Contacts of the helix formed by residues 64 - 77 (chain A) in PDB entry 4E70
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 ALA 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.8 25.6 - - + +
51A ASN* 5.4 1.3 - - - -
54A ALA* 4.4 16.4 - - + -
60A PRO 3.5 3.9 + - - -
61A GLN* 3.0 23.1 + - - +
63A LYS* 1.3 77.3 - - - +
65A PRO* 1.4 61.1 - - + +
67A LEU* 3.1 10.3 + - - +
68A SER* 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 5.2 1.3 - - + -
61A GLN 4.0 3.1 - - - +
62A THR 3.6 13.2 - - - +
63A LYS* 3.3 5.2 - - - -
64A ALA* 1.4 91.8 - - + +
66A PHE* 1.3 69.3 + - + +
68A SER* 3.5 9.6 + - - -
69A ARG* 3.2 28.9 + - - +
----------------------------------------------------------
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 THR 4.6 4.7 - - - -
63A LYS* 3.0 34.4 + - + +
65A PRO* 1.3 80.8 - - + +
67A LEU* 1.3 66.4 + - - +
69A ARG* 3.2 21.9 + - - +
70A LEU* 3.0 21.5 + - - +
1137B TRP* 3.7 29.8 - + + -
1138B LEU* 3.8 16.6 - - + -
1149B PRO 4.8 6.3 - - - -
1327B MET* 3.7 38.6 - - + +
1331B GLU 6.6 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
35A LEU* 5.2 0.2 - - + -
37A ILE* 4.8 1.6 - - + -
50A LEU* 4.0 14.8 - - + -
53A LEU* 4.0 5.8 - - + -
54A ALA* 3.6 39.5 - - + +
57A LEU* 3.9 26.5 - - + -
59A ILE* 4.0 18.8 - - + -
63A LYS 3.2 7.9 + - - +
64A ALA* 3.1 9.3 + - - +
66A PHE* 1.3 78.7 - - - +
68A SER* 1.3 57.3 + - - +
70A LEU* 3.2 18.1 + - + +
71A MET* 2.8 47.4 + - + +
1138B LEU* 4.4 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.8 18.4 - - - +
64A ALA 2.9 12.0 + - - -
65A PRO* 3.5 13.0 - - - -
66A PHE 3.2 0.2 - - - -
67A LEU* 1.3 76.1 - - - +
69A ARG* 1.3 58.5 + - - +
71A MET* 3.2 3.3 + - - +
72A ARG* 2.9 27.9 + - - +
96A PRO* 4.2 8.0 - - - +
98A TYR* 3.6 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.2 18.1 + - - +
66A PHE* 3.2 32.7 + - - +
68A SER* 1.3 75.6 - - - +
70A LEU* 1.3 64.9 + - - +
72A ARG* 3.3 22.9 + - - +
73A MET* 3.1 17.3 + - - +
1320B LEU* 5.9 0.5 - - - +
1323B ASP* 2.9 58.5 + - - +
1324B MET* 3.4 15.6 - - + +
1327B MET* 3.4 18.7 - - - +
1331B GLU 6.1 0.2 - - - -
1332B GLY 3.0 26.9 + - - -
1333B SER* 3.5 15.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
28A THR* 4.0 38.4 - - + +
31A CYS* 4.4 12.8 - - + -
35A LEU* 4.1 25.1 - - + -
37A ILE* 4.4 12.8 - - + -
66A PHE 3.0 12.9 + - - +
67A LEU* 3.5 14.4 - - + +
69A ARG* 1.3 75.0 - - - +
71A MET* 1.3 63.3 + - - +
73A MET* 3.2 4.7 + - - +
74A LEU* 3.0 34.5 + - + +
1131B TRP* 5.3 3.6 - - + -
1134B MET* 6.1 0.7 - - + -
1138B LEU* 4.2 15.0 - - + -
1324B MET* 3.7 13.1 - - - +
1327B MET* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.0 30.1 - - - -
41A ILE* 4.0 10.5 - - + -
53A LEU* 4.1 11.0 - - + -
67A LEU* 2.8 31.0 + - + +
68A SER 3.6 3.4 - - - +
70A LEU* 1.3 77.3 - - - +
72A ARG* 1.3 51.9 + - - +
74A LEU* 3.1 9.6 + - - +
75A VAL* 2.7 41.3 + - - +
80A PHE* 3.8 28.7 - - + -
98A TYR* 3.5 55.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER 2.9 14.0 + - - +
69A ARG* 3.5 23.0 + - - +
70A LEU 3.3 0.2 - - - -
71A MET* 1.3 74.6 - - - +
73A MET* 1.3 62.2 + - - +
75A VAL* 3.5 7.6 + - - +
76A HIS* 3.1 22.3 + - - +
82A GLN* 6.2 0.2 - - - -
98A TYR* 5.1 1.7 - - - -
1305B LEU* 3.4 28.7 - - - +
1316B MET* 6.3 0.4 - - - -
1320B LEU* 3.6 25.0 - - + +
1323B ASP* 3.1 33.7 + - - +
1333B SER* 5.8 0.8 - - - -
1334B LEU 4.2 5.5 + - - -
1336B THR* 4.5 12.1 - - - +
1339B GLN* 5.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.2 10.3 - - + -
25A ASN* 3.2 27.8 - - - +
28A THR* 3.9 26.5 - - + +
69A ARG 3.1 12.5 + - - +
70A LEU 3.4 9.0 - - - +
72A ARG* 1.3 77.1 - - - +
74A LEU* 1.3 57.6 + - - +
76A HIS* 3.2 8.4 + - - +
77A LEU* 3.0 37.6 + - + +
1317B GLY 5.0 0.9 - - - +
1320B LEU* 3.8 32.5 - - + +
1321B ILE* 3.5 17.9 - - + -
1324B MET* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.9 17.0 - - - +
29A LEU* 4.4 5.2 - - + -
32A ALA* 3.7 33.0 - - + -
37A ILE* 4.0 13.0 - - + -
70A LEU* 3.0 39.2 + - + +
71A MET* 3.1 8.9 + - - +
73A MET* 1.3 73.0 - - + +
75A VAL* 1.3 65.5 + - - +
77A LEU* 3.4 14.0 + - + +
78A GLY 3.1 4.9 + - - -
79A TYR* 3.1 40.8 + - + +
80A PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET 2.7 26.1 + - - +
72A ARG* 3.7 7.9 - - - +
74A LEU* 1.3 70.2 - - - +
76A HIS* 1.3 68.5 + - - +
78A GLY* 3.0 14.6 + - - -
80A PHE* 3.4 37.9 - - + +
81A THR* 4.1 10.8 - - - +
82A GLN* 4.3 17.3 - - + +
98A TYR* 4.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 3.1 7.0 + - - +
73A MET* 3.2 11.0 + - + +
75A VAL* 1.3 80.1 - - - +
77A LEU* 1.3 66.2 + - + +
78A GLY* 3.2 1.2 + - - -
402A GOL 4.0 19.3 + - - -
1313B SER* 3.4 32.6 + - - -
1316B MET* 4.0 15.8 - - + +
1317B GLY* 3.3 29.6 - - - -
1320B LEU* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.7 28.5 - - - +
28A THR* 4.1 19.5 - - - +
29A LEU* 5.3 2.5 - - + +
73A MET* 3.0 27.3 + - + +
74A LEU* 3.7 18.6 - - + +
75A VAL 3.2 0.2 - - - -
76A HIS* 1.3 80.8 - - + +
78A GLY* 1.3 59.0 + - - +
79A TYR* 3.7 22.2 - - + -
103A LEU* 4.0 6.2 - - - +
402A GOL 3.8 17.0 - - - +
1015B GLN* 5.6 0.3 - - - +
1019B HIS* 3.2 43.6 + - + +
----------------------------------------------------------
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