - - - +
90D GLY* 1.3 57.2 + - - +
92D LEU* 4.9 0.2 - - - -
93D HIS* 2.8 26.7 + - - -
94D THR* 3.0 39.5 + - - +
95D SER 4.8 0.9 - - - -
96D PHE* 3.6 28.3 - - + -
109D PHE* 3.8 13.2 - - + +
110D VAL* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 5.0 2.0 - - - -
86D THR 3.2 13.6 + - - -
87D SER* 3.7 3.7 + - - -
88D PHE 3.4 0.4 - - - -
89D CYS* 1.3 80.6 - - - +
91D ALA* 1.3 58.1 + - - +
93D HIS* 3.9 20.1 + - - -
108D GLN* 4.5 6.1 - - - -
109D PHE* 4.0 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 3.5 36.3 + - - +
56B PHE* 3.8 22.7 - - + -
87D SER 3.4 13.6 + - - +
88D PHE 4.2 0.7 - - - +
89D CYS 3.3 0.4 - - - -
90D GLY* 1.3 76.5 - - - +
92D LEU* 1.3 63.0 + - - +
93D HIS* 3.3 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.4 37.5 - - + -
62D PHE* 3.6 31.6 - - + -
63D CYS* 6.0 3.1 - - - -
66D PHE* 3.7 38.9 - - + -
88D PHE* 3.1 17.8 + - + +
89D CYS* 4.5 0.4 - - - +
91D ALA* 1.3 76.5 - - - +
93D HIS* 1.3 70.2 + - - +
94D THR* 3.4 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D CYS 2.8 10.8 + - - -
90D GLY 3.9 10.6 + - - -
91D ALA* 3.3 17.0 + - - -
92D LEU* 1.3 81.1 - - - +
94D THR* 1.3 55.2 + - - +
95D SER* 4.3 0.7 + - - -
109D PHE* 3.2 47.4 - + + -
----------------------------------------------------------
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