Contacts of the helix formed by residues 60 - 79 (chain G) in PDB entry 5GAG
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 ASP 60 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757A A 5.3 5.6 + - - +
38G ASN* 5.4 1.2 - - - +
40G ALA* 3.3 22.0 - - - +
58G TYR* 4.0 5.9 - - - +
59G ALA* 1.3 79.1 - - + +
61G GLY* 1.3 56.4 + - - +
62G TRP 3.1 2.7 - - - -
63G ALA* 2.7 38.8 + - + +
64G GLN* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ALA* 4.2 15.8 - - - +
54G PRO* 3.8 26.8 - - - +
55G ARG 5.1 0.2 - - - -
58G TYR* 4.2 6.6 + - - -
59G ALA 3.3 5.3 + - - -
60G ASP* 1.3 82.3 + - - +
62G TRP* 1.3 56.8 + - - +
64G GLN* 3.9 1.7 - - - +
65G ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749A A 4.7 5.6 - - - +
2G SER* 4.0 33.8 + - - -
5G ALA* 3.7 30.3 - - + -
6G LYS* 3.7 41.8 - - + +
52G PHE 4.4 6.5 - - - -
53G GLY* 4.6 2.7 - - - -
54G PRO* 3.7 38.9 - - + +
59G ALA 5.2 0.2 + - - -
60G ASP 2.8 3.4 + - - -
61G GLY* 1.3 70.4 - - - +
63G ALA* 1.3 61.9 + - - +
65G ALA* 3.7 2.0 - - + +
66G GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748A A 2.8 21.0 + - + +
2749A A 3.5 37.9 + - - +
2757A A 4.1 17.7 - - + +
60G ASP* 2.7 24.2 + - + +
62G TRP* 1.3 70.4 - - - +
64G GLN* 1.3 66.7 + - - +
66G GLY 3.1 0.7 + - - -
67G THR* 3.0 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757A A 3.4 33.9 + - - +
2758A A 3.4 24.0 + - - +
38G ASN* 3.1 38.4 + - - +
40G ALA* 4.3 4.5 - - + -
41G VAL* 3.5 18.7 - - + +
60G ASP* 3.1 38.8 + - - +
61G GLY 3.9 5.8 - - - +
63G ALA* 1.3 78.2 - - - +
65G ALA* 1.3 62.3 + - - +
67G THR* 3.3 9.3 + - - +
68G ALA* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ALA* 3.6 21.1 - - + -
41G VAL* 3.9 14.5 - - + +
52G PHE* 4.6 6.5 - - + +
53G GLY 4.2 22.7 - - - +
61G GLY 2.9 21.2 + - - +
62G TRP* 3.7 6.3 - - + +
64G GLN* 1.3 74.9 - - - +
66G GLY* 1.3 64.7 + - - +
68G ALA* 2.9 5.2 + - - +
69G ARG* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748A A 3.4 17.0 - - - +
2G SER 4.9 1.1 - - - -
4G VAL* 3.5 14.6 - - - +
5G ALA* 3.6 22.6 - - - +
62G TRP 2.9 13.5 + - - -
63G ALA 3.1 0.2 + - - -
65G ALA* 1.3 74.3 - - - +
67G THR* 1.3 62.3 + - - +
69G ARG* 3.3 3.3 + - - +
70G ALA* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747A G 3.2 23.5 + - - +
2748A A 3.3 7.7 + - - -
2757A A 2.8 28.3 + - - -
2758A A 4.0 30.7 - - + +
63G ALA 3.0 7.0 + - - -
64G GLN* 3.4 13.5 - - - +
66G GLY* 1.3 74.1 - - - +
68G ALA* 1.3 65.5 + - - +
70G ALA* 2.9 16.2 + - - +
71G LEU* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 4.1 23.3 - - + -
41G VAL* 3.7 25.1 - - + -
52G PHE* 4.4 6.3 - - + -
64G GLN 2.9 12.0 + - - +
65G ALA 2.9 9.0 + - - +
67G THR* 1.3 77.2 - - - +
69G ARG* 1.3 63.1 + - - +
71G LEU* 3.1 9.2 + - - +
72G LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 3.3 36.6 + - + +
5G ALA* 4.2 5.6 - - - -
7G ALA* 2.9 26.2 + - - +
8G PRO 3.8 13.5 + - - -
9G VAL* 3.3 24.0 - - + +
10G VAL 5.5 0.2 - - - +
52G PHE* 3.5 32.9 - - + -
65G ALA 2.9 9.7 + - - +
66G GLY 3.3 11.0 - - - +
68G ALA* 1.3 77.0 - - - +
70G ALA* 1.3 67.5 + - - +
72G LEU* 3.2 0.9 + - - -
73G ASN* 2.9 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747A G 3.7 17.3 - - - +
2748A A 3.4 29.4 - - - +
4G VAL* 4.9 3.4 - - + -
66G GLY 3.0 10.1 + - - +
67G THR 2.9 9.0 + - - +
69G ARG* 1.3 81.4 - - - +
71G LEU* 1.3 57.4 + - - +
73G ASN* 3.2 8.5 + - - +
74G SER* 2.6 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746A U 4.0 11.4 - - - +
2747A G 3.8 34.1 - - - +
2758A A 4.1 9.4 - - + +
35G ARG* 3.4 49.4 - - - +
37G LEU* 5.8 2.0 - - + -
67G THR* 3.0 32.5 + - + +
68G ALA* 3.5 8.5 - - - +
70G ALA* 1.3 77.3 - - - +
72G LEU* 1.3 61.7 + - + +
74G SER* 3.3 5.8 + - - +
75G MET* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 4.6 2.7 - - + -
24G ILE* 4.0 32.8 - - + -
26G ILE* 4.2 14.9 - - + +
35G ARG* 4.8 2.5 - - + -
37G LEU* 3.7 25.8 - - + -
43G VAL* 4.7 4.3 - - + -
50G LEU* 4.6 12.3 - - + -
52G PHE* 3.5 33.2 - - + -
68G ALA 2.9 22.1 + - - +
69G ARG 4.0 0.4 - - - +
71G LEU* 1.3 81.8 - - + +
73G ASN* 1.3 61.0 + - - +
75G MET* 3.6 16.1 - - - +
76G VAL* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 4.1 14.1 - - + +
69G ARG* 2.9 54.0 + - - +
70G ALA* 3.5 5.6 + - - +
72G LEU* 1.3 78.0 - - - +
74G SER* 1.3 58.9 + - - +
76G VAL* 3.1 8.5 + - - +
77G ILE* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746A U 5.2 1.6 + - - -
2747A G 4.4 9.4 + - - -
33G LEU* 5.1 0.3 - - - +
70G ALA 2.6 20.1 + - - -
71G LEU* 3.5 8.6 + - - +
73G ASN* 1.3 77.0 - - - +
75G MET* 1.3 57.2 + - - +
77G ILE* 3.8 13.0 - - - -
78G GLY* 2.9 23.4 + - - -
83G PHE* 3.6 14.8 - - - -
136G ALA 4.7 0.7 - - - +
138G LYS* 4.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 4.5 4.7 - - + +
26G ILE* 4.2 18.3 - - + +
33G LEU* 3.6 50.0 - - + +
34G THR 3.9 1.3 - - - +
35G ARG* 3.6 52.5 - - + +
71G LEU* 2.9 27.4 + - + +
72G LEU* 3.6 15.5 - - + +
73G ASN 3.1 0.2 - - - -
74G SER* 1.3 77.1 - - - +
76G VAL* 1.3 61.1 + - - +
78G GLY 3.7 0.2 - - - -
79G VAL* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 4.1 16.4 - - + -
10G VAL 4.2 8.7 - - - +
11G VAL* 4.8 4.7 - - + -
12G PRO* 3.7 30.5 - - + -
15G VAL* 4.7 7.2 - - + -
17G VAL* 6.2 0.2 - - + -
26G ILE* 4.7 17.0 - - + -
50G LEU* 4.9 4.7 - - + -
72G LEU 2.9 16.8 + - - +
73G ASN* 3.3 14.1 - - - +
75G MET* 1.3 74.2 - - - +
77G ILE* 1.3 71.5 + - + +
78G GLY 3.0 2.0 + - - -
79G VAL* 3.5 7.2 + - - +
80G THR* 3.0 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ASN* 3.0 36.4 + - - +
74G SER* 3.6 15.5 + - - +
76G VAL* 1.3 78.1 - - + +
78G GLY* 1.3 55.7 + - - +
80G THR* 3.6 6.1 - - - +
81G GLU* 3.1 48.3 + - + +
82G GLY 3.2 7.7 + - - +
83G PHE* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ASN* 3.4 2.8 - - - +
33G LEU* 4.6 1.8 - - - -
74G SER 2.9 15.2 + - - -
75G MET 3.6 3.3 + - - -
76G VAL 3.0 0.8 - - - -
77G ILE* 1.3 79.1 - - - +
79G VAL* 1.3 57.4 + - - +
80G THR 3.2 0.7 - - - -
82G GLY* 3.1 25.8 + - - -
83G PHE* 4.4 3.1 - - - -
136G ALA* 3.4 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G VAL* 4.0 7.9 - - + -
26G ILE* 3.8 28.0 - - + +
27G LYS 4.0 9.6 - - - +
28G GLY* 3.5 4.7 - - - +
29G LYS* 3.4 11.1 + - - +
30G ASN* 3.1 26.3 + - - -
31G GLY 3.1 27.6 - - - +
33G LEU* 3.6 32.8 - - + -
75G MET 3.2 14.5 + - - +
76G VAL* 3.8 6.7 - - - +
78G GLY* 1.3 74.4 - - - +
80G THR* 1.3 59.7 + - - +
136G ALA* 4.8 2.2 - - + -
----------------------------------------------------------
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