Contacts of the helix formed by residues 11 - 21 (chain F) in PDB entry 4GTU
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 GLY 11 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F TYR* 3.5 12.8 - - - -
9F ILE* 3.4 2.1 - - - -
10F ARG* 1.3 92.5 - - - +
12F LEU* 1.3 63.9 + - - -
13F ALA 2.9 3.8 + - - -
14F HIS* 3.4 11.3 + - - +
161F ASP* 4.4 5.7 - - - +
207F LEU 2.9 21.9 + - - -
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Residues in contact with LEU 12 (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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6F TYR* 3.5 12.0 + - + +
11F GLY* 1.3 72.5 - - - -
13F ALA* 1.3 58.3 + - - +
14F HIS 3.7 0.2 - - - -
15F ALA* 5.0 5.5 + - - +
16F ILE* 3.7 14.6 - - - +
60F PRO* 4.4 13.3 - - + +
72F SER* 4.2 18.3 - - - +
104F MET* 3.6 31.4 - - + -
107F SER* 4.6 16.2 - - - +
108F ASN* 5.9 4.3 - - - +
111F ALA* 5.9 6.7 - - + -
161F ASP* 5.7 0.7 - - - -
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Residues in contact with ALA 13 (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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4F LEU* 5.6 3.1 - - + -
6F TYR* 3.4 30.7 - - + -
10F ARG 3.6 0.4 - - - +
11F GLY 2.9 1.6 + - - -
12F LEU* 1.3 77.9 - - - +
14F HIS* 1.3 67.6 + - - +
15F ALA 3.3 2.2 - - - -
16F ILE* 3.1 25.1 + - + +
17F ARG* 3.2 41.5 + - + +
60F PRO* 4.3 4.0 - - + -
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Residues in contact with HIS 14 (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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10F ARG* 3.0 54.2 + - + +
11F GLY 3.4 2.2 + - - +
13F ALA* 1.3 76.9 - - - +
15F ALA* 1.3 64.9 + - - +
17F ARG* 3.0 19.5 + - - +
18F LEU* 3.0 46.3 + - + +
160F TYR* 5.9 2.9 - + - -
161F ASP* 3.2 11.2 - - - +
196F TYR* 5.2 4.5 - + - -
202F PHE* 3.3 33.5 - + - -
203F LEU 3.0 30.4 + - - -
204F PRO* 4.4 0.2 - - + -
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Residues in contact with ALA 15 (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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12F LEU 5.0 3.3 + - - +
13F ALA 3.3 1.2 - - - -
14F HIS* 1.3 78.7 - - - +
16F ILE* 1.3 56.8 + - + +
18F LEU* 2.8 40.2 + - - +
19F LEU* 3.2 11.3 + - - +
76F LEU* 4.5 11.2 - - + -
157F PHE* 4.3 5.5 - - + +
158F LEU* 4.4 30.7 - - + +
161F ASP* 3.2 14.0 + - + +
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Residues in contact with ILE 16 (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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4F LEU* 3.7 24.5 - - + -
12F LEU 3.7 21.1 - - - +
13F ALA* 3.1 16.1 + - + +
15F ALA* 1.3 75.5 - - + +
17F ARG* 1.3 63.8 + - - +
18F LEU 3.3 0.2 + - - -
19F LEU* 3.4 15.5 + - + +
20F LEU* 3.1 34.4 + - + +
60F PRO* 4.3 11.7 - - + -
72F SER* 4.5 7.9 - - - +
75F ILE* 3.7 41.3 - - + -
76F LEU* 4.0 19.0 - - + +
79F ILE* 5.9 0.7 - - + -
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Residues in contact with ARG 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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4F LEU* 3.6 20.7 - - + +
6F TYR* 3.6 8.1 - - - +
7F TRP 4.1 6.7 + - - -
8F ASP 5.2 0.2 - - - -
9F ILE 3.4 20.6 + - - -
10F ARG* 3.6 8.7 + - - +
13F ALA* 3.2 37.8 - - - +
14F HIS* 3.0 14.1 + - - +
16F ILE* 1.3 76.7 - - - +
18F LEU* 1.3 57.0 + - - +
20F LEU* 3.3 10.1 - - - +
21F GLU* 2.9 35.1 + - - +
27F TYR* 6.4 2.9 - - + -
29F GLU* 3.9 20.6 + - - -
31F LYS* 5.5 4.1 - - - +
196F TYR* 3.8 26.2 - - + +
203F LEU* 3.2 41.1 + - - +
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Residues in contact with LEU 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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14F HIS* 3.0 40.4 + - + +
15F ALA* 2.8 26.8 + - - +
17F ARG* 1.3 77.2 - - - +
19F LEU* 1.3 54.6 + - - +
20F LEU 3.0 5.0 + - - -
21F GLU* 3.9 2.6 - - - +
22F TYR* 3.1 26.7 + - - +
157F PHE* 3.4 34.5 - - + +
160F TYR* 4.3 22.7 - - + -
161F ASP* 4.9 4.3 - - - +
187F PHE* 4.9 5.2 - - + -
193F ILE* 4.0 15.4 - - + +
196F TYR* 4.4 19.5 - - + -
197F MET* 5.8 1.6 - - + -
202F PHE* 5.4 2.0 - - + -
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Residues in contact with LEU 19 (chain F).
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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15F ALA 3.2 15.3 + - - +
16F ILE* 3.5 12.1 - - + +
18F LEU* 1.3 76.4 - - - +
20F LEU* 1.3 51.8 + - - +
22F TYR* 4.5 1.3 - - - -
23F THR* 2.6 34.6 + - + +
76F LEU* 3.4 34.8 - - + +
79F ILE* 3.3 33.4 - - + +
80F ALA* 4.0 8.1 - - + -
85F LEU* 4.7 4.3 - - + -
154F PHE* 3.6 30.7 - - + -
157F PHE* 3.5 32.7 - - + -
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Residues in contact with LEU 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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2F MET* 3.6 34.1 - - + -
4F LEU* 3.9 27.4 - - + -
16F ILE* 3.1 30.7 + - + +
17F ARG* 3.3 7.4 - - - +
18F LEU 3.0 0.2 - - - -
19F LEU* 1.3 78.7 - - - +
21F GLU* 1.3 61.4 + - - +
23F THR* 3.0 15.1 + - - -
25F SER* 3.1 28.3 + - - +
27F TYR* 3.8 26.7 - - + -
62F LEU* 5.6 1.1 - - + -
75F ILE* 5.9 0.2 - - + -
79F ILE* 3.7 29.6 - - + -
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Residues in contact with GLU 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 ARG 2.9 15.2 + - - +
18F LEU 3.9 2.2 - - - +
20F LEU* 1.3 75.5 - - - +
22F TYR* 1.3 59.3 + - - +
24F ASP* 2.9 27.2 + - - +
25F SER 5.1 0.7 - - - +
27F TYR* 3.2 27.9 + - + -
192F LYS* 4.1 11.7 - - - +
193F ILE* 5.3 1.1 - - + -
196F TYR* 3.2 49.5 - - + -
201F ARG* 3.1 32.1 + - - -
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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