Contacts of the helix formed by residues 57 - 63 (chain A) in PDB entry 5E0F
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 PRO 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.7 0.2 - - - +
51A ILE* 3.6 15.5 - - + +
54A PRO* 3.4 20.9 - - + +
55A PHE 3.5 1.3 - - - -
56A ARG* 1.3 94.1 - - - +
58A TRP* 1.3 65.7 + - - +
59A TRP* 3.1 51.7 + - + -
60A GLU* 3.1 23.7 + - - +
72A ARG* 4.5 1.9 + - - -
357A TRP* 3.1 21.5 - - + +
359A GLY 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.8 14.9 - + + -
18A GLU* 3.3 26.7 - - - +
57A PRO* 1.3 71.1 - - - +
59A TRP* 1.3 94.4 + + + +
60A GLU 3.1 1.6 + - - -
61A ARG* 3.2 15.1 + - - +
62A TYR* 4.0 10.2 - + - -
299A HIS* 3.4 28.7 - + - -
300A ASP* 3.2 21.3 - - - -
303A ARG* 3.3 23.6 - - - +
305A HIS* 4.3 9.4 - + - -
342A TYR* 3.4 17.9 - - - +
356A ASP 2.9 23.6 + - - -
357A TRP* 3.2 26.7 + - - -
358A VAL 3.6 9.4 - - - -
359A GLY* 3.6 6.6 - - - -
360A PRO* 4.7 0.4 - - - -
501A 5J7 3.5 36.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.6 26.5 - - + -
53A ASN 4.9 0.9 - - - -
54A PRO* 3.7 34.5 - - + -
57A PRO* 3.6 13.0 - - + +
58A TRP* 1.3 117.2 - + + +
60A GLU* 1.3 67.3 + - - +
61A ARG 3.1 1.8 - - - -
62A TYR* 3.1 22.2 + - + +
63A GLN* 4.0 19.4 + - - +
356A ASP* 5.1 1.0 + - - -
357A TRP* 3.5 20.2 - - + +
501A 5J7 3.4 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.0 28.5 + - - +
49A VAL 3.2 16.9 - - - +
51A ILE* 2.9 50.3 + - + +
56A ARG* 2.7 43.6 + - - -
57A PRO* 3.1 17.5 + - + +
58A TRP 3.1 2.0 + - - -
59A TRP* 1.3 81.1 - - - +
61A ARG* 1.3 65.5 + - + +
62A TYR 3.0 0.4 - - - -
63A GLN* 3.1 20.5 + - - +
72A ARG* 4.1 9.2 + - - +
114A THR* 4.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 2.9 41.1 + - - +
21A TRP* 3.9 4.2 - - - -
43A SER* 3.5 23.7 - - - -
44A PRO* 2.9 58.0 + - + +
46A ASN* 5.2 1.9 + - - +
48A ASN* 3.8 28.2 + - - +
58A TRP 3.7 11.0 - - - +
59A TRP 3.1 1.2 - - - -
60A GLU* 1.3 86.1 - - + +
62A TYR* 1.3 62.4 + - + +
63A GLN 3.3 2.9 + - - -
64A PRO* 5.1 1.9 - - - +
71A THR* 3.5 19.5 + - - -
72A ARG* 4.9 8.4 - - - +
73A SER* 2.9 35.9 + - - +
98A VAL* 4.2 3.3 - - - +
367A ILE* 4.5 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 5.1 2.9 + - - -
17A PHE* 5.1 6.6 - + - -
43A SER* 5.3 1.0 + - - -
44A PRO* 3.8 20.3 - - + +
58A TRP* 4.0 20.2 - + - -
59A TRP* 3.1 14.4 + - + +
60A GLU 3.0 1.4 - - - -
61A ARG* 1.3 80.8 - - + +
63A GLN* 1.3 64.6 + - - +
64A PRO* 3.7 3.8 - - - -
96A ASP* 2.7 32.0 + - - -
98A VAL* 3.6 13.9 - - + -
101A HIS* 3.0 26.7 + - - -
195A ARG* 4.0 1.1 - - - -
197A ASP* 3.6 16.6 - - - -
299A HIS* 3.3 32.2 + + - -
501A 5J7 3.3 49.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.3 4.1 - - - +
49A VAL* 3.0 31.9 + - + +
51A ILE* 3.8 22.6 - - - +
59A TRP* 4.0 24.4 + - - +
60A GLU 3.1 9.4 + - - +
61A ARG 3.3 1.2 - - - -
62A TYR* 1.3 84.7 - - + +
64A PRO* 1.4 63.6 - - - +
102A MET 3.9 3.1 - - - -
103A CYS* 3.6 12.8 - - + +
104A GLY* 2.9 22.2 + - - -
107A VAL* 3.8 10.8 - - - +
165A LEU* 3.6 22.1 - - + +
501A 5J7 5.1 5.9 + - - +
----------------------------------------------------------
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