Contacts of the helix formed by residues 16 - 25 (chain F) in PDB entry 1GUL
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 MET 16 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F LEU* 3.7 28.0 - - + -
8F HIS 3.3 32.1 - - - +
9F TYR* 3.5 31.2 - - + -
13F ARG 3.0 2.5 + - - +
15F ARG* 1.3 75.3 - - - +
17F GLU* 1.3 65.5 + - - +
18F SER 3.1 2.9 - - - -
19F VAL* 2.8 36.5 + - - +
20F ARG* 2.9 30.0 + - - +
56F PRO* 3.5 22.4 - - + +
57F MET 3.7 13.9 - - - +
58F VAL* 4.0 5.6 - - + -
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ARG* 2.9 36.5 + - + +
14F GLY 4.3 3.8 - - - +
15F ARG 3.3 1.2 - - - -
16F MET* 1.3 77.8 - - - +
18F SER* 1.3 58.0 + - - +
20F ARG* 2.5 40.6 + - - +
21F TRP* 2.8 43.1 + - + +
162F GLN* 3.8 16.4 - - - +
197F PHE* 4.1 3.3 - - - -
204F LYS* 3.5 13.7 + - - +
205F LYS* 2.7 41.0 + - - +
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ARG* 3.9 11.4 + - - -
16F MET 3.0 1.0 + - - -
17F GLU* 1.3 75.9 - - - +
19F VAL* 1.3 58.8 + - - +
21F TRP* 3.1 3.7 + - - +
22F VAL* 2.9 33.6 + - - +
68F THR* 5.0 3.6 - - - +
72F LEU* 4.0 15.9 - - - -
100F LEU* 4.6 4.1 - - - +
103F LEU* 3.8 13.3 - - - +
107F ILE* 6.0 0.2 - - - +
159F ILE* 3.8 15.7 - - - -
162F GLN* 2.7 30.8 + - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LEU* 4.4 2.2 - - + -
16F MET* 2.8 40.7 + - - +
18F SER* 1.3 74.4 - - - +
20F ARG* 1.3 64.4 + - - +
22F VAL* 3.3 1.5 + - - +
23F LEU* 3.0 40.7 + - + +
56F PRO* 5.3 0.7 - - + -
58F VAL* 4.4 11.9 - - + -
68F THR* 4.6 14.8 - - + -
71F ILE* 4.4 16.2 - - + -
72F LEU* 3.9 18.6 - - + -
75F ILE* 4.1 16.2 - - + -
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Residues in contact with ARG 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LEU* 4.0 8.7 - - + -
9F TYR* 3.9 4.0 - - - +
10F PRO 3.7 14.3 + - - -
12F GLY 2.8 29.5 + - - -
13F ARG 3.3 12.5 + - - -
16F MET* 2.9 27.8 + - - +
17F GLU* 2.5 45.1 + - - +
19F VAL* 1.3 78.6 - - - +
21F TRP* 1.3 64.3 + - - +
23F LEU* 3.7 0.9 - - - +
24F ALA* 2.9 24.6 + - - +
30F PHE* 3.9 26.8 - - + -
32F GLU* 2.9 26.3 + - - -
34F PHE* 4.4 0.6 - - - -
197F PHE* 4.0 15.7 - - + -
203F LYS 3.7 17.0 - - - -
205F LYS* 3.6 10.3 - - - +
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Residues in contact with TRP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLU* 2.8 39.4 + - + +
18F SER* 3.1 9.6 + - - +
20F ARG* 1.3 73.0 - - - +
22F VAL* 1.3 57.5 + - - +
24F ALA* 3.4 2.4 + - - +
25F ALA* 2.8 30.0 + - - +
158F VAL* 3.5 28.3 - - + +
159F ILE* 5.6 0.2 - - + -
161F LEU* 3.4 28.3 - - + -
162F GLN* 3.7 43.2 + - + +
165F LEU* 3.8 26.7 - - + -
194F ILE* 4.1 16.8 - - + -
197F PHE* 3.4 27.8 - + + -
198F LEU* 3.9 13.0 - - + -
204F LYS* 3.9 22.8 - - - +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F SER 2.9 20.4 + - - +
19F VAL 3.9 2.7 - - - +
21F TRP* 1.3 74.2 - - - +
23F LEU* 1.3 69.8 + - - +
25F ALA* 3.3 3.1 + - - +
26F ALA* 2.9 22.0 + - - +
72F LEU* 3.8 15.3 - - + +
75F ILE* 3.8 27.4 - - + -
76F ALA 5.0 1.8 - - - +
81F LEU* 3.8 21.0 - - + +
155F LEU* 3.6 30.1 - - + -
158F VAL* 4.2 15.7 - - + -
159F ILE* 4.4 3.4 - - + -
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PRO* 4.5 11.7 - - + -
7F LEU* 4.1 13.7 - - + -
19F VAL* 3.0 33.5 + - + +
20F ARG 3.7 2.2 - - - +
22F VAL* 1.3 77.8 - - - +
24F ALA* 1.3 62.2 + - - +
26F ALA* 3.0 11.8 + - - +
28F VAL* 2.9 51.7 + - + +
30F PHE* 3.7 35.7 - - + -
58F VAL* 5.4 1.8 - - + -
60F ILE* 5.1 3.6 - - + -
75F ILE* 4.0 31.2 - - + -
79F HIS* 5.5 1.1 - - + -
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ARG 2.9 13.2 + - - +
21F TRP 3.7 1.8 - - - +
23F LEU* 1.3 75.3 - - - +
25F ALA* 1.3 64.2 + - - +
27F GLY* 2.9 12.9 + - - -
28F VAL 4.1 7.8 + - - +
30F PHE* 4.4 5.5 - - + -
193F THR* 3.2 16.0 - - - +
197F PHE* 3.2 44.6 - - + -
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TRP* 2.8 19.1 + - + +
22F VAL 3.7 3.6 - - - +
24F ALA* 1.3 77.3 - - - +
26F ALA* 1.3 58.3 + - - +
27F GLY 2.9 3.7 + - - -
81F LEU* 5.7 2.2 - - + -
153F LEU* 4.7 14.0 - - + +
158F VAL* 4.0 24.7 - - + -
191F ILE* 5.5 0.2 - - - +
193F THR* 3.0 25.6 + - - +
194F ILE* 4.1 21.1 - - + -
197F PHE* 5.7 0.2 - - - +
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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