Contacts of the helix formed by residues 54 - 68 (chain B) 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 ASN 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP* 3.6 11.0 + - + +
52B SER 3.3 1.8 - - - +
53B SER* 1.3 77.2 + - - +
55B SER* 1.3 64.5 + - - +
56B PHE* 3.2 10.6 - - - +
57B SER* 3.2 26.2 + - - +
58B VAL* 3.4 12.0 - - - +
87D SER* 4.1 6.3 - - - +
90D GLY 5.0 0.7 - - - -
91D ALA* 3.5 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER 4.5 1.1 - - - -
53B SER 3.2 6.0 + - - -
54B ASN* 1.3 69.3 - - - +
56B PHE* 1.3 64.3 + - - +
58B VAL* 3.2 13.4 + - - +
59B THR* 3.1 22.9 + - - +
80B MET 5.6 0.2 + - - -
81B SER* 5.6 2.8 - - - -
84B THR* 3.6 23.7 + - - +
83D ASN* 4.8 5.2 - - - -
84D THR* 4.6 1.9 + - - -
87D SER* 3.1 31.0 + - - -
88D PHE* 3.9 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 3.2 4.7 - - - +
55B SER* 1.3 77.4 - - - +
57B SER* 1.3 62.0 + - - +
59B THR* 2.8 23.7 + - - -
60B ASN* 3.1 35.8 + - + +
87D SER 4.7 3.2 + - - +
88D PHE* 4.4 21.1 - + + -
91D ALA* 3.8 27.6 - - + -
92D LEU* 3.4 48.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.2 8.7 - - - +
51B ASP* 3.8 25.8 + - - +
54B ASN* 3.2 23.2 + - - +
56B PHE* 1.3 80.1 - - - +
58B VAL* 1.3 61.9 + - - +
60B ASN* 4.5 4.3 - - - +
61B ALA* 3.5 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.4 1.1 - - + +
50B LEU* 4.5 16.7 - - + +
51B ASP 4.1 6.5 - - - +
52B SER* 3.4 21.1 - - - +
54B ASN 3.4 16.4 - - - +
55B SER* 3.4 13.0 - - - +
56B PHE 3.1 0.6 - - - -
57B SER* 1.3 77.7 - - - +
59B THR* 1.3 63.3 + - + +
61B ALA* 3.7 4.3 + - - +
62B PHE* 3.3 21.0 + - - +
81B SER* 4.0 18.8 - - - +
84B THR* 5.4 5.8 - - + -
85B LEU* 3.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER 3.1 12.9 + - - +
56B PHE* 2.8 24.8 + - - -
58B VAL* 1.3 75.5 - - - +
60B ASN* 1.3 63.0 + - - +
62B PHE* 3.2 9.0 + - - +
63B CYS* 2.9 34.2 + - - +
84B THR* 3.7 27.8 - - + -
85B LEU* 6.0 0.7 - - - -
88B PHE* 3.9 19.7 - - + -
88D PHE* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.1 38.9 + - + +
57B SER* 4.5 4.7 - - - +
59B THR* 1.3 80.8 + - - +
61B ALA* 1.3 60.4 + - - +
63B CYS* 3.9 7.1 - - - +
64B SER* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.8 21.3 - - + -
48B ASP* 4.6 14.2 - - + +
50B LEU* 3.9 12.8 - - + -
57B SER 3.5 18.8 + - - +
58B VAL 3.8 4.0 - - - +
59B THR 3.3 0.4 - - - -
60B ASN* 1.3 76.1 - - - +
62B PHE* 1.3 63.1 + - - +
64B SER* 3.4 6.7 + - - -
65B GLN* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.6 9.5 - - + +
58B VAL 3.3 11.0 + - - +
59B THR* 3.2 11.6 + - - +
61B ALA* 1.3 78.8 - - - +
63B CYS* 1.3 63.8 + - - +
65B GLN* 3.3 7.7 + - - +
66B PHE* 2.9 28.4 + - + +
73B ILE* 3.7 25.2 - - + +
85B LEU* 4.0 23.3 - - + -
88B PHE* 3.6 49.6 - + + -
89B CYS* 3.6 26.0 - - - -
92B LEU* 3.7 28.9 - - + -
94B THR* 5.0 4.5 - - - -
96B PHE* 5.7 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 2.9 20.5 + - - +
60B ASN* 3.9 10.1 - - - +
61B ALA 3.3 0.2 - - - -
62B PHE* 1.3 80.1 - - - +
64B SER* 1.3 57.0 + - - +
66B PHE* 3.2 2.8 + - - +
67B SER* 2.7 41.6 + - - +
88B PHE* 4.8 8.1 - - - -
312B CYS* 2.2 49.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 4.4 10.0 + - - -
60B ASN 3.0 19.7 + - - -
61B ALA* 3.4 6.9 + - - -
63B CYS* 1.3 75.4 - - - +
65B GLN* 1.3 57.8 + - - +
67B SER* 3.7 6.9 + - - -
68B ARG* 2.6 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 3.2 20.5 - - - -
10B GLY 3.2 16.9 + - - -
11B LEU* 4.1 14.3 - - + +
46B HIS* 2.8 39.0 + - - +
48B ASP* 3.5 21.2 + - - +
61B ALA 3.0 20.1 + - - +
62B PHE* 3.5 9.4 - - - +
63B CYS 3.2 0.2 - - - -
64B SER* 1.3 75.2 - - - +
66B PHE* 1.3 63.5 + - - +
68B ARG* 3.2 18.2 + - - +
69B GLY 3.4 6.9 + - - -
70B VAL* 3.7 27.0 - - + +
73B ILE* 4.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 2.9 22.6 + + + +
63B CYS* 3.2 6.9 + - - +
65B GLN* 1.3 74.0 - - - +
67B SER* 1.3 58.0 + - - +
69B GLY* 2.8 26.6 + - - +
70B VAL* 5.0 7.9 - - + +
73B ILE* 5.4 1.1 - - - +
92B LEU* 3.7 46.4 - - + -
94B THR* 3.8 28.0 - - + -
310B GLY* 3.7 39.2 + - - +
311B ASP* 3.7 12.6 - - - -
312B CYS* 4.7 3.1 - - - -
319B PRO* 6.1 1.1 - - + -
322B GLN* 4.7 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B CYS* 2.7 27.7 + - - +
64B SER* 3.9 8.5 - - - -
65B GLN 3.3 0.2 - - - -
66B PHE* 1.3 72.4 - - - +
68B ARG* 1.3 60.7 + - - +
69B GLY* 3.1 1.1 + - - -
310B GLY 3.9 24.7 + - - +
311B ASP* 4.3 8.6 + - - -
312B CYS* 5.3 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 5.1 3.8 + - - -
46B HIS* 4.3 45.5 + - - -
48B ASP* 5.3 0.4 + - - -
64B SER* 2.6 62.2 + - - +
65B GLN* 3.2 13.0 + - - +
66B PHE 3.1 0.4 - - - -
67B SER* 1.3 78.7 - - - +
69B GLY* 1.3 63.1 + - - +
70B VAL* 3.5 10.0 + - + +
----------------------------------------------------------
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