Contacts of the helix formed by residues 73 - 90 (chain D) in PDB entry 3F27
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 73 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A T 2.9 22.2 + - - -
10A G 3.1 45.9 + - - +
11A T 4.3 13.7 - - - +
8B A 3.3 15.2 + - - -
71D PRO 3.6 3.9 + - - +
72D MET* 1.3 75.3 - - - +
74D ALA* 1.3 64.8 + - - +
75D PHE* 2.6 34.7 + - - +
76D MET* 3.0 11.6 + - - +
77D VAL* 2.9 21.0 + - - +
121D ALA* 3.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A G 4.6 12.0 + - - +
11A T 5.2 4.5 + - - +
73D ASN* 1.3 74.3 - - - +
75D PHE* 1.3 64.7 + - - +
77D VAL* 3.4 4.7 + - - +
78D TRP* 3.2 20.4 + - - +
106D TRP* 3.9 22.2 - - + -
117D PHE* 4.1 6.8 - - - +
118D VAL* 4.3 29.2 - - + +
121D ALA* 3.5 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A T 3.3 41.7 - + + -
9A T 3.4 48.0 - + - +
10A G 4.4 6.2 - - - -
9B A 6.0 0.2 - + - -
73D ASN* 2.6 15.7 + - - +
74D ALA* 1.3 70.3 - - - +
76D MET* 1.3 86.6 + - - +
78D TRP* 2.8 29.0 + + - +
79D ALA* 2.7 34.2 + - + +
102D LEU* 4.0 27.6 - - + -
103D GLY 4.6 0.7 - - - -
106D TRP* 4.0 21.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A T 4.8 3.4 - - - +
9A T 4.8 0.4 - - - -
8B A 3.5 47.1 - - + +
9B A 3.5 57.5 - - + +
72D MET* 3.6 23.9 - - + +
73D ASN* 3.5 18.8 - - - +
75D PHE* 1.3 100.5 - - - +
77D VAL* 1.3 52.2 + - - +
79D ALA* 3.6 5.1 - - + +
80D LYS* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D MET* 4.0 12.1 - - + -
73D ASN 2.9 15.8 + - - +
74D ALA* 3.6 9.0 - - - +
75D PHE 2.8 3.4 + - - -
76D MET* 1.3 73.6 - - - +
78D TRP* 1.3 62.1 - - - +
80D LYS* 3.3 19.2 - - - +
81D ASP* 3.9 10.0 + - - +
117D PHE* 3.8 20.0 - - + +
120D GLU* 3.2 40.2 - - + +
121D ALA* 4.2 9.4 - - - -
124D LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ALA 3.2 12.2 + - - +
75D PHE* 2.8 18.9 + + - +
77D VAL* 1.3 70.8 - - - +
79D ALA* 1.3 80.6 + - - +
81D ASP* 3.2 6.5 + - - +
82D GLU* 3.0 49.1 + - + +
102D LEU* 3.3 52.3 - - + -
105D SER* 3.5 19.7 - - - -
106D TRP* 3.5 31.0 - + + -
109D LEU* 3.5 26.4 - - + +
117D PHE* 3.8 41.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B A 6.2 0.7 - - + +
75D PHE* 2.7 47.7 + - + +
76D MET* 3.6 7.9 - - + +
78D TRP* 1.3 78.6 - - + +
80D LYS* 1.3 67.0 + - - +
81D ASP 3.0 0.2 + - - -
83D ARG* 2.8 38.1 + - - +
102D LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B A 3.7 17.2 + - - +
10B T 3.0 40.6 + - - +
72D MET* 4.4 20.8 - - + +
76D MET 2.7 22.7 + - - +
77D VAL* 3.3 13.0 - - - +
79D ALA* 1.3 73.3 - - - +
81D ASP* 1.3 76.0 + - - +
83D ARG* 4.5 3.5 - - - +
84D LYS* 4.1 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL 3.9 8.2 + - - +
78D TRP 3.2 4.9 + - - +
79D ALA 3.1 0.4 - - - -
80D LYS* 1.3 93.0 - - - +
82D GLU* 1.3 56.6 + - - +
83D ARG 3.1 1.3 - - - -
84D LYS* 2.6 41.0 + - + +
85D ARG* 3.0 8.5 + - - -
117D PHE* 5.4 6.8 - - - -
120D GLU* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TRP* 3.0 50.5 + - + +
81D ASP* 1.3 76.7 - - - +
83D ARG* 1.3 52.4 + - - +
85D ARG* 2.8 49.6 + - - +
86D LEU* 2.6 54.1 + - - +
102D LEU* 3.4 17.7 - - + +
105D SER* 4.9 2.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
7A A 4.4 0.8 - - - -
8A T 4.4 4.6 + - - -
9B A 3.3 32.7 + - - -
10B T 3.5 36.1 + - - +
11B A 6.3 1.6 - - - -
79D ALA* 2.8 27.3 + - - +
80D LYS* 4.5 2.9 - - - +
81D ASP 2.8 4.2 + - - -
82D GLU* 1.3 69.8 - - - +
84D LYS* 1.3 57.7 + - + +
86D LEU* 3.6 4.9 - - - +
87D ALA* 2.7 36.3 + - + +
95D ASN* 3.2 21.9 + - - +
98D LEU* 4.0 12.3 - - + +
99D SER* 2.7 34.4 + - - +
102D LEU* 3.3 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LYS 4.1 7.4 + - - +
81D ASP* 2.6 23.6 + - + +
83D ARG* 1.3 77.2 - - - +
85D ARG* 1.3 59.2 + - - +
87D ALA* 3.4 6.5 + - - +
88D GLN* 3.0 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ASP 3.0 5.1 + - - +
82D GLU* 2.8 52.6 + - - +
84D LYS* 1.3 76.5 - - - +
86D LEU* 1.3 73.0 + - - +
88D GLN* 2.9 35.1 + - - +
89D GLN* 3.1 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU* 2.6 37.6 + - - +
83D ARG* 3.8 3.4 - - - +
85D ARG* 1.3 93.0 - - - +
87D ALA* 1.3 51.4 + - - +
89D GLN* 4.6 2.2 - - + +
90D ASN* 2.6 52.6 + - - +
98D LEU* 3.8 18.3 - - + +
101D MET* 4.1 33.4 - - + -
102D LEU* 4.1 22.4 - - + +
105D SER* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B A 6.4 2.2 - - - -
83D ARG* 2.7 24.8 + - + +
84D LYS* 3.7 7.4 - - - +
85D ARG 3.2 0.2 - - - -
86D LEU* 1.3 72.9 - - - +
88D GLN* 1.3 58.9 + - + +
90D ASN 3.7 7.6 - - - -
91D PRO* 3.0 29.9 - - + +
98D LEU* 3.8 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LYS* 3.0 52.5 + - + +
85D ARG* 2.9 15.9 + - - +
87D ALA* 1.3 75.5 - - + +
89D GLN* 1.3 69.4 + - + +
90D ASN 3.1 1.3 - - - -
91D PRO* 3.3 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 3.1 45.1 + - - +
86D LEU* 4.7 1.3 - - + -
88D GLN* 1.3 80.7 + - + +
90D ASN* 1.3 77.2 + - - +
91D PRO* 3.7 3.7 - - - +
92D ASP* 4.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 2.6 47.3 + - - +
87D ALA* 3.2 11.0 - - - +
89D GLN* 1.3 93.1 - - - +
91D PRO* 1.4 62.3 - - - +
92D ASP* 2.9 26.4 + - - +
93D LEU* 3.3 37.6 + - + +
98D LEU* 4.8 2.7 - - + +
101D MET* 5.2 3.5 - - - +
----------------------------------------------------------
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