Contacts of the helix formed by residues 60 - 70 (chain A) in PDB entry 3EHN
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 THR 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 1.3 96.1 - - + +
61A GLY* 1.3 69.2 + - - +
62A PRO 3.4 1.6 - - - -
63A GLY* 3.2 3.3 + - - +
64A ASN* 3.1 24.6 + - - -
271A LEU* 6.3 0.4 - - + -
276A ALA* 3.7 23.8 - - + -
280A GLU* 4.8 10.8 - - + +
281A TYR* 3.2 28.6 + - + +
2C GAL 4.6 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.9 12.8 + - - -
59A THR* 4.7 0.2 - - - -
60A THR* 1.3 81.9 + - - +
62A PRO* 1.3 65.9 - - - +
64A ASN* 3.0 22.0 + - - +
65A ASP* 3.4 10.6 + - - +
2C GAL 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 3.8 1.8 - - - +
53A ILE* 3.7 15.7 - - - +
54A GLY* 3.7 36.8 - - - +
55A SER 5.1 0.4 - - - +
58A LEU* 3.6 28.5 - - + +
59A THR 4.0 6.1 - - - +
60A THR 3.8 0.7 - - - -
61A GLY* 1.3 88.3 - - - +
63A GLY* 1.3 57.3 + - - +
65A ASP* 2.9 14.2 + - + +
66A LEU* 2.8 28.2 + - - +
271A LEU 5.7 0.9 - - - +
273A SER* 4.0 5.8 - - - -
----------------------------------------------------------
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 THR 5.2 0.2 + - - -
60A THR* 3.2 9.9 + - - +
62A PRO* 1.3 79.7 - - - +
64A ASN* 1.3 59.1 + - - +
66A LEU* 3.4 1.4 + - - +
67A GLN* 2.9 30.9 + - - +
71A LEU* 5.0 2.1 - - - +
273A SER* 3.2 28.5 - - - +
276A ALA* 4.1 16.1 - - - +
277A SER* 5.1 1.6 - - - -
281A TYR* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.1 16.8 + - - +
61A GLY* 3.0 12.3 + - - +
63A GLY* 1.3 76.2 - - - +
65A ASP* 1.3 58.7 + - - +
67A GLN* 3.5 9.6 + - - +
68A ASN* 3.3 14.7 + - - +
101A ARG* 5.1 1.4 + - - -
104A TYR* 3.0 24.5 + - + +
281A TYR* 2.8 35.6 + - - -
1C NDG 3.4 24.5 + - + +
2C GAL 3.5 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 4.3 15.9 + - - -
52A PRO* 3.5 17.7 - - + +
61A GLY 3.4 12.1 + - - +
62A PRO* 2.9 13.3 + - + +
64A ASN* 1.3 74.8 - - - +
66A LEU* 1.3 65.1 + - - +
67A GLN 3.0 1.8 - - - -
68A ASN* 3.1 3.3 + - - +
69A THR* 3.1 27.5 + - - +
104A TYR* 2.7 30.6 + - - -
108A ASN* 2.7 26.7 - - - +
112A GLN* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.5 31.2 - - + -
52A PRO* 3.5 13.0 - - + +
62A PRO 2.8 17.9 + - - +
63A GLY 3.9 3.6 - - - +
65A ASP* 1.3 72.4 - - - +
67A GLN* 1.3 59.2 + - - +
69A THR* 3.8 4.7 - - - +
70A ASP* 2.8 41.7 + - + +
71A LEU* 3.0 19.7 + - + -
273A SER* 3.3 40.6 - - - +
274A MET* 3.6 22.9 - - + -
353A LEU* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 2.9 16.8 + - - +
64A ASN* 3.5 10.2 + - - +
66A LEU* 1.3 81.7 - - - +
68A ASN* 1.3 59.9 + - - +
69A THR 3.6 0.2 + - - -
71A LEU* 3.7 9.6 + - + +
72A ILE* 3.0 59.2 + - + +
73A SER 3.9 1.2 + - - -
101A ARG* 5.7 0.4 - - - +
277A SER* 2.8 34.3 + - - +
281A TYR* 3.5 10.5 - - - -
283A GLU* 3.0 22.6 + - - -
1C NDG 3.2 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.3 1.4 + - - +
65A ASP 3.1 7.5 + - - +
67A GLN* 1.3 81.3 - - - +
69A THR* 1.3 59.2 + - - +
73A SER* 2.9 17.9 + - - -
92A GLU* 2.7 37.1 + - - +
101A ARG* 3.6 24.1 + - - +
102A MET* 5.3 0.6 - - - +
104A TYR* 3.6 31.7 - - + -
105A ALA* 3.1 22.0 - - - +
108A ASN* 3.0 16.6 + - - +
503A PHE* 4.3 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 4.0 10.8 - - + +
65A ASP 3.1 17.4 + - - +
66A LEU* 3.6 6.8 + - - -
68A ASN* 1.3 78.8 - - - +
70A ASP* 1.3 75.4 + - - +
73A SER* 3.1 11.0 + - - -
74A SER* 2.7 23.7 + - - -
108A ASN* 3.5 30.1 - - + +
109A PHE* 3.4 34.4 - - + -
149A ARG* 3.8 6.7 + - - +
464A VAL* 3.5 8.0 - - - +
467A TRP* 5.8 0.3 - - - -
503A PHE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.2 8.5 - - - +
66A LEU* 2.8 34.4 + - + +
69A THR* 1.3 105.0 + - - +
71A LEU* 1.3 66.0 + - + +
72A ILE 3.8 0.9 - - - -
73A SER* 4.3 1.6 - - - -
74A SER* 3.3 3.4 - - - -
75A GLY* 2.6 33.8 + - - -
81A PHE* 3.9 0.6 - - + -
149A ARG* 3.2 23.4 + - - -
461A PRO 4.3 5.1 - - - +
462A ASN* 4.7 2.4 - - - +
463A ALA* 3.7 23.2 + - + +
464A VAL* 3.7 6.3 + - - +
----------------------------------------------------------
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