Contacts of the helix formed by residues 21 - 32 (chain F) in PDB entry 5GJQ
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 LEU 21 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F VAL 5.5 2.2 - - - +
13F ASN* 4.8 4.3 - - - -
14F THR 3.6 17.5 - - - +
15F PHE* 3.7 25.6 - - + -
20F ARG* 1.3 74.8 - - - +
22F PHE* 1.3 66.1 + - - +
23F GLN* 4.5 3.1 - - + +
24F VAL* 3.0 34.0 + - + +
25F GLU* 3.1 14.6 + - - +
121F LEU* 3.8 16.4 - - + -
123F PHE* 4.8 5.2 - - + -
77G LEU* 4.0 12.7 - - + +
126G ARG* 3.5 51.6 - - - +
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Residues in contact with PHE 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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10F ARG* 3.5 50.5 - - - +
14F THR* 3.7 20.1 + - + +
15F PHE 3.6 7.6 - - - -
16F SER* 3.6 39.0 - - - -
17F PRO* 4.3 8.5 - - + -
20F ARG* 3.5 3.8 + - - +
21F LEU* 1.3 71.5 - - - +
23F GLN* 1.3 62.0 + - + +
25F GLU* 3.3 4.5 + - - +
26F TYR* 2.8 69.2 + + + -
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Residues in contact with GLN 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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9E VAL* 3.8 12.9 - - - +
10E PHE* 2.7 68.4 + - - +
11F GLY 5.2 0.9 - - - +
12F VAL* 3.8 40.0 + - + +
14F THR 5.4 0.4 + - - -
21F LEU* 3.2 2.1 - - + +
22F PHE* 1.3 81.5 - - + +
24F VAL* 1.3 62.0 + - - +
26F TYR* 3.8 11.2 - - - +
27F ALA* 3.0 24.3 + - - +
123F PHE* 4.7 3.1 - - + -
135F ARG* 4.4 0.5 - - - +
136F PRO* 3.8 22.0 - - + +
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Residues in contact with VAL 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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21F LEU* 3.0 30.9 + - + +
23F GLN* 1.3 77.0 - - - +
25F GLU* 1.3 63.0 + - + +
27F ALA* 3.2 6.1 + - - +
28F ILE* 3.0 35.4 + - + +
121F LEU* 3.8 26.5 - - + -
123F PHE* 4.4 2.5 - - + -
136F PRO* 4.2 12.8 - - + -
158F PRO 3.7 6.1 - - - +
159F SER* 3.6 35.9 - - - +
77G LEU* 6.3 3.8 - - + -
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Residues in contact with GLU 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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20F ARG* 3.2 44.6 + - + +
21F LEU 3.1 12.5 + - - +
22F PHE* 3.6 9.2 - - - +
24F VAL* 1.3 81.1 - - - +
26F TYR* 1.3 67.1 + - + +
28F ILE* 3.1 19.2 + - - +
29F GLU* 2.9 29.0 + - - +
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Residues in contact with TYR 26 (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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10E PHE* 3.6 24.0 - - + -
11E SER 3.6 24.7 - - - +
12E PRO* 3.6 45.1 - - + +
14E GLY* 3.3 10.4 - - - -
10F ARG* 3.7 10.9 + - - -
22F PHE* 2.8 59.1 + + + +
23F GLN* 3.8 9.0 - - - +
25F GLU* 1.3 83.9 - - + +
27F ALA* 1.3 57.1 + - - +
29F GLU* 3.3 11.6 - - + +
30F ALA* 2.9 21.0 + - - +
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Residues in contact with ALA 27 (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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10E PHE* 3.4 34.1 - - + -
23F GLN 3.0 10.6 + - - +
24F VAL 3.4 9.0 - - - +
26F TYR* 1.3 75.1 - - - +
28F ILE* 1.3 61.4 + - - +
30F ALA* 2.8 18.2 + - - +
31F ILE* 3.0 15.4 + - - +
136F PRO* 4.3 5.2 - - + -
137F PHE 4.2 4.7 - - - +
138F GLY* 4.5 1.3 - - - -
158F PRO* 3.8 22.3 - - + +
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Residues in contact with ILE 28 (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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24F VAL* 3.0 21.1 + - + +
25F GLU* 3.3 22.0 - - - +
27F ALA* 1.3 76.3 - - - +
29F GLU* 1.3 61.1 + - - +
31F ILE* 3.1 24.7 + - + +
32F LYS* 3.7 18.5 + - + +
157F ASP* 3.4 28.3 - - + +
158F PRO* 3.8 23.1 - - + -
159F SER* 4.4 3.1 - - - +
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Residues in contact with GLU 29 (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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12E PRO 4.1 13.5 - - - +
13E ASP* 4.2 10.0 - - - +
14E GLY* 4.2 10.1 - - - -
25F GLU* 2.9 17.9 + - + +
26F TYR* 3.3 14.4 - - + +
27F ALA 3.1 0.2 - - - -
28F ILE* 1.3 76.2 - - + +
30F ALA* 1.3 62.6 + - - +
32F LYS* 2.7 57.0 + - - +
33F LEU* 4.2 8.3 + - - +
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Residues in contact with ALA 30 (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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10E PHE* 3.7 19.1 - - + -
14E GLY* 3.2 26.4 - - - +
26F TYR 2.9 10.6 + - - +
27F ALA* 2.8 11.7 + - - +
29F GLU* 1.3 77.1 - - - +
31F ILE* 1.3 61.7 + - - +
33F LEU* 3.5 19.9 + - - +
34F GLY 4.2 1.6 + - - -
80F GLY* 4.6 7.9 - - - -
81F LEU* 5.0 12.3 + - + +
138F GLY* 4.9 6.5 - - - -
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Residues in contact with ILE 31 (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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27F ALA 3.0 10.3 + - - +
28F ILE* 3.3 18.8 - - + +
29F GLU 3.1 0.4 - - - -
30F ALA* 1.3 73.3 - - - +
32F LYS* 1.3 57.9 + - + +
33F LEU 2.9 5.4 - - - -
34F GLY* 2.8 24.1 + - - +
79F SER* 4.4 7.6 - - - +
80F GLY* 4.8 5.4 - - - -
138F GLY 4.8 0.4 - - - -
139F VAL* 4.2 7.4 - - - +
140F ALA* 3.6 38.8 - - + +
157F ASP* 4.7 3.4 - - + -
158F PRO* 3.3 35.7 - - + -
170F ILE* 5.2 0.7 - - + -
171F GLY* 4.1 21.0 - - - +
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Residues in contact with LYS 32 (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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28F ILE* 3.8 21.1 - - + +
29F GLU* 2.7 49.4 + - - +
31F ILE* 1.3 75.0 - - + +
33F LEU* 1.3 62.2 + - + +
34F GLY 3.4 0.4 - - - -
171F GLY 4.2 14.4 - - - +
172F SER* 3.2 25.1 - - - +
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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