Contacts of the helix formed by residues 51 - 67 (chain A) in PDB entry 1G24
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.7 1.4 - - - +
50A THR* 1.3 82.6 + - - +
52A ILE* 1.3 66.7 + - - +
53A ASP* 3.3 17.7 + - - +
54A GLN* 3.1 34.9 + - + +
55A ALA* 2.9 21.5 + - - +
178A MET* 3.9 2.7 - - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR 4.2 0.2 + - - -
51A ASN* 1.3 72.5 + - - +
53A ASP* 1.3 67.4 + - - +
55A ALA* 3.2 1.9 + - - +
56A LYS* 2.9 25.7 + - + +
178A MET* 3.5 29.1 - - + -
180A VAL* 5.8 4.0 - - + -
212A GLN* 4.3 24.0 - - - +
213A LEU* 4.1 19.3 - - + -
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASN* 3.3 15.2 + - - +
52A ILE* 1.3 80.3 - - - +
54A GLN* 1.3 59.2 + - + +
56A LYS* 3.6 8.9 + - - +
57A ALA* 3.1 24.9 + - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.6 6.2 - - + -
51A ASN* 3.1 33.7 + - + +
53A ASP* 1.3 78.8 - - + +
55A ALA* 1.3 56.3 + - - +
56A LYS 3.2 0.2 - - - -
57A ALA* 3.6 17.3 - - - +
58A TRP* 2.7 36.8 + - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.6 35.6 - - + -
51A ASN 2.9 13.6 + - - +
52A ILE* 3.2 9.8 + - - +
54A GLN* 1.3 76.0 - - - +
56A LYS* 1.3 58.5 + - - +
58A TRP* 3.3 0.9 + - - +
59A GLY* 2.8 25.5 + - - -
177A LEU* 3.5 18.6 - - + +
178A MET* 4.2 0.9 - - - -
213A LEU* 3.9 21.8 - - + -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 2.9 19.3 + - + +
53A ASP* 3.7 8.1 - - - +
55A ALA* 1.3 75.1 - - - +
57A ALA* 1.3 59.3 + - - +
59A GLY 3.4 0.5 + - - -
60A ASN* 2.8 52.6 + - - +
202A TYR* 3.5 17.8 + - - +
204A ASP* 4.2 17.0 + - - -
213A LEU* 3.9 7.3 - - + +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP 3.1 19.1 + - - +
54A GLN* 3.2 19.3 + - - +
56A LYS* 1.3 75.4 - - - +
58A TRP* 1.3 57.9 + - - +
60A ASN* 3.7 7.3 - - - +
61A ALA* 3.0 30.2 + - - +
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Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.3 35.6 - + + -
54A GLN 2.7 21.1 + - - +
55A ALA 3.6 2.2 - - - +
57A ALA* 1.3 74.2 - - - +
59A GLY* 1.3 70.2 + - - +
61A ALA* 3.2 5.1 + - + +
62A GLN* 3.0 52.0 + - + +
120A THR* 3.7 19.1 - - - -
121A PRO* 3.6 29.5 - - + +
122A GLU* 4.2 22.1 + - + +
124A ILE* 4.2 8.1 - - + -
177A LEU* 4.0 12.8 - - + -
215A MET* 3.6 29.6 - - + -
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 2.8 14.0 + - - -
58A TRP* 1.3 82.4 - - - +
60A ASN* 1.3 66.3 + - - +
62A GLN* 3.1 6.1 + - - +
63A TYR 2.9 18.9 + - - -
202A TYR* 3.2 41.0 - - - -
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 2.8 41.7 + - - +
57A ALA* 3.7 6.9 - - - +
59A GLY* 1.3 75.2 - - - +
61A ALA* 1.3 57.6 + - - +
63A TYR* 3.2 9.5 + - + +
64A LYS* 3.0 29.5 + - - +
202A TYR* 3.5 18.9 + - - -
204A ASP* 5.2 1.0 + - - -
205A PRO* 3.8 21.6 - - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.0 18.6 + - - +
58A TRP* 3.4 8.3 - - + +
59A GLY 3.1 0.2 - - - -
60A ASN* 1.3 78.7 - - - +
62A GLN* 1.3 64.4 + - - +
64A LYS* 3.5 1.4 + - - -
65A LYS* 2.7 51.9 + - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 3.0 62.6 + - + +
59A GLY* 3.1 7.3 + - - +
61A ALA* 1.3 81.7 - - - +
63A TYR* 1.3 66.7 + - - +
65A LYS* 3.0 16.6 + - - +
66A TYR* 3.2 36.8 + - + +
119A LYS 5.0 3.3 - - - +
120A THR* 6.1 0.2 - - - -
121A PRO* 3.3 31.6 - - + +
202A TYR* 5.1 0.9 - - + -
215A MET* 5.7 1.3 - - + -
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 2.9 12.2 + - - +
60A ASN* 3.4 11.7 - - + +
62A GLN* 1.3 77.7 - - - +
64A LYS* 1.3 64.9 + - - +
65A LYS 3.0 1.6 + - - -
66A TYR* 3.1 38.8 + + + +
67A GLY 4.4 1.6 + - - -
68A LEU* 4.2 4.9 - - + -
73A LYS* 3.1 40.2 + - - +
202A TYR 4.3 3.6 - - - +
205A PRO* 3.7 32.9 + - + -
206A ILE* 3.3 40.3 - - + +
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASN 3.0 16.5 + - - +
61A ALA* 4.6 0.4 - - - -
62A GLN 3.2 0.4 - - - -
63A TYR* 1.3 80.4 - - + +
65A LYS* 1.3 85.0 + - + +
67A GLY* 4.7 3.9 + - - -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 2.7 45.1 + - - +
62A GLN* 3.0 9.9 + - - +
64A LYS* 1.3 105.7 - - + +
66A TYR* 1.3 65.8 + - + +
67A GLY* 3.4 2.8 - - - -
117A LYS 5.1 0.3 - - - +
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.2 33.7 - - + +
63A TYR* 3.1 34.2 + + - +
65A LYS* 1.3 79.7 - - + +
67A GLY* 1.3 63.6 + - - +
68A LEU* 3.3 20.2 - - + -
117A LYS* 3.3 40.6 - - - +
118A MET* 3.7 41.7 - - + -
119A LYS 4.5 8.7 + - - -
200A ALA 3.9 3.5 + - - -
201A GLY* 3.6 3.3 - - - -
202A TYR* 2.9 42.2 + - - +
206A ILE* 5.3 0.2 - - + -
215A MET* 5.0 2.6 - - - +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR 4.4 2.2 + - - -
64A LYS 4.7 3.3 + - - -
65A LYS* 3.4 3.5 - - - +
66A TYR* 1.3 79.1 - - - +
68A LEU* 1.3 66.1 + - - +
69A SER* 4.6 0.2 - - - -
117A LYS* 3.0 20.1 + - - +
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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