Contacts of the helix formed by residues 10 - 19 (chain C) in PDB entry 1DGH
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A GLN* 5.6 0.2 - - - -
4C SER* 3.3 29.6 - - - -
5C ARG* 2.7 51.5 + - - +
6C ASP 3.3 6.7 + - - +
7C PRO* 3.2 7.9 + - - +
9C SER* 1.3 74.4 - - - +
11C GLN* 1.3 64.9 + - - +
12C MET 3.3 2.7 - - - -
13C GLN* 3.0 15.9 + - + +
14C HIS* 2.9 50.3 + - + +
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Residues in contact with GLN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 2.9 39.6 + - - +
172A PRO* 5.0 1.4 - - - +
173A GLN* 2.9 35.8 + - + +
174A THR* 4.0 9.0 - - + -
178A ASP* 5.1 0.7 - - - +
7C PRO 3.4 5.4 + - - +
8C ALA 3.3 15.9 + - - +
9C SER 3.2 4.5 - - - +
10C ASP* 1.3 75.4 - - - +
12C MET* 1.3 76.1 + - - +
14C HIS* 3.5 5.4 + - - +
15C TRP* 3.0 30.2 + - - +
266C PHE* 5.3 2.9 - - + -
400D GLY* 2.8 30.9 + - - +
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Residues in contact with MET 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 4.2 7.0 - - - +
172A PRO* 6.1 1.1 - - + -
178A ASP* 4.2 5.1 + - - +
180A ASP* 3.5 29.8 - - + +
181A MET* 3.5 36.6 - - + +
9C SER 4.8 1.8 + - - -
10C ASP 3.3 0.4 - - - -
11C GLN* 1.3 91.8 + - - +
13C GLN* 1.3 65.8 + - - +
15C TRP* 3.3 5.9 + - - +
16C LYS* 2.9 19.4 + - - +
402D PRO* 4.3 20.9 - - + -
404D TYR* 3.7 19.3 - - - +
409D PHE* 3.4 40.9 - - + +
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 5.4 1.7 + - - +
471A GLN* 3.0 44.6 + - - +
473A PHE* 4.4 6.6 - - - -
10C ASP* 3.0 23.9 + - + +
12C MET* 1.3 77.4 - - - +
14C HIS* 1.3 63.1 + - + +
16C LYS* 3.2 16.9 + - - +
17C GLU* 2.8 66.1 + - - +
409D PHE* 3.7 13.0 - - - -
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Residues in contact with HIS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER* 5.8 2.9 - - - -
7C PRO* 4.4 16.0 + - + +
10C ASP* 2.9 46.1 + - + +
11C GLN* 3.8 4.5 - - - +
13C GLN* 1.3 77.6 - - + +
15C TRP* 1.3 67.1 + - - +
17C GLU* 3.2 20.5 + - - +
18C GLN* 2.9 39.5 + - + +
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Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN* 5.8 0.2 - - - -
11C GLN* 3.0 21.2 + - - +
12C MET* 3.6 8.1 - - - +
13C GLN 3.3 0.2 - - - -
14C HIS* 1.3 76.8 - - - +
16C LYS* 1.3 64.5 + - - +
18C GLN* 3.3 22.9 + - + +
19C ARG* 3.3 44.7 + - + +
398D GLN 5.5 0.2 + - - -
400D GLY* 3.7 26.5 - - - +
401D ALA* 3.6 29.5 - - + +
402D PRO* 3.5 20.2 - - + -
409D PHE 3.1 29.4 - - - -
410D GLY* 3.7 15.9 - - - -
411D ALA* 4.2 5.4 - - - -
412D PRO* 5.5 2.0 - - + -
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A PHE* 5.2 7.1 - - - -
12C MET 2.9 13.7 + - - +
13C GLN* 3.3 23.9 + - - +
15C TRP* 1.3 78.9 - - - +
17C GLU* 1.3 63.0 + - + +
19C ARG* 3.1 10.0 + - - +
22C GLN* 3.0 41.7 + - - +
408D SER* 2.8 31.7 + - - +
409D PHE* 3.7 34.3 - - + +
410D GLY 4.9 0.9 - - - +
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLN* 2.8 43.5 + - - +
14C HIS* 3.2 24.0 + - - +
16C LYS* 1.3 73.5 - - + +
18C GLN* 1.3 58.4 + - - +
19C ARG 2.9 10.0 + - - -
20C ALA* 3.2 17.7 + - - +
22C GLN* 5.0 1.3 - - - +
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C HIS* 2.9 30.8 + - + +
15C TRP* 3.3 14.8 + - + +
17C GLU* 1.3 73.9 - - + +
19C ARG* 1.3 60.1 + - + +
20C ALA* 3.4 4.2 + - - +
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TRP* 3.3 47.9 + - + +
16C LYS* 3.1 9.3 + - - +
17C GLU 2.9 1.6 + - - -
18C GLN* 1.3 81.8 - - + +
20C ALA* 1.3 65.0 + - - +
21C ALA 3.0 8.9 + - - +
22C GLN* 3.0 36.6 + - - +
23C LYS 3.2 14.5 + - - +
24C ALA* 3.2 33.9 - - - +
25C ASP* 4.1 18.0 + - - -
410D GLY* 3.4 13.2 + - - -
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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