Contacts of the helix formed by residues 55 - 70 (chain A) in PDB entry 1DJ9
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 HIS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 4.9 1.3 - - - +
52A LEU* 2.8 26.4 + - + +
53A SER 3.5 0.8 + - - -
54A HIS* 1.3 76.2 - - - +
56A PRO* 1.3 65.0 - - + +
57A GLN* 2.7 62.7 + - + +
58A ILE* 2.8 17.5 + - + +
59A ILE* 2.8 35.2 + - - +
282A VAL* 3.7 20.4 - - + +
287A GLU* 3.0 39.5 + - - -
291A ARG* 4.1 11.0 - - - +
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Residues in contact with PRO 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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54A HIS 3.3 8.5 - - - +
55A HIS* 1.3 98.3 - - + +
57A GLN* 1.3 62.2 + - + +
59A ILE* 3.2 11.3 + - + +
60A ARG* 2.8 25.2 + - - +
291A ARG* 5.9 1.8 - - - +
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Residues in contact with GLN 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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55A HIS* 2.7 37.6 + - + +
56A PRO* 1.3 74.9 - - - +
58A ILE* 1.3 62.4 + - - +
60A ARG* 3.1 8.0 + - - +
61A ALA* 3.0 24.1 + - - +
278A ALA* 4.1 11.2 - - + +
281A ALA* 5.1 6.4 - - - +
282A VAL* 3.8 17.1 - - + +
287A GLU* 4.5 5.5 + - - -
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Residues in contact with ILE 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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52A LEU* 3.1 46.9 - - + +
53A SER 5.7 2.5 - - - +
55A HIS* 2.8 20.0 + - + +
57A GLN* 1.3 78.2 - - - +
59A ILE* 1.3 67.6 + - + +
61A ALA* 3.2 2.6 + - - +
62A TRP* 3.0 22.7 + - + +
238A PHE 4.0 2.5 - - - +
239A GLY 5.4 1.6 - - - +
240A VAL* 4.3 11.4 - - + -
275A ALA* 3.8 26.0 - - + +
278A ALA* 4.3 7.9 - - - +
279A SER* 3.7 35.0 - - - +
282A VAL* 4.9 2.5 - - + -
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Residues in contact with ILE 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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53A SER 4.6 7.9 - - - +
54A HIS* 4.2 29.6 - - + +
55A HIS 2.8 19.5 + - - +
56A PRO* 3.6 9.0 - - + +
58A ILE* 1.3 79.4 - - + +
60A ARG* 1.3 61.9 + - - +
62A TRP* 3.3 8.0 + - + +
63A GLN* 3.1 52.1 + - + +
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Residues in contact with ARG 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 PRO 2.8 17.2 + - - +
57A GLN* 3.8 7.6 - - - +
58A ILE 3.1 0.4 - - - -
59A ILE* 1.3 75.6 - - - +
61A ALA* 1.3 69.6 + - - +
63A GLN* 3.8 11.8 - - - +
64A GLN* 2.9 63.0 + - - +
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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 GLN 3.0 16.5 + - - +
58A ILE 3.9 2.2 - - - +
60A ARG* 1.3 80.1 - - - +
62A TRP* 1.3 64.1 + - - +
64A GLN* 4.7 4.0 - - - +
65A GLY* 3.0 22.2 + - - -
271A ALA 4.3 0.2 - - - +
274A GLN* 3.6 37.4 - - + +
275A ALA* 4.2 0.4 - - - -
278A ALA* 3.8 13.0 - - + -
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Residues in contact with TRP 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 ILE* 3.0 12.8 + - + +
59A ILE* 3.5 11.9 - - + +
61A ALA* 1.3 78.3 - - - +
63A GLN* 1.3 73.6 + - + +
66A ALA* 3.7 13.9 + - - +
240A VAL* 4.5 10.8 - - + -
271A ALA* 3.7 22.6 - - + +
272A GLN* 3.9 37.9 - - + -
275A ALA* 3.9 20.9 - - + +
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Residues in contact with GLN 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 ILE* 3.1 37.0 + - + +
60A ARG* 3.8 11.0 - - - +
62A TRP* 1.3 85.0 - - + +
64A GLN* 1.3 68.7 + - - +
66A ALA* 3.0 18.6 + - - +
67A GLU* 3.3 11.1 + - - +
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Residues in contact with GLN 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 ARG* 2.9 65.3 + - - +
61A ALA* 4.3 3.7 - - - +
63A GLN* 1.3 78.0 - - - +
65A GLY* 1.3 64.4 + - - +
67A GLU* 3.0 14.7 + - + +
68A GLN* 2.9 25.4 + - - +
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Residues in contact with GLY 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 3.0 19.6 + - - -
64A GLN* 1.3 76.6 - - - +
66A ALA* 1.3 51.8 + - - +
68A GLN* 3.2 2.7 + - - -
69A PHE* 2.6 53.7 + - - +
271A ALA* 3.8 13.7 - - - -
274A GLN* 4.3 12.3 - - - +
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Residues in contact with ALA 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 TRP 3.7 7.6 + - - +
63A GLN* 3.0 12.0 + - - +
65A GLY* 1.3 71.2 - - - +
67A GLU* 1.3 67.0 + - - +
70A GLY* 2.9 34.3 + - - -
71A ILE* 3.6 24.8 - - + +
271A ALA* 3.6 8.7 - - + +
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Residues in contact with GLU 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 GLN 3.3 4.5 + - - +
64A GLN* 3.0 22.7 + - + +
66A ALA* 1.3 80.1 - - - +
68A GLN* 1.3 62.0 + - - +
70A GLY 4.6 0.9 + - - -
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Residues in contact with GLN 68 (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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64A GLN* 2.9 13.1 + - - +
65A GLY* 3.6 6.8 - - - +
67A GLU* 1.3 79.0 - - - +
69A PHE* 1.3 99.4 + - + +
70A GLY 3.6 0.4 - - - -
274A GLN* 4.8 8.3 - - - +
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Residues in contact with PHE 69 (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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65A GLY* 2.6 33.3 + - - +
68A GLN* 1.3 113.0 - - + +
70A GLY* 1.3 64.1 + - - +
71A ILE 3.9 1.0 + - - +
72A GLY 4.5 7.3 - - - +
83A SER* 4.4 8.7 - - - -
84A VAL* 4.8 11.0 - - + -
85A VAL* 3.5 32.3 - - + -
270A PRO* 3.7 33.4 - - + +
271A ALA 5.0 0.4 - - - +
274A GLN* 4.3 12.3 - - + -
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Residues in contact with GLY 70 (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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65A GLY 4.6 0.3 - - - -
66A ALA* 2.9 28.1 + - - -
67A GLU 4.6 0.6 + - - -
68A GLN 3.6 1.2 - - - -
69A PHE* 1.3 87.2 - - - +
71A ILE* 1.3 69.2 + - - +
271A ALA* 4.6 4.3 + - - +
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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