Contacts of the helix formed by residues 56 - 74 (chain B) in PDB entry 3IFS
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 ASP 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 3.6 1.7 + - - -
55B TYR* 1.3 70.8 - - - +
57B LYS* 1.3 58.8 + - - +
58B GLU* 3.1 15.5 + - - +
59B GLU* 2.8 46.3 + - + +
60B PHE* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 2.8 28.4 + - - -
54B GLN* 3.7 3.6 - - - +
55B TYR* 2.8 51.9 + - + +
56B ASP* 1.3 71.5 + - - +
58B GLU* 1.3 80.1 + - - +
60B PHE* 3.3 7.7 + - - +
61B ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 3.1 10.9 + - - +
57B LYS* 1.3 85.1 + - - +
59B GLU* 1.3 65.1 + - - +
61B ALA* 3.3 8.4 + - - +
62B ARG* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 2.8 38.3 + - + +
58B GLU* 1.3 76.3 - - - +
60B PHE* 1.3 57.5 + - - +
62B ARG* 3.1 19.1 + - - +
63B ILE* 2.9 34.7 + - + +
199B PHE* 3.7 19.7 - - + -
200B VAL* 2.9 40.3 + - - +
214B PRO* 3.3 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.5 35.2 - + + -
56B ASP 3.0 18.2 + - - +
57B LYS* 3.4 7.4 - - - +
58B GLU 3.2 0.2 - - - -
59B GLU* 1.3 77.1 - - - +
61B ALA* 1.3 61.8 + - - +
63B ILE* 3.2 20.6 + - + +
64B GLN* 3.2 43.9 + - - +
217B LEU* 3.7 25.6 - - + -
227B ILE* 3.6 37.0 - - + +
228B GLU* 3.8 14.6 - - + -
231B MSE 3.6 23.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
57B LYS 3.0 12.2 + - - +
58B GLU* 3.5 11.7 - - - +
60B PHE* 1.3 79.5 - - - +
62B ARG* 1.3 61.0 + - - +
64B GLN* 3.3 18.2 + - - +
65B LYS* 3.1 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.1 12.7 + - - +
59B GLU* 3.1 24.1 + - - +
61B ALA* 1.3 74.7 - - - +
63B ILE* 1.3 60.1 + - - +
65B LYS* 3.2 13.0 + - + +
66B CYS* 2.9 30.7 + - - -
197B GLU* 2.6 46.0 + - - +
198B THR 2.9 30.9 + - - +
199B PHE* 3.5 24.0 - - + +
200B VAL* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 2.9 20.9 + - + +
60B PHE* 3.2 15.7 + - - +
62B ARG* 1.3 76.6 - - - +
64B GLN* 1.3 57.4 + - - +
66B CYS* 3.3 3.1 + - - +
67B ALA* 2.8 29.3 + - - +
199B PHE* 3.5 25.1 - - + -
214B PRO* 3.8 37.9 - - + -
217B LEU* 4.0 15.7 - - + +
218B LEU* 3.7 33.5 - - + +
221B ALA* 4.7 1.8 - - + -
227B ILE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.2 23.7 + - - +
61B ALA* 3.6 18.8 - - - +
63B ILE* 1.3 78.3 - - - +
65B LYS* 1.3 61.4 + - - +
67B ALA* 3.4 7.2 + - - +
68B GLU* 3.1 30.6 + - + +
221B ALA* 5.3 2.0 - - + -
226B ASN* 5.6 0.2 + - - -
227B ILE* 3.9 21.5 - - + +
228B GLU* 3.1 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.1 14.2 + - - +
62B ARG* 3.2 15.7 + - + +
64B GLN* 1.3 74.3 - - - +
66B CYS* 1.3 66.5 + - - +
68B GLU* 3.3 7.7 + - - +
69B LYS* 3.1 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.9 20.8 + - - +
63B ILE 3.7 3.8 - - - +
65B LYS* 1.3 76.0 - - - +
67B ALA* 1.3 65.7 + - - +
69B LYS* 3.2 9.6 + - - +
70B ILE* 3.0 31.4 + - - +
177B TYR* 3.8 22.2 - - + -
197B GLU* 3.7 26.2 - - - -
199B PHE* 3.7 21.3 - - + -
218B LEU* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 2.8 17.6 + - - +
64B GLN* 3.6 6.7 - - - +
66B CYS* 1.3 77.2 - - - +
68B GLU* 1.3 57.6 + - - +
70B ILE* 3.4 1.9 + - - +
71B LYS* 3.0 37.5 + - - +
218B LEU* 4.1 3.1 - - + +
221B ALA* 3.7 38.8 - - + +
222B VAL* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 3.1 19.0 + - + +
65B LYS* 3.8 6.5 - - - +
67B ALA* 1.3 75.6 - - - +
69B LYS* 1.3 65.0 + - - +
71B LYS* 2.9 36.7 + - - +
72B ASN* 3.1 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.1 15.0 + - + +
66B CYS* 3.4 12.6 - - - +
68B GLU* 1.3 77.3 - - - +
70B ILE* 1.3 62.8 + - - +
72B ASN* 3.1 7.3 + - - +
73B ASP* 2.8 53.5 + - - +
174B LYS* 3.0 48.5 + - - +
175B ARG* 4.9 2.8 - - - +
177B TYR* 3.2 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B CYS 3.0 20.4 + - - +
67B ALA 3.8 3.6 - - - +
69B LYS* 1.3 77.6 - - - +
71B LYS* 1.3 61.5 + - - +
73B ASP* 3.4 6.5 - - - -
74B SER* 2.9 40.7 + - - +
77B LEU* 4.4 17.9 - - + -
112B PRO* 4.1 2.0 - - + +
139B SER* 4.3 9.4 - - - +
177B TYR* 3.6 44.0 - - + +
218B LEU* 4.4 10.5 - - + -
222B VAL* 3.9 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 3.0 23.1 + - - +
68B GLU* 2.9 38.5 + - - +
69B LYS 3.3 0.2 - - - -
70B ILE* 1.3 76.4 - - - +
72B ASN* 1.3 66.5 + - - +
74B SER 4.1 2.3 - - - +
110B LYS 5.4 4.2 - - - +
111B THR* 4.5 10.4 - - + +
112B PRO* 3.9 19.5 - - + +
221B ALA 3.2 27.8 + - - -
222B VAL* 3.7 19.7 - - - +
224B GLY* 4.0 15.0 - - - -
225B LEU 5.7 0.4 + - - -
454B PGE 3.6 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 3.1 24.4 + - - +
69B LYS* 3.1 7.5 + - - +
71B LYS* 1.3 87.3 + - - +
73B ASP* 1.3 57.3 + - + +
74B SER 3.7 0.2 - - - -
454B PGE 3.2 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 2.8 52.1 + - - +
70B ILE* 3.3 7.0 - - - +
72B ASN* 1.3 77.7 - - + +
74B SER* 1.3 84.4 + - - +
137B ASP* 3.5 4.7 - - - +
139B SER* 3.8 2.0 + - - -
175B ARG* 2.9 44.9 + - - +
454B PGE 3.1 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 2.9 18.9 + - - +
71B LYS 4.1 1.4 - - - +
72B ASN 3.7 1.0 - - - -
73B ASP* 1.3 90.5 + - - +
75B ASP* 1.3 62.0 + - - +
76B ILE 3.6 20.9 - - - -
112B PRO* 3.6 17.9 - - - +
137B ASP 3.8 5.6 - - - -
138B PHE* 4.1 1.1 - - - -
139B SER* 2.6 28.2 + - - -
175B ARG* 3.2 6.1 + - - -
454B PGE 3.6 14.8 - - - +
----------------------------------------------------------
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