Contacts of the helix formed by residues 10 - 20 (chain D) 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 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B GLN* 5.6 0.5 - - - -
5D ARG* 2.8 57.8 + - - +
6D ASP 3.3 7.2 + - - +
7D PRO* 2.9 5.6 + - - +
9D SER* 1.3 75.5 - - - +
11D GLN* 1.3 65.4 + - - +
12D MET 3.3 2.5 - - - -
13D GLN* 2.9 14.9 + - + +
14D HIS* 2.9 53.7 + - + +
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Residues in contact with GLN 11 (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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400A GLY* 2.9 29.1 + - - +
171B ASN* 2.8 44.9 + - - +
172B PRO* 4.8 1.6 - - - +
173B GLN* 3.0 30.0 + - + +
174B THR* 3.7 13.9 - - + -
178B ASP* 5.1 0.2 - - - +
7D PRO 3.2 4.9 + - - +
8D ALA 2.9 17.2 + - - +
9D SER 3.2 2.1 - - - +
10D ASP* 1.3 78.4 - - - +
12D MET* 1.3 78.0 + - - +
14D HIS* 3.4 7.2 + - - +
15D TRP* 3.2 22.2 + - - +
266D PHE* 5.3 2.9 - - + -
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Residues in contact with MET 12 (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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402A PRO* 4.1 24.5 - - + -
404A TYR* 3.6 35.9 - - - +
409A PHE* 3.7 29.5 - - + +
171B ASN* 4.0 8.3 - - - +
172B PRO* 6.0 1.1 - - + -
178B ASP* 4.2 3.1 + - - +
180B ASP* 3.7 22.7 - - + +
181B MET* 3.3 28.9 - - + +
9D SER 4.8 2.0 + - - +
10D ASP 3.3 0.6 - - - -
11D GLN* 1.3 93.2 + - - +
13D GLN* 1.3 60.3 + - - +
15D TRP* 3.0 7.7 + - - +
16D LYS* 2.8 29.5 + - - +
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Residues in contact with GLN 13 (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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409A PHE* 3.4 15.8 - - - -
180B ASP* 5.5 0.2 + - - -
471B GLN* 2.9 45.9 + - - +
473B PHE* 4.3 4.3 - - - -
10D ASP* 2.9 21.7 + - + +
12D MET* 1.3 77.2 - - - +
14D HIS* 1.3 61.6 + - + +
16D LYS* 3.1 21.8 + - - +
17D GLU* 2.8 65.9 + - - +
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Residues in contact with HIS 14 (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 PRO* 4.3 17.8 + - + +
10D ASP* 2.9 48.3 + - + +
11D GLN* 3.7 5.9 + - - +
13D GLN* 1.3 78.1 - - + +
15D TRP* 1.3 57.5 + - - +
17D GLU* 3.5 22.4 - - - +
18D GLN* 2.8 33.3 + - - +
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Residues in contact with TRP 15 (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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400A GLY* 3.7 22.5 - - - +
401A ALA* 3.6 29.6 - - + +
402A PRO* 3.7 19.5 - - + -
409A PHE 3.1 26.7 - - - -
410A GLY 3.6 18.8 - - - -
411A ALA* 4.2 4.9 - - - -
412A PRO* 5.5 1.8 - - + -
173B GLN* 5.8 0.2 - - - -
11D GLN* 3.2 19.2 + - - +
12D MET* 3.0 12.0 + - - +
14D HIS* 1.3 74.1 - - - +
16D LYS* 1.3 66.9 + - - +
18D GLN* 3.3 32.8 + - - +
19D ARG* 3.4 42.7 + - + +
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Residues in contact with LYS 16 (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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408A SER* 3.3 28.1 + - - +
409A PHE* 3.6 37.0 - - + +
410A GLY* 5.5 1.1 - - - +
473B PHE* 4.6 17.2 - - - -
12D MET 2.8 12.3 + - - +
13D GLN* 3.4 26.0 - - - +
15D TRP* 1.3 78.7 - - - +
17D GLU* 1.3 58.0 + - + +
19D ARG* 3.1 7.6 + - - +
20D ALA* 2.8 24.7 + - - -
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Residues in contact with GLU 17 (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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13D GLN* 2.8 47.2 + - - +
14D HIS* 3.5 25.2 - - - +
16D LYS* 1.3 74.0 - - + +
18D GLN* 1.3 62.4 + - - +
19D ARG 2.9 6.3 + - - -
20D ALA* 3.1 23.2 + - - +
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Residues in contact with GLN 18 (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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14D HIS 2.8 22.5 + - - +
15D TRP* 3.4 25.4 - - - +
16D LYS 3.3 0.2 - - - -
17D GLU* 1.3 72.1 - - - +
19D ARG* 1.3 61.8 + - + +
22D GLN* 4.3 3.5 - - - +
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Residues in contact with ARG 19 (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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382A ARG* 5.0 5.1 - - - +
410A GLY* 4.0 12.7 + - - -
15D TRP* 3.4 47.7 - - + +
16D LYS* 3.1 6.4 + - - +
17D GLU 3.0 0.4 - - - -
18D GLN* 1.3 83.0 - - + +
20D ALA* 1.3 64.7 + - - +
21D ALA* 2.8 12.1 + - - +
22D GLN* 3.5 58.8 + - + +
23D LYS 2.7 30.9 + - - -
24D ALA* 4.0 8.5 - - - +
25D ASP* 3.9 23.2 + - - +
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Residues in contact with ALA 20 (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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16D LYS* 2.8 15.3 + - - -
17D GLU* 3.3 17.0 - - - +
19D ARG* 1.3 74.9 - - - +
21D ALA* 1.3 68.8 + - + +
22D GLN 3.5 5.8 + - - +
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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