Contacts of the helix formed by residues 49 - 66 (chain G) in PDB entry 1GLE
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 49 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G HIS 3.5 10.0 - - - +
48G ASP* 1.3 89.1 - - - +
50G MET* 1.3 60.8 + - - +
51G GLU 3.2 1.0 + - - -
52G ILE* 3.5 13.9 + - + +
53G TRP* 3.0 23.6 + - - +
87G ILE* 3.9 20.9 - - + -
96G PRO* 3.7 31.9 - - + -
98G TYR 3.8 10.8 - - - +
99G ASN* 3.9 7.2 - - - +
100G ALA* 3.6 13.7 - - + +
168G TRP* 3.5 19.5 + - + +
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Residues in contact with MET 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ASP* 2.9 13.5 + - - +
49G PRO* 1.3 79.7 - - - +
51G GLU* 1.3 53.6 + - - +
53G TRP* 3.4 18.2 - - + +
54G ALA* 2.7 35.7 + - - +
94G GLY 4.2 9.6 - - - +
95G LYS* 4.4 7.9 - - + -
96G PRO* 3.6 36.3 - - + +
168G TRP* 4.2 13.5 - - - -
172G LYS* 5.2 3.6 - - - +
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Residues in contact with GLU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLU 4.8 1.0 - - - +
35G PHE* 3.3 31.8 - - + +
36G GLU* 3.7 27.5 + - - +
48G ASP* 2.5 41.6 + - + +
50G MET* 1.3 71.8 - - - +
52G ILE* 1.3 52.0 + - - +
53G TRP 3.2 0.7 - - - -
54G ALA* 4.2 6.1 - - + +
55G THR* 2.7 41.3 + - - -
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLN* 3.0 45.8 - - + +
16G SER* 4.6 0.2 - - - -
35G PHE* 5.0 8.2 - - + -
47G HIS* 4.5 18.8 - - + -
48G ASP 3.5 15.3 - - - +
49G PRO* 3.5 14.6 - - + +
51G GLU* 1.3 71.1 - - - +
53G TRP* 1.3 57.9 + - - +
55G THR* 2.8 9.6 - - - +
56G GLN* 2.3 41.8 + - + +
82G GLN* 4.7 6.3 - - - +
85G THR* 5.7 0.9 - - - +
87G ILE* 5.4 3.4 - - + -
100G ALA* 5.2 8.7 - - + -
165G VAL* 4.2 21.1 - - + -
168G TRP* 4.8 9.2 - - + +
169G LEU* 5.3 1.8 - - + -
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Residues in contact with TRP 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PRO 3.0 18.2 - - - +
50G MET* 3.4 20.2 - - + +
52G ILE* 1.3 79.0 - - - +
54G ALA* 1.3 56.9 + - + +
56G GLN* 4.7 1.1 - - + -
57G SER* 2.7 66.0 + - - -
168G TRP* 3.9 13.7 - + + +
169G LEU* 4.1 26.9 - - + -
172G LYS* 3.3 64.1 - - + +
173G MET* 5.2 14.8 - - + -
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Residues in contact with ALA 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G MET 2.7 22.9 + - - +
51G GLU* 4.0 9.0 - - + +
53G TRP* 1.3 74.5 - - + +
55G THR* 1.3 61.0 + - - +
57G SER* 2.9 18.6 + - - -
58G SER* 3.0 18.8 + - - -
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Residues in contact with THR 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G SER* 2.8 31.2 - - - +
33G ARG* 3.8 24.6 + - - +
34G GLU 3.9 10.7 + - - -
35G PHE* 4.0 13.5 - - + +
51G GLU* 2.7 23.8 + - - +
52G ILE* 2.8 19.5 - - - +
54G ALA* 1.3 75.8 - - - +
56G GLN* 1.3 54.4 + - - +
58G SER* 3.9 4.3 - - - -
59G THR* 3.0 29.6 + - - -
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Residues in contact with GLN 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU* 3.7 22.6 - - + +
10G ASP 3.4 5.5 + - - +
11G GLN* 2.8 50.4 - - + +
16G SER* 3.5 6.4 - - - -
17G ARG 2.7 23.2 - - - +
52G ILE 2.3 32.8 + - - +
53G TRP* 3.9 2.2 - - + +
55G THR* 1.3 65.4 - - - +
57G SER* 1.3 71.2 + - - +
59G THR* 2.9 34.5 - - - +
60G LEU* 3.4 5.9 + - - +
169G LEU* 3.6 34.5 - - + +
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Residues in contact with SER 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G TRP* 2.7 55.4 + - - -
54G ALA* 2.9 17.5 + - - -
56G GLN* 1.3 70.4 - - - +
58G SER* 1.3 51.1 + - - -
59G THR 2.7 0.3 + - - -
60G LEU* 2.6 43.9 + - - +
61G VAL* 3.8 5.8 + - - +
173G MET* 6.4 1.3 - - - -
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Residues in contact with SER 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ALA 3.0 16.5 + - - -
55G THR* 3.9 4.9 - - - -
57G SER* 1.3 77.3 + - - +
59G THR* 1.3 61.8 + - - +
60G LEU 3.3 0.9 + - - -
61G VAL* 3.7 10.1 + - - +
62G GLU* 3.4 29.4 + - - +
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Residues in contact with THR 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G SER 4.2 5.6 - - - -
17G ARG* 3.3 18.8 - - - +
18G ALA* 3.7 1.9 - - + +
31G SER* 2.6 43.0 + - - -
32G GLN* 4.3 4.2 - - - -
33G ARG* 5.2 4.0 - - - +
55G THR 3.0 16.7 + - - +
56G GLN* 2.9 43.5 - - - +
57G SER 2.7 6.9 + - - -
58G SER* 1.3 75.3 - - - +
60G LEU* 1.3 50.6 + - - +
62G GLU* 3.9 3.7 - - - +
63G VAL* 2.8 28.6 + - - +
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.8 20.0 - - + -
9G LEU* 3.4 44.9 - - + -
18G ALA* 3.9 5.4 - - + -
56G GLN 3.4 5.0 + - - +
57G SER* 2.6 22.3 + - - +
59G THR* 1.3 69.3 - - - +
61G VAL* 1.3 68.5 - - + +
63G VAL* 2.8 21.9 + - + +
64G LEU* 3.2 25.6 + - + +
77G ILE* 5.3 7.0 - - + -
173G MET* 4.4 15.7 - - + -
229G ILE* 5.7 8.5 - - + -
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Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G SER* 4.1 15.3 - - - +
58G SER* 3.7 9.6 - - - +
60G LEU* 1.3 76.3 - - + +
62G GLU* 1.3 58.1 + - + +
63G VAL 3.1 0.3 + - - -
64G LEU* 3.1 11.1 + - - +
65G ALA* 2.7 41.0 + - + +
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Residues in contact with GLU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL 5.2 0.2 - - - +
31G SER* 3.5 23.9 + - - +
32G GLN 4.5 8.5 - - - +
33G ARG* 5.6 3.8 - - - +
58G SER* 3.4 22.6 + - - +
59G THR* 3.9 6.1 - - - +
61G VAL* 1.3 81.9 - - + +
63G VAL* 1.4 54.9 + - - +
65G ALA* 3.9 7.0 - - - +
66G LYS* 2.9 27.8 + - - +
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Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA* 3.0 42.4 - - + +
20G VAL* 4.1 13.9 - - + +
29G SER* 2.7 50.5 + - - +
30G VAL* 3.5 1.1 - - - +
31G SER* 3.1 12.1 + - - +
59G THR 2.8 20.0 - - - +
60G LEU* 2.8 25.8 - - + +
62G GLU* 1.4 74.1 - - - +
64G LEU* 1.4 58.7 - - - +
65G ALA 3.3 0.4 - - - -
66G LYS* 3.4 1.4 + - - -
67G ALA* 3.2 21.5 + - - +
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 4.4 17.0 - - + -
20G VAL* 4.4 6.1 - - + -
60G LEU* 3.2 21.9 + - + +
61G VAL* 3.3 13.0 - - - +
63G VAL* 1.4 75.7 - - - +
65G ALA* 1.3 59.2 + - - +
67G ALA* 3.6 0.8 + - - -
68G ASP 2.9 23.6 + - - -
69G ILE* 3.0 51.4 + - + +
70G SER* 5.7 3.6 - - - -
71G SER 5.7 1.6 - - - +
74G ILE* 4.2 16.6 - - + -
229G ILE* 4.3 25.6 - - + -
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Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G VAL* 2.7 28.0 + - + +
62G GLU* 3.9 8.5 - - - +
64G LEU* 1.3 75.5 - - - +
66G LYS* 1.3 61.6 + - - +
68G ASP* 3.2 16.3 + - - +
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Residues in contact with LYS 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G SER* 4.1 11.2 - - - +
30G VAL 5.8 2.0 - - - +
31G SER* 5.5 0.9 - - - +
62G GLU 2.9 18.8 + - - +
63G VAL* 3.5 8.3 - - - +
65G ALA* 1.3 78.8 - - - +
67G ALA* 1.3 58.6 + - - +
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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) + - + + + + + -
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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