Contacts of the helix formed by residues 58 - 74 (chain A) in PDB entry 5O5E
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 GLN 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.5 27.6 - - + +
33A ARG* 5.2 0.8 + - - -
36A PHE* 3.3 36.7 - - - +
55A PRO* 4.0 7.1 - - - +
56A GLU 3.3 19.1 + - - +
57A SER* 1.3 71.4 - - - +
59A GLY* 1.3 55.9 + - - +
60A VAL 3.0 5.2 - - - -
61A ILE* 3.0 41.1 + - - +
62A SER* 3.4 8.3 + - - -
238A LEU* 3.8 23.7 - - + +
248A VAL* 3.4 31.8 - - + +
249A PHE 3.0 15.7 + - - +
250A VAL 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 3.1 0.2 - - - -
58A GLN* 1.3 76.5 - - - +
60A VAL* 1.4 53.9 + - - +
61A ILE 3.3 0.2 - - - -
62A SER* 3.4 11.2 + - - -
63A GLY* 2.8 30.8 + - - -
109A ILE* 4.5 0.3 - - - +
238A LEU* 4.0 3.8 - - - -
250A VAL* 3.0 19.6 + - - +
253A THR* 3.9 9.7 - - - +
254A PHE* 3.7 19.5 - - - -
257A PHE* 4.4 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.5 27.8 - - + -
57A SER 3.1 20.2 + - - +
58A GLN 3.0 0.2 - - - -
59A GLY* 1.4 76.9 - - - +
61A ILE* 1.4 62.3 + - + +
64A ALA* 2.9 30.0 + - - +
109A ILE* 4.5 8.1 - - + +
113A PHE* 3.5 38.4 - - + -
253A THR* 3.6 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 4.6 2.9 - - - +
28A LEU* 3.8 25.8 - - + -
29A ILE* 3.8 22.2 - - + +
32A PHE* 3.7 22.2 - - + -
36A PHE* 3.6 26.9 - - + -
58A GLN* 3.0 35.2 + - - +
60A VAL* 1.4 80.0 - - + +
62A SER* 1.4 59.3 + - - +
64A ALA* 3.3 6.7 + - - +
65A VAL* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 3.7 31.2 - - - +
29A ILE* 5.2 0.2 - - - +
58A GLN 3.4 3.9 + - - -
59A GLY* 3.4 8.7 + - - -
61A ILE* 1.4 77.2 - - - +
63A GLY* 1.3 54.2 + - - +
65A VAL* 3.3 3.3 + - - +
66A PHE* 2.8 35.9 + - - +
234A THR* 4.0 21.8 - - - -
235A THR 4.9 0.6 + - - -
238A LEU* 3.6 25.9 - - - +
254A PHE* 4.5 1.6 - - - -
257A PHE* 4.2 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 2.8 22.3 + - - -
60A VAL 4.1 0.7 - - - -
62A SER* 1.3 74.9 + - - +
64A ALA* 1.4 55.8 + - - +
66A PHE* 3.3 3.6 - - - +
67A LEU* 3.1 31.0 + - - +
109A ILE* 3.5 18.9 - - - +
257A PHE* 3.7 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL 2.9 21.0 + - - +
61A ILE* 3.4 8.1 - - - +
62A SER 3.3 0.2 - - - -
63A GLY* 1.4 72.4 - - - +
65A VAL* 1.4 67.4 + - + +
67A LEU* 2.9 22.4 + - - +
68A ILE* 3.0 24.2 + - + +
109A ILE* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 3.5 28.5 - - - +
24A ALA* 3.9 7.9 - - + -
25A THR* 3.5 18.8 - - - +
28A LEU* 3.9 27.8 - - + -
61A ILE* 3.0 20.2 + - + +
62A SER 3.5 7.2 - - - +
64A ALA* 1.4 71.9 - - + +
66A PHE* 1.4 63.4 + - - +
68A ILE* 3.1 11.5 + - - +
69A ILE* 2.9 40.9 + - + +
234A THR* 4.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER 2.8 17.7 + - - +
63A GLY 3.3 11.0 - - - +
65A VAL* 1.4 72.1 - - - +
67A LEU* 1.4 70.5 + - + +
69A ILE* 3.5 12.0 + - - +
70A LEU* 3.2 50.4 + - + +
102A LEU* 4.3 7.2 - - + -
105A ILE* 3.9 15.3 - - + -
227A PHE* 3.3 29.6 - + - -
230A PRO* 3.9 9.2 - - + -
231A PHE* 3.5 25.4 - - + -
234A THR* 4.1 4.7 - - - +
257A PHE* 3.5 35.9 - + + -
261A THR* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 3.1 16.8 + - - +
64A ALA* 2.9 12.4 + - - +
66A PHE* 1.4 77.2 - - + +
68A ILE* 1.4 58.0 + - + +
70A LEU* 3.3 3.4 + - - +
71A PHE* 2.8 58.4 + - + -
102A LEU* 4.0 22.9 - - + -
105A ILE* 4.5 1.3 - - + -
106A CYS* 3.7 46.0 - - + +
109A ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 3.0 23.4 + - + +
65A VAL* 3.7 7.0 - - - +
67A LEU* 1.4 77.8 - - + +
69A ILE* 1.4 63.3 + - + +
71A PHE* 3.4 13.3 + - + +
72A CYS* 3.1 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.6 44.5 - - + +
18A SER* 4.8 2.7 - - - -
21A GLY* 3.6 29.2 - - - +
65A VAL* 2.9 29.7 + - + +
66A PHE* 3.5 8.1 - - - +
68A ILE* 1.4 74.6 - - + +
70A LEU* 1.3 54.0 + - + +
72A CYS* 3.1 10.6 + - - +
73A PHE* 2.8 30.7 + - - +
230A PRO* 4.2 24.2 - - + -
234A THR* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 4.2 9.4 - - - +
66A PHE* 3.2 48.3 + - + +
67A LEU 4.0 0.7 - - - +
69A ILE* 1.3 77.3 - - + +
71A PHE* 1.3 60.9 + - - +
73A PHE* 3.5 14.3 - - + +
74A ILE* 3.0 32.8 + - - +
98A LEU* 5.5 0.3 - - - +
102A LEU* 3.8 20.8 - - + +
226A TYR* 3.3 24.7 - - + +
227A PHE* 3.6 25.1 - - + -
230A PRO* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 2.8 56.6 + - + +
68A ILE* 3.8 14.1 - - + +
70A LEU* 1.3 77.0 - - - +
72A CYS* 1.3 62.5 + - - +
74A ILE* 3.5 29.4 - - + +
75A PRO* 4.1 3.3 - - - +
102A LEU* 3.8 28.7 - - + -
106A CYS* 5.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 5.7 8.3 - - + -
68A ILE* 3.1 34.4 + - - +
69A ILE* 3.3 10.5 - - - +
71A PHE* 1.3 78.0 - - - +
73A PHE* 1.3 60.6 + - - +
74A ILE 3.5 0.2 - - - -
75A PRO* 3.4 9.2 - - - +
76A PHE* 3.3 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.1 29.2 - - + -
13A ILE* 4.4 4.0 - - + -
14A ASN* 3.3 40.8 - - + +
17A VAL* 4.8 8.3 - - + -
69A ILE 2.8 15.6 + - - +
70A LEU* 3.2 20.4 + - + +
72A CYS* 1.3 77.2 - - - +
74A ILE* 1.4 65.5 + - - +
75A PRO* 3.3 0.2 - - - +
76A PHE* 2.9 41.8 + + + -
77A PRO* 3.2 27.7 - - + +
98A LEU* 5.2 6.1 - - + -
226A TYR* 3.5 34.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU 3.0 15.5 + - - +
71A PHE* 3.5 35.2 - - + +
73A PHE* 1.4 73.3 - - - +
75A PRO* 1.4 64.8 - - + +
77A PRO* 3.3 4.1 - - - +
78A PHE* 3.3 24.4 - - - -
95A PHE* 3.5 30.6 - - + -
98A LEU* 4.0 17.9 - - + -
99A ILE* 3.7 23.6 - - + -
102A LEU* 4.2 12.1 - - + -
----------------------------------------------------------
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