Contacts of the helix formed by residues 24 - 43 (chain A) in PDB entry 1F89
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 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.1 8.6 + - - +
23A PRO* 1.3 77.4 - - - +
25A LYS* 1.3 61.6 + - - +
26A MET* 3.1 13.5 + - - +
27A ALA* 2.8 40.5 + - + +
28A ASN* 3.1 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 4.3 0.2 + - - -
23A PRO 3.4 4.9 + - - -
24A ASP* 1.3 69.9 + - - +
26A MET* 1.3 63.8 + - + +
28A ASN* 2.8 19.1 + - - +
29A LEU* 2.9 29.9 + - + +
56A ASN* 3.5 33.7 + - + +
67A TYR* 3.6 28.3 + - + +
69A GLU* 3.6 33.6 + - - +
70A VAL* 3.2 26.1 - - - +
78A THR* 4.8 10.5 - - + -
79A SER* 3.2 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.1 9.3 + - - +
25A LYS* 1.3 80.0 - - + +
27A ALA* 1.3 57.7 + - - +
29A LEU* 3.4 15.1 + - + +
30A GLN* 2.9 36.8 + - - +
78A THR* 3.7 29.8 - - + -
82A PHE* 5.6 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 4.6 2.9 - - - +
24A ASP* 2.8 35.2 + - + +
26A MET* 1.3 72.9 - - - +
28A ASN* 1.3 60.6 + - - +
30A GLN* 3.6 7.4 - - - +
31A ARG* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.2 4.3 - - - +
20A GLY* 4.1 6.8 - - - -
21A SER 3.3 8.7 + - - +
22A SER* 2.9 55.7 + - - +
24A ASP 3.1 6.9 + - - +
25A LYS 2.8 9.2 + - - +
27A ALA* 1.3 77.0 - - - +
29A LEU* 1.3 65.5 + - - +
31A ARG* 3.1 7.6 + - - +
32A ALA* 2.9 23.0 + - - +
55A PHE* 3.8 12.8 - - - +
56A ASN* 2.9 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 2.9 22.8 + - + +
26A MET* 3.8 30.3 - - + +
28A ASN* 1.3 75.3 - - - +
30A GLN* 1.3 57.5 + - - +
32A ALA* 2.9 7.5 + - - +
33A ALA 2.8 26.0 + - - -
55A PHE* 3.9 25.6 - - + -
56A ASN* 4.1 5.2 - - + -
78A THR* 4.2 13.0 - - + +
79A SER* 3.9 27.6 - - - +
82A PHE* 3.1 47.8 - - + -
83A LEU* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 2.9 23.5 + - - +
27A ALA* 3.6 9.2 - - - +
29A LEU* 1.3 76.1 - - - +
31A ARG* 1.3 58.1 + - - +
33A ALA* 3.2 8.0 + - - +
34A THR* 2.9 34.1 + - - +
82A PHE* 3.4 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.6 13.9 - - + -
19A SER* 3.5 21.5 + - - -
20A GLY* 4.7 3.4 - - - -
27A ALA 3.0 18.3 + - - +
28A ASN* 3.1 7.2 + - - +
30A GLN* 1.3 71.2 - - - +
32A ALA* 1.3 60.9 + - - +
33A ALA 3.0 1.6 - - - -
34A THR* 3.2 6.9 + - - -
35A PHE* 2.9 49.0 + - + -
255A GLU* 2.5 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.7 18.1 - - + +
28A ASN 2.9 8.4 + - - +
29A LEU* 3.4 8.3 - - - +
31A ARG* 1.3 76.5 - - - +
33A ALA* 1.3 58.2 + - - +
35A PHE* 4.1 2.0 - - - +
36A ILE* 2.9 36.3 + - + +
51A LEU* 4.5 14.5 - - + +
55A PHE* 3.6 32.5 - - + -
82A PHE* 5.4 1.6 - - + -
83A LEU* 5.4 2.7 - - + -
86A LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 2.8 11.8 + - - +
30A GLN* 3.2 13.5 - - - +
32A ALA* 1.3 74.9 - - - +
34A THR* 1.3 67.4 + - - +
36A ILE* 3.1 3.9 + - - +
37A GLU* 3.1 36.3 + - - +
82A PHE* 3.7 21.7 - - + -
86A LEU* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN* 2.9 20.7 + - - +
31A ARG* 3.5 12.5 - - + -
33A ALA* 1.3 76.3 - - - +
35A PHE* 1.3 68.5 + - + +
37A GLU* 3.2 18.6 + - - +
38A ARG* 3.2 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.8 22.9 - - + +
18A LEU* 3.6 12.6 - - + -
31A ARG* 2.9 42.3 + - + +
32A ALA 4.3 2.0 - - - +
34A THR* 1.3 81.6 - - + +
36A ILE* 1.3 60.8 + - - +
37A GLU 3.2 0.2 - - - -
38A ARG* 3.5 34.7 + - - -
39A ALA* 3.1 19.9 + - - +
255A GLU* 3.4 45.5 - - + -
256A GLU* 5.0 8.1 - - - -
257A ILE* 3.2 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.4 3.6 - - + -
32A ALA 2.9 24.0 + - - +
33A ALA* 3.1 6.5 + - - +
35A PHE* 1.3 76.3 - - - +
37A GLU* 1.3 64.8 + - - +
39A ALA* 3.3 6.0 + - - +
40A MET* 3.0 25.5 + - + +
49A VAL* 4.2 20.2 - - + -
51A LEU* 3.7 35.9 - - + -
86A LEU* 4.1 20.0 - - + -
90A PHE* 4.2 15.3 - - + -
92A ILE* 4.0 24.5 - - + -
94A LEU* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.1 34.4 + - - +
34A THR* 3.2 15.6 + - - +
36A ILE* 1.3 77.9 - - - +
38A ARG* 1.3 58.9 + - + +
40A MET* 3.3 3.5 + - - +
41A LYS* 2.9 29.6 + - - +
86A LEU* 4.8 5.0 - - - +
89A LYS* 4.7 12.9 + - - +
90A PHE* 3.8 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.2 34.4 + - + +
35A PHE* 3.7 39.3 - - - +
36A ILE 3.3 0.4 - - - -
37A GLU* 1.3 75.8 - - + +
39A ALA* 1.3 59.0 + - - +
41A LYS* 3.8 6.9 - - - +
42A GLU* 2.9 39.1 + - + +
257A ILE* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 4.2 23.8 - - + -
16A VAL* 4.8 4.7 - - + -
35A PHE 3.1 15.2 + - - +
36A ILE* 3.5 13.7 - - + +
38A ARG* 1.3 76.9 - - - +
40A MET* 1.3 63.7 + - - +
43A GLN* 3.0 32.9 + - - +
46A THR* 4.3 1.2 + - - -
49A VAL* 5.2 2.7 - - + -
257A ILE* 3.7 9.1 - - + +
259A TYR* 3.7 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.0 19.2 + - + +
37A GLU 3.8 4.0 - - - +
39A ALA* 1.3 74.5 - - - +
41A LYS* 1.3 64.6 + - - +
43A GLN 3.9 2.0 - - - -
44A PRO* 3.1 40.2 - - - +
46A THR* 3.8 29.2 - - - +
49A VAL* 4.2 8.1 - - - -
90A PHE* 3.5 42.6 - - + -
91A LYS* 4.8 4.0 - - + +
92A ILE* 3.4 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 2.9 17.7 + - - +
38A ARG* 3.8 7.4 - - - +
40A MET* 1.3 77.4 - - - +
42A GLU* 1.3 71.9 + - + +
43A GLN 3.5 0.3 + - - -
44A PRO* 3.8 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 2.9 17.5 + - + +
41A LYS* 1.3 83.6 - - + +
43A GLN* 1.3 59.5 + - - +
44A PRO* 3.8 4.7 - - - +
257A ILE* 5.2 2.4 - - - +
259A TYR* 2.8 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.3 33.8 - - + +
13A VAL 3.2 25.1 + - - +
39A ALA 3.0 13.1 + - - +
40A MET* 3.4 5.3 - - - +
42A GLU* 1.3 79.3 - - - +
44A PRO* 1.4 61.9 - - - +
45A ASP* 3.3 16.6 - - - +
46A THR* 2.6 47.1 + - - +
259A TYR* 3.4 32.1 - - + +
260A ALA 4.4 1.9 - - - +
----------------------------------------------------------
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