Contacts of the helix formed by residues 50 - 63 (chain D) in PDB entry 6GL7
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 GLU 50 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU 5.0 3.1 - - - +
47D CYS* 2.8 40.4 + - + +
49D ALA* 1.3 80.1 - - + +
51D SER* 1.3 61.7 + - - +
52D ASN* 4.0 11.4 + - + +
53D CYS 4.3 0.7 - - - +
54D SER* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ALA 3.6 2.8 + - - -
50D GLU* 1.3 75.4 + - - +
52D ASN* 1.3 67.7 + - - +
54D SER* 4.3 5.6 - - - -
55D SER* 3.0 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D CYS* 5.6 0.7 - - - -
50D GLU* 3.1 8.0 + - + +
51D SER* 1.3 87.6 + - - +
53D CYS* 1.3 63.4 + - - +
55D SER* 4.1 1.0 - - - -
56D ARG* 3.0 38.6 + - - +
84D VAL* 4.1 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASN* 5.8 2.5 - - - +
47D CYS* 2.1 61.0 - - - +
48D ALA* 4.4 3.8 - - - -
50D GLU* 3.5 2.2 + - - +
52D ASN* 1.3 79.3 - - - +
54D SER* 1.3 54.6 + - - +
57D TYR* 2.7 38.7 + - + +
84D VAL* 5.6 3.1 - - - -
85D LEU* 3.6 26.7 - - + +
88D SER* 3.8 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA* 3.7 14.7 + - - +
49D ALA 5.2 0.9 - - - -
50D GLU 2.8 20.6 + - - -
51D SER* 4.1 5.2 - - - -
53D CYS* 1.3 80.0 - - - +
55D SER* 1.3 62.9 + - - +
57D TYR* 3.8 3.8 - - - +
58D ARG* 2.6 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D SER* 3.0 22.9 + - - -
52D ASN* 4.2 1.6 - - - -
54D SER* 1.3 77.4 + - - +
56D ARG* 1.3 63.2 + - - +
58D ARG* 3.4 26.2 + - - +
59D THR* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ASN* 3.0 22.6 + - - +
55D SER* 1.3 77.7 - - - +
57D TYR* 1.3 65.4 + - - +
59D THR* 3.2 10.4 + - - -
60D LEU* 3.1 20.8 + - - +
77D GLU* 2.9 41.0 + - - +
80D ALA* 4.3 12.8 - - - +
81D ALA* 3.3 31.9 - - + +
84D VAL* 4.0 30.5 - - + +
85D LEU* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASN* 4.5 19.1 - - - -
53D CYS 2.7 25.6 + - - +
54D SER* 3.8 4.9 - - - +
56D ARG* 1.3 74.0 - - - +
58D ARG* 1.3 74.2 + - + +
60D LEU* 3.3 4.3 + - - +
61D ARG* 3.2 37.3 + - + +
85D LEU* 3.8 12.4 - - + +
107D GLN 4.9 0.5 + - - -
108D ILE* 4.2 14.5 + - + +
111D SER* 3.3 38.4 + - - +
112D ILE* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D SER* 2.6 41.7 + - - +
55D SER* 3.4 32.6 + - - +
56D ARG 3.3 0.2 - - - -
57D TYR* 1.3 85.2 - - + +
59D THR* 1.3 63.8 + - - +
61D ARG* 3.1 47.2 + - - +
62D GLN* 3.1 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER* 2.9 16.9 + - - -
56D ARG* 3.4 19.3 + - - +
57D TYR 3.2 0.2 - - - -
58D ARG* 1.3 76.2 - - - +
60D LEU* 1.3 62.4 + - - +
62D GLN* 3.0 17.9 + - + +
63D CYS 3.2 0.7 + - - -
74D ALA* 4.8 0.7 - - + +
77D GLU* 3.6 45.0 - - + +
78D CYS* 3.2 24.5 - - - +
81D ALA* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ARG 3.1 4.7 + - - +
57D TYR 3.8 6.1 - - - +
59D THR* 1.3 75.1 - - - +
61D ARG* 1.3 64.2 + - - +
63D CYS* 2.8 28.6 + - - -
78D CYS* 3.1 30.7 - - + +
81D ALA* 3.6 11.9 - - + -
82D LEU* 4.1 9.9 - - + +
85D LEU* 3.4 27.8 - - + -
111D SER 4.1 11.7 - - - +
112D ILE* 3.3 31.4 - - - +
113D HIS 5.0 4.1 - - - +
114D LEU* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 3.2 29.6 + - + +
58D ARG* 3.1 45.9 + - - +
60D LEU* 1.3 75.9 - - - +
62D GLN* 1.3 63.4 + - - +
63D CYS* 4.4 0.2 - - - -
111D SER* 4.5 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ARG 3.1 8.6 + - - +
59D THR* 3.0 14.5 + - + +
61D ARG* 1.3 78.1 - - - +
63D CYS* 1.3 60.5 + - + +
74D ALA* 4.5 19.5 - - + -
78D CYS* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR 3.2 5.7 + - - -
60D LEU* 2.8 27.4 + - - -
61D ARG 4.4 0.4 - - - -
62D GLN* 1.3 76.1 - - + +
74D ALA* 3.3 30.5 - - + -
75D ASN* 3.5 17.5 - - - +
78D CYS* 2.1 52.7 - - - -
113D HIS 5.3 1.3 - - - -
114D LEU* 3.9 7.5 - - - +
115D GLY 3.4 38.3 + - - -
----------------------------------------------------------
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