Contacts of the helix formed by residues 54 - 65 (chain A) in PDB entry 1DGB
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 ASP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.2 10.0 - - - +
42A ILE* 2.9 43.4 + - + +
50A LEU* 4.4 4.3 - - + -
51A LEU* 3.2 14.8 + - - +
52A VAL 2.9 4.7 + - - +
53A GLN* 1.3 72.9 - - - +
55A VAL* 1.3 59.2 + - - +
56A VAL 3.3 0.3 + - - -
57A PHE* 2.9 35.3 + - + +
58A THR* 3.2 21.1 + - - -
431C ARG* 2.9 31.8 + - - +
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Residues in contact with VAL 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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29A THR* 5.7 5.2 - - + -
52A VAL 4.1 7.9 - - - +
53A GLN 2.7 20.9 + - - +
54A ASP* 1.3 70.6 - - - +
56A VAL* 1.3 66.1 + - + +
58A THR* 3.8 9.0 - - - -
59A ASP* 2.7 37.7 + - + +
431C ARG* 5.2 0.2 - - - +
337D SER* 3.6 42.6 - - - +
339D MET* 6.3 1.1 - - + -
355D LEU* 4.4 17.7 - - + +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 4.4 17.7 - - + -
34A PRO 5.9 0.7 - - - +
35A VAL* 3.8 36.8 - - + -
37A ASP 4.9 0.2 - - - +
38A LYS* 4.1 17.0 - - + -
54A ASP* 3.2 7.3 - - - +
55A VAL* 1.3 84.9 - - + +
57A PHE* 1.3 64.5 + - - +
59A ASP* 3.7 5.3 - - - +
60A GLU* 3.1 23.8 + - + +
159C ILE* 4.1 6.5 - - + -
431C ARG* 3.5 20.9 - - - +
420D GLU* 4.1 7.6 - - - +
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Residues in contact with PHE 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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41A VAL* 3.8 15.9 - - + -
50A LEU* 4.0 22.4 - - + -
51A LEU 6.1 0.2 - - - -
54A ASP* 2.9 30.1 + - + +
56A VAL* 1.3 75.7 - - - +
58A THR* 1.3 69.7 + - - +
60A GLU* 3.8 1.2 - - - +
61A MET* 2.7 61.8 + - + +
52B VAL* 6.1 2.2 - - + -
158C PRO* 3.4 23.1 - - + -
159C ILE* 3.8 28.9 - - + +
353C GLY* 3.8 25.1 - - - -
356C PHE* 4.4 20.4 - + + -
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Residues in contact with THR 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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51A LEU 5.6 0.2 + - - -
52A VAL* 4.5 8.5 + - - +
54A ASP 3.2 14.0 + - - -
55A VAL* 3.9 10.3 - - - -
56A VAL 3.4 0.2 - - - -
57A PHE* 1.3 88.2 - - - +
59A ASP* 1.3 56.7 + - - +
61A MET* 3.1 3.5 + - - -
62A ALA* 2.6 40.9 + - + +
52B VAL* 6.0 1.6 - - - +
356C PHE* 3.8 29.0 - - + -
356D PHE* 5.2 12.6 - - + -
359D PRO* 6.0 4.3 - - + -
363D ARG* 4.9 8.5 - - - +
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 3.6 12.5 - - + -
30A GLY* 2.9 25.6 + - - -
31A ALA 5.1 0.6 + - - -
55A VAL* 2.7 24.3 + - + +
56A VAL* 3.7 5.5 - - - +
58A THR* 1.3 75.8 - - - +
60A GLU* 1.3 63.8 + - - +
62A ALA* 3.6 2.1 + - - +
63A HIS* 3.4 17.3 + - - +
363D ARG* 4.5 15.9 + - - +
371D LEU* 4.7 9.2 - - - +
387D GLN* 2.8 27.3 + - - +
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Residues in contact with GLU 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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38A LYS* 2.8 47.7 + - + +
56A VAL 3.1 13.9 + - - +
57A PHE* 3.9 2.2 - - - +
59A ASP* 1.3 79.8 - - - +
61A MET* 1.3 64.2 + - - +
63A HIS* 3.3 6.1 + - - +
64A PHE* 3.0 19.2 + - - +
159C ILE* 3.2 20.0 - - - +
162C PRO* 4.2 20.7 - - + +
163C SER* 4.5 3.7 + - - -
385D ASN* 6.0 0.3 - - - +
386D TYR* 4.1 19.6 + - - +
387D GLN* 3.6 26.3 - - + +
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Residues in contact with MET 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 PHE* 2.7 52.6 + - + +
58A THR 3.7 1.3 - - - +
60A GLU* 1.3 72.1 + - - +
62A ALA* 1.3 68.2 + - - +
64A PHE* 2.8 20.1 + - - +
65A ASP* 2.8 45.7 + - - +
158C PRO* 3.9 13.5 - - + +
159C ILE* 5.4 0.4 - - - -
161C PHE* 4.5 0.2 - - + -
162C PRO* 4.0 15.7 - - + -
356C PHE* 3.7 26.7 - - + -
357C ALA* 4.2 4.9 - - + -
1202C HEM 3.7 28.3 - - + -
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Residues in contact with ALA 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 THR* 2.6 22.1 + - + +
59A ASP 3.9 1.8 - - - +
61A MET* 1.3 73.8 - - - +
63A HIS* 1.3 62.2 + - - +
65A ASP* 3.3 7.8 + - - +
66A ARG* 2.8 28.7 + - - +
356C PHE* 4.2 6.4 - - + -
360C ASP* 3.5 14.1 - - - +
363D ARG* 3.2 43.1 - - - +
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Residues in contact with HIS 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 ASP 3.4 4.7 + - - +
60A GLU 3.3 7.0 + - - +
61A MET 3.1 0.6 - - - -
62A ALA* 1.3 76.2 - - - +
64A PHE* 1.3 68.6 + - - +
66A ARG* 2.9 18.1 + - + +
67A GLU* 3.2 8.8 + - + +
363D ARG* 5.4 0.6 - - - +
368D PRO* 4.5 12.6 + - + +
369D ASN* 2.9 34.5 + - - -
372D HIS* 5.4 0.7 - - - -
387D GLN* 3.5 31.9 + - + +
388D ARG 2.8 44.0 + - - -
389D ASP 3.1 11.5 + - - -
390D GLY* 4.8 2.6 - - - -
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Residues in contact with PHE 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 GLU 3.0 12.6 + - - +
61A MET* 2.8 18.8 + - - +
63A HIS* 1.3 76.2 - - - +
65A ASP* 1.3 72.0 + - - +
66A ARG 2.9 6.4 + - - -
67A GLU* 3.1 46.0 + - - +
68A ARG* 5.6 0.4 - - - -
73C VAL* 3.7 40.4 - - + +
74C VAL* 4.1 3.4 - - + -
161C PHE* 3.7 31.6 - + - -
162C PRO* 3.8 35.9 - - + -
165C ILE* 4.0 22.9 - - + -
166C HIS* 4.2 2.7 - + - -
1202C HEM 4.5 3.6 - - + -
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Residues in contact with ASP 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 MET* 2.8 33.1 + - - +
62A ALA 3.3 10.8 - - - +
63A HIS 3.1 0.2 - - - -
64A PHE* 1.3 83.3 - - - +
66A ARG* 1.3 58.6 + - - +
67A GLU 3.6 0.6 + - - -
68A ARG 5.4 0.2 + - - -
73C VAL* 5.1 6.9 - - - +
356C PHE* 4.0 0.3 - - - -
357C ALA* 3.2 31.0 - - - +
360C ASP* 2.7 23.4 - - - +
361C THR* 3.1 31.7 + - - -
364C HIS* 3.6 11.1 - - - -
1202C HEM 3.8 11.4 - - - +
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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