Contacts of the helix formed by residues 34 - 47 (chain I) 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 THR 34 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1055A G 3.4 14.8 - - - +
1056A G 3.3 22.9 - - - +
1084A A 6.3 0.2 - - - -
1085A A 5.6 0.4 - - - -
32I GLY 4.4 0.2 + - - -
33I VAL* 1.3 77.6 - - - +
35I VAL* 1.3 63.1 + - - +
36I ASP* 3.1 17.9 + - - +
37I LYS* 3.2 29.9 + - - +
38I MET* 3.3 22.3 + - - +
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Residues in contact with VAL 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A G 3.2 9.5 + - - +
1056A G 3.5 15.3 + - - -
1057A A 3.5 24.5 + - - +
1082A U 4.4 1.1 - - - +
1085A A 3.2 36.8 - - - +
1086A A 3.1 40.2 - - - +
34I THR* 1.3 70.6 - - - +
36I ASP* 1.3 55.9 + - - +
38I MET* 4.5 3.1 - - + -
39I THR* 2.5 48.9 + - - +
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Residues in contact with ASP 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A G 4.1 2.3 + - - -
1057A A 3.2 40.0 + - - +
1058A U 4.1 9.5 + - - +
34I THR* 3.1 20.2 - - - +
35I VAL* 1.3 76.2 - - - +
37I LYS* 1.3 63.3 + - + +
39I THR* 3.4 5.0 + - - -
40I GLU* 3.0 30.1 + - - +
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Residues in contact with LYS 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I VAL* 3.6 17.7 - - + -
34I THR* 3.2 21.0 + - - +
36I ASP* 1.3 77.2 - - + +
38I MET* 1.3 56.9 + - - +
40I GLU* 3.1 10.7 - - - +
41I LEU 3.0 14.4 + - - -
99I PHE* 2.9 21.5 - - + -
103I ASN* 2.9 40.1 + - - +
105I LYS* 3.1 25.4 - - - +
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Residues in contact with MET 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A A 5.5 8.3 - - - +
1085A A 5.0 9.2 - - - +
30I SER* 4.0 18.2 - - - +
33I VAL* 3.6 22.2 - - + +
34I THR 3.3 18.8 + - - +
35I VAL* 4.5 5.6 - - + -
37I LYS* 1.3 75.3 - - - +
39I THR* 1.3 58.8 + - - +
40I GLU 3.1 1.3 - - - -
41I LEU* 3.3 7.9 + - - +
42I ARG* 2.9 67.6 + - - +
52I MET* 5.3 1.1 - - + -
54I VAL* 4.6 4.0 - - + -
81I LEU* 3.6 28.0 - - + -
99I PHE* 4.1 20.0 - - - -
106I PHE* 5.7 1.3 - - - -
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Residues in contact with THR 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A A 4.7 5.6 + - - -
1082A U 3.1 33.7 + - + +
35I VAL* 2.5 38.5 + - - +
36I ASP* 3.8 5.2 - - - -
38I MET* 1.3 75.1 - - - +
40I GLU* 1.3 57.2 + - - +
42I ARG* 3.4 2.2 + - - +
43I LYS* 3.0 41.1 + - + +
118J THR* 3.7 34.2 - - + +
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ASP 3.0 15.4 + - - +
37I LYS* 3.1 16.4 - - - +
38I MET 3.1 0.4 - - - -
39I THR* 1.3 78.4 - - - +
41I LEU* 1.3 54.5 + - - +
43I LYS* 3.5 33.0 + - - +
44I ALA* 3.0 28.1 + - - +
99I PHE* 4.7 6.7 - - + -
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Residues in contact with LEU 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I LYS 3.0 5.7 + - - -
38I MET* 3.3 15.6 + - - +
40I GLU* 1.3 75.3 - - - +
42I ARG* 1.3 59.9 + - - +
44I ALA* 4.4 1.6 - - + +
45I GLY* 2.9 23.0 + - - -
52I MET* 3.6 20.5 - - + +
81I LEU* 4.9 1.6 - - + -
95I LEU* 3.5 39.7 - - + +
96I PHE* 3.4 29.2 - - + -
99I PHE* 3.4 54.7 - - + -
106I PHE* 5.6 0.2 - - + -
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Residues in contact with ARG 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082A U 3.3 22.7 - - - +
1083A U 2.8 66.7 + - - +
1084A A 3.3 20.2 + - - -
1085A A 5.3 1.8 - - - +
38I MET* 2.9 59.3 + - - +
39I THR* 3.6 2.0 - - - +
40I GLU 3.3 0.4 - - - -
41I LEU* 1.3 75.9 - - - +
43I LYS* 1.3 55.9 + - - +
45I GLY* 3.7 2.2 - - - +
46I ARG* 2.8 40.6 + - - +
52I MET* 3.2 30.7 - - - +
54I VAL* 3.9 7.1 - - - +
81I LEU* 3.7 13.7 - - - +
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Residues in contact with LYS 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I THR* 3.0 32.8 + - + +
40I GLU* 3.5 35.2 + - - +
42I ARG* 1.3 76.4 - - - +
44I ALA* 1.3 56.6 + - - +
45I GLY 3.2 1.3 - - - -
46I ARG* 3.3 26.0 + - - +
47I GLU* 3.0 36.0 + - - +
117J MET 3.3 19.4 + - - +
118J THR* 3.6 29.4 - - - +
119J GLY 5.8 0.2 - - - +
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Residues in contact with ALA 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I GLU 3.0 17.9 + - - +
41I LEU* 4.5 3.6 - - + -
43I LYS* 1.3 74.6 - - - +
45I GLY* 1.3 57.3 + - - +
47I GLU* 4.2 14.0 - - - +
48I ALA* 3.2 17.8 + - - +
95I LEU* 3.1 39.8 - - + +
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Residues in contact with GLY 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I LEU 2.9 23.4 + - - -
42I ARG 4.0 0.7 - - - -
43I LYS 3.2 0.2 - - - -
44I ALA* 1.3 76.2 - - - +
46I ARG* 1.3 59.1 + - - +
47I GLU 3.3 1.6 - - - -
49I GLY 3.6 1.7 + - - -
50I VAL* 2.8 45.0 + - - +
52I MET* 4.2 15.0 - - - -
95I LEU* 4.3 2.5 - - - -
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Residues in contact with ARG 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082A U 3.1 34.5 + - - -
1083A U 3.9 15.3 - - - +
42I ARG* 2.8 48.5 + - - +
43I LYS* 3.3 31.8 + - - +
45I GLY* 1.3 71.7 - - - +
47I GLU* 1.3 60.7 + - - +
48I ALA 3.8 0.3 + - - -
49I GLY* 3.9 7.9 + - - -
50I VAL 4.3 6.7 - - - +
118J THR 3.9 9.9 + - - -
119J GLY 3.9 10.7 + - - -
120J ALA* 3.5 31.8 + - - +
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Residues in contact with GLU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LYS* 3.0 22.4 + - - +
44I ALA* 4.2 11.2 - - - +
46I ARG* 1.3 78.2 - - - +
48I ALA* 1.3 56.1 + - - +
49I GLY 3.4 3.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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