Contacts of the helix formed by residues 61 - 78 (chain A) in PDB entry 3HEG
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 SER 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE 4.0 0.7 - - - -
60A GLN* 1.3 81.1 - - - +
62A ILE* 1.3 59.9 + - - +
63A ILE* 3.6 6.4 + - - +
64A HIS* 3.1 28.8 + - - +
65A ALA* 2.9 29.5 + - - +
334A ILE* 3.5 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 1.3 74.1 - - - +
63A ILE* 1.3 61.7 + - + +
65A ALA* 3.3 3.2 + - - +
66A LYS* 2.9 31.4 + - + +
331A ASP* 6.0 0.7 - - - -
332A LEU 3.2 28.7 - - - +
333A LEU* 4.6 8.1 - - + -
334A ILE* 3.6 24.7 - - + +
337A TRP* 3.8 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 3.4 5.8 + - - +
62A ILE* 1.3 80.9 - - + +
64A HIS* 1.3 56.9 + - - +
66A LYS* 3.6 13.8 + - + +
67A ARG* 3.0 57.3 + - - +
70A ARG* 5.4 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.9 10.2 + - - -
57A ARG* 2.6 45.7 + - + +
58A PRO* 2.9 8.5 - - + +
60A GLN* 4.3 14.1 + - + -
61A SER* 3.1 28.6 + - - +
63A ILE* 1.3 78.1 - - - +
65A ALA* 1.3 53.6 + - - +
67A ARG* 3.4 27.7 + - - +
68A THR* 2.8 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 3.4 7.4 + - - -
59A PHE* 4.0 21.7 - - + -
61A SER 2.9 21.5 + - - +
62A ILE 3.8 2.7 - - - +
64A HIS* 1.3 74.1 - - - +
66A LYS* 1.3 64.4 + - - +
68A THR* 3.5 3.3 + - - -
69A TYR* 3.1 22.7 + - - +
334A ILE* 4.2 11.7 - - - +
337A TRP* 3.5 26.3 - - + +
341A THR* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 2.9 21.4 + - + +
63A ILE* 3.9 14.4 - - + +
65A ALA* 1.3 71.9 - - - +
67A ARG* 1.3 57.0 + - - +
69A TYR* 3.4 1.9 + - - +
70A ARG* 2.9 46.8 + - - +
327A PHE* 3.6 21.1 - - + -
328A GLU* 2.7 42.5 + - - +
330A ARG 3.0 19.8 + - - +
331A ASP* 4.6 5.1 + - - -
337A TRP* 3.6 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.0 45.1 + - - +
64A HIS* 3.4 43.4 + - - +
65A ALA 3.2 0.4 - - - -
66A LYS* 1.3 77.4 - - - +
68A THR* 1.3 56.4 + - - +
70A ARG* 3.3 23.9 + - - +
71A GLU* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.1 20.2 - - + +
58A PRO* 2.9 31.6 + - + +
59A PHE* 3.6 27.4 - - + -
64A HIS* 2.8 20.9 + - - -
65A ALA 3.6 5.2 - - - -
67A ARG* 1.3 76.4 - - - +
69A TYR* 1.3 56.7 + - - +
71A GLU* 3.4 6.1 + - - +
72A LEU* 3.0 28.4 + - - +
102A VAL* 4.5 3.1 - - + -
341A THR* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 3.1 16.4 + - - +
66A LYS 3.8 2.5 - - - +
68A THR* 1.3 73.2 - - - +
70A ARG* 1.3 61.3 + - - +
72A LEU* 3.4 4.1 + - + +
73A ARG* 2.8 67.3 + - + +
327A PHE* 3.6 37.0 - + + +
337A TRP* 3.7 28.9 - + + +
340A LEU* 3.5 37.1 - - + +
341A THR* 3.4 32.9 + - - +
344A GLU* 3.7 17.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.4 2.0 + - - +
66A LYS* 2.9 42.6 + - - +
67A ARG* 3.5 34.7 - - - +
69A TYR* 1.3 76.5 - - - +
71A GLU* 1.3 64.1 + - - +
73A ARG* 3.8 1.7 - - - +
74A LEU* 3.0 29.1 + - + +
323A TYR* 4.4 2.1 + - - +
327A PHE* 3.7 19.3 - - + -
328A GLU* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BAX 2.7 57.5 + - - -
53A LYS* 3.0 23.1 + - - +
55A LEU* 5.5 5.2 - - + -
67A ARG* 3.0 18.2 + - + +
68A THR* 3.8 6.1 - - - +
70A ARG* 1.3 75.2 - - - +
72A LEU* 1.3 61.5 + - - +
74A LEU* 3.2 4.0 + - - +
75A LEU* 2.9 38.3 + - + +
104A LEU* 4.0 16.6 - - + -
168A ASP 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.0 17.2 + - + +
69A TYR* 3.9 5.2 - - - +
71A GLU* 1.3 79.4 - - - +
73A ARG* 1.3 63.3 + - - +
75A LEU* 4.0 2.4 - - - -
76A LYS* 3.1 44.5 + - + +
86A LEU* 3.8 16.8 - - + -
89A VAL* 4.1 16.2 - - + -
102A VAL* 5.1 4.0 - - + -
104A LEU* 4.6 11.9 - - + -
341A THR* 3.7 15.0 - - + +
344A GLU* 3.6 26.7 - - + -
345A VAL* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.8 60.4 + - + +
70A ARG 3.8 2.7 - - - +
72A LEU* 1.3 72.5 - - - +
74A LEU* 1.3 61.2 + - - +
76A LYS* 3.6 6.7 + - - +
77A HIS* 3.3 21.3 + - - +
323A TYR* 3.6 28.2 - - - +
324A ASP* 2.5 46.1 + - - +
327A PHE* 3.6 22.6 - - + +
344A GLU* 3.3 35.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
1A BAX 3.4 63.5 - - + +
70A ARG* 3.0 22.7 + - + +
71A GLU* 3.8 4.9 - - - +
72A LEU 3.2 0.4 - - - -
73A ARG* 1.3 75.1 - - - +
75A LEU* 1.3 69.9 + - + +
77A HIS* 3.0 12.7 + - - +
78A MET* 3.1 26.2 + - + +
146A ILE* 3.8 37.5 - - + -
323A TYR* 3.6 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BAX 3.7 32.8 - - + +
71A GLU* 2.9 42.8 + - + +
72A LEU* 4.1 2.7 - - - +
74A LEU* 1.3 80.3 - - + +
76A LYS* 1.3 60.7 + - - +
77A HIS 3.3 0.9 + - - -
78A MET* 3.4 20.2 + - + +
84A ILE* 3.9 28.5 - - + +
85A GLY 5.2 2.5 - - - -
86A LEU* 3.8 40.8 + - + +
104A LEU* 3.7 23.3 - - + -
106A THR* 5.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.1 42.9 + - + +
73A ARG* 3.8 6.1 - - - +
75A LEU* 1.3 75.4 - - - +
77A HIS* 1.3 59.8 + - - +
78A MET 4.9 0.2 - - - -
79A LYS* 3.6 21.4 + - - -
86A LEU* 3.7 15.5 - - + -
344A GLU* 2.5 56.9 + - + +
347A SER* 3.0 19.8 + - - -
348A PHE* 4.2 22.9 - - + +
349A VAL 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG 3.3 12.9 + - - +
74A LEU 3.0 10.0 + - - +
76A LYS* 1.3 77.6 - - - +
78A MET* 1.3 86.7 + - + +
79A LYS* 3.2 9.6 + - - +
140A TYR* 3.0 15.9 + - - -
144A ALA* 4.3 4.3 - - + -
320A ALA* 4.2 7.5 - - + +
321A ASP* 2.7 35.7 + - + -
322A PRO 3.1 24.5 - - - -
323A TYR* 3.4 34.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BAX 3.7 17.7 - - - -
74A LEU* 3.1 30.5 + - + +
75A LEU* 3.4 13.7 + - + +
76A LYS 4.9 0.2 - - - +
77A HIS* 1.3 109.6 - - + +
79A LYS* 1.3 64.2 + - - +
80A HIS 3.9 1.8 - - - -
83A VAL* 3.9 15.3 - - + -
84A ILE 3.4 20.0 - - - +
85A GLY* 4.0 13.7 - - - -
86A LEU 4.7 0.9 + - - -
140A TYR* 3.8 19.1 - - + -
141A ILE* 4.1 8.5 - - + -
144A ALA* 4.7 4.0 - - + -
146A ILE* 3.6 23.6 - - + -
----------------------------------------------------------
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