Contacts of the helix formed by residues 9 - 20 (chain A) in PDB entry 1G1E
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 ILE 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG 5.3 0.2 - - - +
8A ASN* 1.3 91.1 - - + +
10A GLN* 1.3 58.8 + - + +
12A LEU* 3.0 10.1 + - + +
13A LEU* 2.7 39.6 + - - +
332B LEU* 3.5 40.3 - - + +
335B TYR* 2.9 39.7 - - + -
336B GLN* 3.3 31.2 - - + +
339B GLN* 4.0 2.9 - - - +
355B GLU* 4.4 13.9 - - - +
358B VAL* 4.4 8.3 - - + -
379B PHE* 5.9 0.4 - - - +
380B LEU* 4.5 6.5 - - + -
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Residues in contact with GLN 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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6A ARG 2.9 24.8 + - - +
7A MET* 3.0 6.7 + - - +
9A ILE* 1.3 79.0 - - + +
11A MET* 1.3 56.5 + - - +
13A LEU* 4.0 9.4 - - + -
14A GLU* 3.0 45.5 + - + +
333B HIS* 5.8 1.3 - - + +
336B GLN* 3.3 49.5 - - + +
339B GLN* 5.4 2.1 + - - -
340B ARG* 4.4 16.1 + - - +
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Residues in contact with MET 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 MET* 2.5 61.6 + - + +
8A ASN* 3.0 24.2 - - - +
10A GLN* 1.3 74.1 - - - +
12A LEU* 1.3 56.9 + - - +
14A GLU* 3.9 8.8 + - - +
15A ALA 3.8 2.8 + - - -
303B GLU* 3.4 29.2 - - + +
304B PHE* 3.2 62.8 - - + +
307B ALA* 4.6 9.6 - - + -
308B ILE* 3.6 2.8 - - - +
379B PHE* 4.9 9.2 - - + -
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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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8A ASN 2.9 11.5 + - - +
9A ILE* 3.5 7.4 - - + +
11A MET* 1.3 76.6 - - - +
13A LEU* 1.3 61.7 + - - +
15A ALA* 2.8 27.2 - - - +
16A ALA* 3.6 0.5 + - - +
307B ALA* 3.2 36.3 - - + +
310B TYR* 4.0 9.2 - - + -
311B VAL* 2.9 40.2 - - + +
328B PHE* 3.8 14.4 - - + -
329B LEU* 5.2 0.4 - - + +
332B LEU* 3.5 26.5 - - + -
376B PHE* 4.0 17.9 - - + -
379B PHE* 4.6 11.9 - - + -
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Residues in contact with LEU 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 ILE* 2.7 26.8 + - + +
10A GLN* 3.8 9.9 - - - +
12A LEU* 1.3 71.7 - - - +
14A GLU* 1.3 64.9 + - + +
15A ALA 2.9 1.4 + - - -
16A ALA* 2.9 17.2 + - - +
17A ASP* 3.2 12.9 - - - +
329B LEU* 2.9 47.5 - - + +
332B LEU* 3.1 39.7 - - + +
333B HIS* 3.3 46.0 - - + +
336B GLN* 4.4 3.8 - - + -
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Residues in contact with GLU 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 GLN* 3.0 31.8 + - + +
11A MET* 3.9 10.6 - - - +
13A LEU* 1.3 75.9 - - + +
15A ALA* 1.3 64.9 + - - +
17A ASP* 3.3 15.0 + - - +
18A TYR* 3.2 17.2 + - - +
304B PHE* 4.8 11.1 - - + -
333B HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 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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11A MET 3.8 2.2 + - - -
12A LEU 2.8 19.1 + - - +
13A LEU 2.9 0.8 + - - -
14A GLU* 1.3 76.5 - - - +
16A ALA* 1.3 52.7 + - - +
18A TYR* 2.7 27.6 + - - +
19A LEU* 2.7 19.1 + - + +
304B PHE* 4.7 2.0 - - - -
308B ILE* 2.8 51.8 - - + +
311B VAL* 3.6 6.5 - - + -
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Residues in contact with ALA 16 (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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12A LEU 3.6 0.8 + - - -
13A LEU 2.9 12.8 + - - +
15A ALA* 1.3 78.3 - - - +
17A ASP* 1.3 55.7 + - - +
18A TYR 2.9 0.3 + - - -
19A LEU* 3.0 3.6 + - - +
20A GLU* 2.6 42.3 + - - +
311B VAL* 3.8 5.7 - - + +
325B TYR* 3.1 29.6 + - + +
329B LEU* 3.5 32.3 - - + -
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Residues in contact with ASP 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 LEU 3.2 17.2 - - - +
14A GLU* 3.5 12.7 - - - +
15A ALA 3.3 0.4 - - - -
16A ALA* 1.3 74.4 - - - +
18A TYR* 1.3 56.7 + - - +
20A GLU* 3.2 17.6 + - - +
21A ARG* 3.0 33.7 + - - +
329B LEU* 4.8 5.6 - - - +
333B HIS* 5.1 6.2 + - - -
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Residues in contact with TYR 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 GLU 3.2 7.5 + - - +
15A ALA* 2.7 18.5 + - - +
17A ASP* 1.3 72.4 - - - +
19A LEU* 1.3 76.9 + - + +
20A GLU 3.1 1.8 + - - -
21A ARG* 3.4 20.6 + - - +
304B PHE* 6.0 9.0 - + + -
308B ILE* 6.0 3.1 - - + -
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Residues in contact with LEU 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 ALA* 2.7 36.6 + - + +
16A ALA* 3.8 2.2 - - - +
18A TYR* 1.3 82.7 - - + +
20A GLU* 1.3 65.6 + - - +
21A ARG* 3.2 9.2 - - - +
308B ILE* 3.3 34.1 - - + +
311B VAL* 3.1 43.5 - - + -
312B ASN* 3.5 20.0 - - + +
315B LYS* 3.8 16.5 - - + -
325B TYR* 3.9 1.8 - - - +
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Residues in contact with GLU 20 (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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16A ALA* 2.6 29.3 + - - +
17A ASP* 3.2 36.9 + - - +
18A TYR 3.1 0.4 - - - -
19A LEU* 1.3 73.2 - - - +
21A ARG* 1.3 76.5 + - - +
315B LYS* 3.6 29.9 + - - +
325B TYR* 3.8 12.3 - - + -
326B LYS* 4.8 12.7 + - - -
329B LEU* 4.1 8.2 - - - +
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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