Contacts of the helix formed by residues 56 - 69 (chain D) in PDB entry 4GOO
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 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ASP* 3.0 14.9 + - - +
55D ILE* 1.3 81.1 - - + +
57D SER* 1.3 61.6 + - - +
58D ASP* 2.9 20.9 + - - +
59D LEU* 3.1 24.2 + - + +
60D ILE* 3.4 14.9 + - - +
111D PHE* 4.9 0.8 - - - -
123D CYS* 3.9 13.5 - - - -
125D TYR* 3.5 30.2 + - - -
162D CYS* 4.1 0.2 - - - -
301D 0Y2 4.0 19.3 + - + +
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ILE 3.2 3.9 + - - -
56D ASN* 1.3 74.7 + - - +
58D ASP* 1.3 71.8 + - - +
60D ILE* 3.9 0.5 - - - +
61D SER* 2.9 29.4 + - - -
162D CYS* 3.5 26.7 - - - -
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASN* 2.9 7.8 + - - +
57D SER* 1.3 87.2 + - - +
59D LEU* 1.3 56.1 + - - +
61D SER* 3.9 4.8 - - - -
62D LEU* 3.0 28.6 + - - +
98D PHE* 3.7 11.7 - - + -
107D ARG* 2.7 35.4 + - - +
108D ALA* 5.7 1.4 - - - +
111D PHE* 3.8 20.4 - - + +
125D TYR* 2.6 36.4 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.5 30.7 - - + -
36D VAL* 4.7 1.3 - - + -
37D GLY* 3.4 35.7 - - - +
54D ASP* 4.1 18.8 - - + +
56D ASN* 3.1 22.0 + - + +
58D ASP* 1.3 73.3 - - - +
60D ILE* 1.3 63.3 + - + +
62D LEU* 3.4 5.1 + - + +
63D TYR* 2.8 50.5 + - + +
111D PHE* 4.2 9.3 - - + -
301D 0Y2 3.9 25.4 - - + +
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.3 10.8 - - + -
52D LEU 4.5 4.5 - - - +
53D ALA* 4.3 4.3 - - - -
54D ASP* 3.9 25.8 - - + +
56D ASN 3.4 12.5 + - - +
57D SER 3.3 6.9 + - - +
59D LEU* 1.3 76.5 - - + +
61D SER* 1.3 57.6 + - - +
63D TYR* 3.1 10.5 + - + +
64D ASN* 2.9 45.9 + - - +
160D PHE* 3.9 13.9 - - + +
161D TYR* 3.7 23.8 - - - +
162D CYS* 3.9 30.1 - - + +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER* 2.9 19.0 + - - -
58D ASP* 3.9 5.2 - - - -
60D ILE* 1.3 77.3 - - - +
62D LEU* 1.3 64.1 + - - +
64D ASN* 3.2 7.4 + - - +
65D ILE* 3.1 33.0 + - - +
104D PRO* 4.1 23.9 + - - +
108D ALA* 5.4 0.3 - - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.6 30.5 - - + -
8D LEU* 3.8 17.9 - - + -
58D ASP 3.0 15.8 + - - +
59D LEU* 3.5 7.9 - - + +
61D SER* 1.3 72.7 + - - +
63D TYR* 1.3 68.2 + - + +
65D ILE* 3.0 4.3 + - - +
66D VAL* 2.9 46.8 + - + +
73D TYR* 3.4 31.2 - - + +
108D ALA* 4.0 21.1 - - + +
111D PHE* 3.7 28.5 - - + -
112D LEU* 5.4 1.8 - - + +
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.5 31.0 - + - -
8D LEU* 3.9 12.6 - - + +
36D VAL* 4.5 11.0 - - + -
37D GLY 2.7 27.5 + - - -
38D ALA* 3.3 18.3 + - - -
39D GLY* 5.4 0.4 - - - -
59D LEU* 2.8 46.6 + - + +
60D ILE* 3.1 11.0 + - + +
62D LEU* 1.3 77.2 - - + +
64D ASN* 1.3 56.4 + - - +
66D VAL* 3.9 4.7 - - - +
67D LYS* 3.0 27.0 + - - +
151D PHE* 3.4 31.6 - + + -
160D PHE* 3.8 36.8 - + + -
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 2.9 38.9 + - - +
61D SER* 3.2 5.8 + - - +
63D TYR* 1.3 77.2 - - - +
65D ILE* 1.3 59.9 + - + +
67D LYS* 3.2 14.1 + - - +
68D MET* 2.8 40.1 + - + +
160D PHE* 3.7 30.3 + - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D SER* 3.1 19.9 + - - +
62D LEU* 3.0 8.9 + - - +
64D ASN* 1.3 76.8 - - + +
66D VAL* 1.3 60.1 + - - +
68D MET* 4.3 0.7 - - - +
69D ARG* 2.7 55.1 + - + +
73D TYR* 4.0 21.1 - - + -
104D PRO* 4.0 12.1 - - + +
105D PHE* 3.8 55.0 - - + +
108D ALA* 4.2 6.3 - - + -
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 4.0 15.7 - - + -
62D LEU* 2.9 45.4 + - + +
63D TYR* 3.9 6.1 - - - +
65D ILE* 1.3 72.7 - - - +
67D LYS* 1.3 58.6 - - - +
70D THR* 2.8 31.0 + - + +
73D TYR* 4.2 23.8 - - + -
148D LEU* 4.1 16.2 - - + +
151D PHE* 3.9 23.8 - - + -
152D ALA* 3.5 14.1 - - + +
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR 3.0 20.2 + - - +
64D ASN* 3.6 12.0 + - - +
65D ILE 3.2 0.2 - - - -
66D VAL* 1.3 78.8 - - - +
68D MET* 1.3 83.2 + - + +
70D THR* 4.0 4.5 + - - -
152D ALA* 4.7 1.1 - - - -
155D ALA* 3.3 33.4 - - + +
156D GLN* 3.2 41.9 + - - +
158D ALA 3.3 22.0 + - - +
159D PHE* 3.9 23.6 - - - +
160D PHE* 4.0 12.1 - - + -
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ASN* 2.8 28.6 + - + +
65D ILE* 5.0 0.2 - - - -
67D LYS* 1.3 105.7 - - + +
69D ARG* 1.3 73.1 + - + +
70D THR 3.7 1.5 + - - -
156D GLN* 5.9 1.1 - - - +
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ILE* 2.7 35.9 + - + +
68D MET* 1.3 93.2 - - + +
70D THR* 1.3 52.9 + - - +
71D ASP 3.5 2.0 - - - -
72D GLU* 2.9 49.6 + - + +
73D TYR* 2.8 33.5 + - - +
105D PHE* 3.6 34.5 - - + +
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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