Contacts of the helix formed by residues 60 - 70 (chain B) in PDB entry 1GXD
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 LEU 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 5.0 0.4 - - - +
49B GLN* 3.4 18.0 - - - +
54B LEU* 4.9 2.2 - - + -
55B PRO* 3.8 22.2 - - + +
57B THR* 2.4 42.0 + - + +
59B ASP* 1.3 71.5 - - - +
61B ASP* 1.3 64.8 + - - +
62B GLN* 3.0 28.7 + - + +
63B ASN* 3.1 21.0 + - + +
64B THR* 2.9 32.8 + - - +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 4.7 4.8 - - - +
18B LYS* 3.8 27.4 - - - +
21B ALA* 5.0 5.9 - - - +
45B LEU* 4.4 9.8 - - - +
59B ASP* 2.9 29.3 + - - +
60B LEU* 1.3 68.8 + - - +
62B GLN* 1.3 64.4 + - - +
64B THR* 2.7 15.9 + - + +
65B ILE* 2.3 55.2 + - + +
68B MET* 4.9 4.3 - - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP 5.5 0.9 - - - +
60B LEU* 3.6 25.9 - - + +
61B ASP* 1.3 75.3 - - - +
63B ASN* 1.3 65.9 + - + +
65B ILE* 3.5 16.0 - - - +
66B GLU* 3.9 8.3 + - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.2 28.2 - - - +
55B PRO* 4.1 4.5 - - + +
60B LEU* 3.1 20.1 + - + -
61B ASP 2.9 0.2 + - - -
62B GLN* 1.3 80.0 - - + +
64B THR* 1.3 64.7 + - - +
66B GLU* 3.6 25.8 + - - +
67B THR* 3.3 12.8 + - - -
466B ARG* 5.1 13.9 - - - +
475B MET* 3.9 19.2 - - + +
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.6 4.1 - - + +
48B MET* 3.6 23.6 - - - +
49B GLN* 3.5 18.1 + - - +
54B LEU* 4.5 6.9 - - - +
60B LEU* 2.9 19.3 + - - +
61B ASP* 2.7 40.2 + - + +
63B ASN* 1.3 69.9 - - - +
65B ILE* 1.3 76.9 + - - +
66B GLU 3.0 1.8 - - - -
67B THR* 2.9 11.6 + - - -
68B MET* 2.9 36.8 + - + +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 2.7 64.8 - - - +
20B LEU* 4.0 13.7 - - + -
21B ALA* 5.4 0.4 - - + -
61B ASP* 2.3 52.3 + - + +
62B GLN* 3.5 11.7 - - - +
64B THR* 1.3 68.4 - - - +
66B GLU* 1.3 67.4 + - - +
68B MET* 3.1 29.3 + - + +
69B ARG* 3.2 20.1 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN 4.1 8.7 - - - +
63B ASN* 3.6 25.3 + - - +
65B ILE* 1.3 80.5 - - + +
67B THR* 1.3 59.1 + - - +
69B ARG* 2.7 32.4 + - - +
70B LYS* 3.5 21.6 + - + +
466B ARG* 5.1 10.0 + - - -
483B PHE* 6.1 0.7 - - - -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 4.5 3.6 + - - -
48B MET* 4.5 8.5 - - - -
52B PHE* 4.3 27.1 - - + -
54B LEU* 4.0 15.3 - - + +
63B ASN 3.3 14.4 + - - -
64B THR* 2.9 6.9 + - - -
66B GLU* 1.3 77.8 - - - +
68B MET* 1.3 61.7 + - - +
70B LYS* 2.9 31.7 + - + +
395B ILE* 3.9 24.7 - - + +
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.3 15.9 - - + +
21B ALA* 3.6 41.7 - - + +
24B TYR* 3.4 45.8 - - + -
25B LEU* 5.3 2.5 - - - -
45B LEU* 4.2 12.1 - - + -
48B MET* 3.7 20.4 - - + +
61B ASP* 4.9 2.5 - - - +
64B THR* 2.9 40.0 + - + +
65B ILE* 3.2 28.9 - - + +
66B GLU 3.0 0.6 - - - -
67B THR* 1.3 77.7 - - - +
69B ARG* 1.3 59.2 + - - +
70B LYS 4.5 0.5 - - - +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS* 4.5 25.7 + - - +
17B ASP* 2.9 29.7 + - - +
20B LEU* 3.0 34.4 - - + +
65B ILE* 3.2 19.6 + - - +
66B GLU* 2.7 19.1 + - - +
68B MET* 1.3 73.0 - - - +
70B LYS* 1.3 66.0 + - - +
71B PRO* 3.2 6.8 - - - +
160B GLY* 5.1 6.8 + - - -
341B ASP* 5.9 7.4 - - - -
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 5.1 1.4 - - - -
66B GLU* 3.5 28.9 + - + +
67B THR* 2.9 31.5 + - + +
68B MET 4.5 2.4 - - - +
69B ARG* 1.3 78.0 - - - +
71B PRO* 1.3 77.6 - - + +
72B ARG* 3.3 12.0 + - - +
160B GLY* 4.7 1.2 - - - +
395B ILE* 3.7 33.2 - - + +
482B THR* 5.3 15.0 - - - +
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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