Contacts of the helix formed by residues 55 - 67 (chain T) in PDB entry 4GGF
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 ASN 55 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51T LYS 4.9 3.4 - - - +
52T GLU 3.0 18.1 + - - +
53T ASN 3.1 1.8 - - - -
54T LYS* 1.3 82.1 - - + +
56T GLU* 1.3 59.5 + - - +
57T LYS* 3.0 29.2 + - - +
58T VAL* 2.9 42.4 + - + +
59T ILE* 3.2 4.0 + - - +
97V GLY 5.4 0.4 + - - -
99V GLU* 2.9 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T LYS* 2.6 41.8 + - + +
53T ASN 4.7 2.8 + - - -
54T LYS 4.1 1.8 + - - -
55T ASN* 1.3 74.2 + - - +
57T LYS* 1.3 62.4 + - + +
59T ILE* 3.2 9.9 + - + +
60T GLU* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55T ASN* 3.0 14.9 + - - +
56T GLU* 1.3 78.2 - - + +
58T VAL* 1.3 62.1 + - - +
60T GLU* 3.7 20.4 - - - +
61T HIS 3.0 14.4 + - - -
99V GLU* 3.1 47.9 + - + -
100V GLY 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T GLU* 3.9 36.1 - - + +
55T ASN* 2.9 35.1 + - + +
57T LYS* 1.3 78.8 - - - +
59T ILE* 1.3 63.2 + - - +
61T HIS* 3.1 5.6 + - + +
62T ILE* 3.0 28.6 + - + +
96V GLU* 6.0 0.9 - - - +
97V GLY* 4.0 24.0 - - - +
98V ASP 3.7 20.0 - - - +
99V GLU* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T PHE* 3.9 19.2 - - + -
38T LYS* 3.9 29.4 - - + -
41T VAL* 3.7 28.5 - - + -
49T LEU* 5.1 0.4 - - + -
52T GLU* 3.5 42.2 - - + +
53T ASN* 3.9 12.3 - - - +
55T ASN 3.2 4.9 + - - +
56T GLU* 3.2 12.3 + - + +
58T VAL* 1.3 75.8 - - - +
60T GLU* 1.3 62.9 + - - +
62T ILE* 3.2 13.8 + - + +
63T MET* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T GLN* 3.4 32.6 + - - +
38T LYS* 2.7 29.1 + - - -
56T GLU* 3.0 24.4 + - - +
57T LYS* 3.7 25.5 - - - +
58T VAL 3.1 0.2 - - - -
59T ILE* 1.3 77.4 - - - +
61T HIS* 1.3 61.9 + - - +
63T MET* 3.3 3.8 + - - +
64T GLU* 3.0 23.5 + - - +
100V GLY* 4.8 9.4 - - - +
101V PRO* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57T LYS 3.0 6.7 + - - -
58T VAL* 3.5 4.9 - - + +
60T GLU* 1.3 73.6 - - - +
62T ILE* 1.3 70.1 + - + +
64T GLU* 3.2 6.8 + - - +
65T ASP* 2.9 38.7 + - + +
26U PHE* 3.8 30.4 - + - -
27U HIS* 5.5 0.4 - - - -
95V HIS* 3.8 21.0 + + - +
98V ASP* 3.1 56.9 + - + +
100V GLY* 3.6 21.6 + - - +
102V GLY 4.5 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T PHE* 3.8 12.1 - - + -
49T LEU* 4.8 13.5 - - + -
52T GLU* 4.5 12.1 - - + -
58T VAL* 3.0 32.5 + - + +
59T ILE* 3.2 23.3 + - + +
61T HIS* 1.3 87.5 - - + +
63T MET* 1.3 64.6 + - - +
65T ASP* 3.3 5.6 + - - +
66T LEU* 3.1 42.0 + - + +
82T LEU* 4.3 15.7 - - + -
85T ARG* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T LEU 3.6 18.6 - - - +
34T GLN* 3.8 42.2 - - + +
37T PHE* 3.7 35.8 - - + -
59T ILE 3.0 9.3 + - - +
60T GLU 3.3 7.2 + - - +
62T ILE* 1.3 77.8 - - - +
64T GLU* 1.3 64.5 + - - +
66T LEU* 3.2 4.6 + - - -
67T ASP* 3.0 24.7 + - + +
72T LYS* 3.4 35.7 - - - +
73T GLN* 3.9 8.1 - - - +
74T LEU* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60T GLU 3.0 14.1 + - - +
61T HIS* 3.2 6.8 + - - +
63T MET* 1.3 77.9 - - - +
65T ASP* 1.3 52.1 + - - +
67T ASP* 3.3 13.3 + - - +
25U ASN* 2.8 27.8 + - - +
26U PHE* 3.6 26.7 - - + -
100V GLY* 4.3 5.9 - - - -
101V PRO* 3.3 29.1 - - - +
102V GLY* 3.2 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61T HIS* 2.9 27.3 + - - +
62T ILE* 3.5 8.7 - - - +
64T GLU* 1.3 75.7 - - - +
66T LEU* 1.3 58.9 + - - +
68T THR* 4.6 3.5 + - - +
85T ARG* 3.0 32.8 + - - -
25U ASN* 2.9 18.9 + - - +
26U PHE* 3.7 15.4 - - + -
27U HIS* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T PHE* 3.9 15.0 - - + -
62T ILE* 3.1 35.4 + - + +
63T MET 3.8 3.4 - - - +
65T ASP* 1.3 76.2 - - - +
67T ASP* 1.3 54.0 + - - +
68T THR* 2.8 28.8 + - - +
74T LEU* 3.9 21.1 - - + -
78T GLU* 3.2 32.0 - - - +
79T PHE* 5.3 1.1 - - - -
81T MET* 4.3 3.1 - - + -
82T LEU* 3.8 35.0 - - + +
85T ARG* 3.9 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T MET* 3.0 20.4 + - + +
64T GLU* 3.7 8.6 - - - +
65T ASP 3.3 2.2 - - - -
66T LEU* 1.3 71.2 - - - +
68T THR* 1.3 56.8 + - - +
69T ASN* 3.2 6.1 - - - +
70T ALA* 3.0 18.1 + - - -
71T ASP* 3.2 7.8 + - - +
72T LYS* 2.8 28.0 + - - +
73T GLN 3.5 9.2 - - - -
74T LEU* 3.7 11.9 - - + -
78T GLU* 4.0 1.8 - - - -
204T CA 2.3 30.1 - - - -
25U ASN* 3.2 13.5 + - - +
----------------------------------------------------------
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