Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 1QGI
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 PRO 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 1.3 86.2 - - - +
10A GLU* 1.3 78.6 + - - +
12A LEU* 3.4 8.9 + - + +
13A GLN* 3.3 25.7 + - - +
134A ALA* 5.8 2.0 - - + -
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Residues in contact with GLU 10 (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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8A SER* 3.3 6.7 + - - +
9A PRO* 1.3 91.5 - - - +
11A THR* 1.3 65.0 + - - +
13A GLN* 3.2 10.4 + - - +
14A PHE* 3.0 23.3 + - - +
134A ALA* 5.5 4.7 - - - +
138A LYS* 4.5 19.7 + - + -
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Residues in contact with THR 11 (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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7A PHE* 3.9 14.6 - - + -
8A SER* 2.8 31.8 + - - -
10A GLU* 1.3 78.2 - - - +
12A LEU* 1.3 57.4 + - - +
14A PHE* 3.2 8.6 + - + +
15A LEU* 2.9 31.5 + - + +
137A ARG* 4.0 1.2 - - - +
138A LYS* 3.3 29.2 + - - +
141A TRP* 3.6 42.6 - - + -
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Residues in contact with LEU 12 (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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4A ASP* 3.8 45.5 - - + +
7A PHE* 3.8 25.4 - - + -
8A SER 3.0 18.0 + - - +
9A PRO* 3.8 9.9 - - + +
10A GLU 3.3 0.2 - - - -
11A THR* 1.3 73.2 - - - +
13A GLN* 1.3 63.1 + - - +
15A LEU* 3.9 6.8 - - + +
16A ARG* 2.8 32.8 + - - +
21A LEU 5.1 0.2 - - - +
22A ASP* 4.7 2.0 - - - -
23A GLY* 3.7 32.1 - - - +
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Residues in contact with GLN 13 (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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9A PRO 3.3 15.0 + - - +
10A GLU* 3.2 10.6 + - - +
12A LEU* 1.3 79.4 - - - +
14A PHE* 1.3 58.0 + - - +
16A ARG* 3.4 11.8 + - - +
17A ASN* 2.9 33.0 + - - +
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Residues in contact with PHE 14 (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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10A GLU 3.0 13.3 + - - +
11A THR* 3.4 9.0 - - - +
13A GLN* 1.3 77.8 - - - +
15A LEU* 1.3 76.5 + - + +
17A ASN* 4.9 1.3 - - - -
18A ASN* 2.9 51.5 + - + +
138A LYS* 3.6 25.6 - - - +
141A TRP* 4.3 5.4 - - + -
142A GLU* 4.1 26.7 - - + -
145A TYR* 3.6 49.6 - + + -
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Residues in contact with LEU 15 (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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7A PHE* 3.4 38.1 - - + -
11A THR* 2.9 24.2 + - + +
12A LEU* 3.9 8.1 - - + +
14A PHE* 1.3 92.6 - - + +
16A ARG* 1.3 58.6 + - - +
19A THR* 2.6 48.7 + - + -
21A LEU 4.0 2.7 - - - +
26A TRP* 3.8 33.9 - - + +
141A TRP* 3.8 28.0 - - + +
145A TYR* 5.6 1.3 - - + -
149A ILE* 4.9 4.7 - - + -
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Residues in contact with ARG 16 (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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12A LEU 2.8 18.0 + - - +
13A GLN* 3.9 11.5 + - - +
15A LEU* 1.3 77.3 - - - +
17A ASN* 1.3 85.9 + - - +
20A GLY* 2.8 37.0 + - - +
21A LEU 3.5 19.4 + - - +
22A ASP* 5.2 6.5 - - + +
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Residues in contact with ASN 17 (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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13A GLN 2.9 17.4 + - - +
14A PHE* 4.1 2.9 - - - +
16A ARG* 1.3 100.1 + - - +
18A ASN* 1.3 75.7 + - - +
20A GLY 4.8 0.5 + - - -
157A ARG* 4.8 4.2 + - - -
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Residues in contact with ASN 18 (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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14A PHE* 2.9 53.3 + - + +
15A LEU* 5.1 0.2 - - - -
17A ASN* 1.3 95.4 + - - +
19A THR* 1.3 63.1 + - + +
20A GLY 3.8 0.2 - - - -
145A TYR* 3.7 39.1 + - + +
153A VAL* 3.8 7.1 - - - +
157A ARG* 3.4 21.5 + - - +
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Residues in contact with THR 19 (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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15A LEU* 2.6 30.2 + - + +
18A ASN* 1.3 84.3 - - + +
20A GLY* 1.3 62.7 + - - +
21A LEU* 3.2 17.6 + - - +
26A TRP* 3.0 30.4 + - + +
145A TYR* 4.4 8.5 - - + -
149A ILE* 4.0 26.7 - - + -
153A VAL* 4.1 13.7 - - + -
157A ARG* 3.7 11.4 + - - +
162A THR* 5.3 1.4 - - - +
167A ILE* 3.8 13.0 - - - +
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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