Contacts of the strand formed by residues 22 - 28 (chain F) in PDB entry 1GZ0
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 PHE 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F VAL* 3.4 28.7 - - + -
14F LEU* 3.5 20.6 - - + -
15F LEU* 3.4 29.4 - - + -
19F PRO* 2.9 30.5 + - + +
20F GLU 4.2 4.9 - - - +
21F ARG* 1.3 79.9 - - - +
23F GLN* 1.3 61.2 + - - +
25F VAL* 3.6 32.8 - - + -
43F LEU* 4.0 11.7 - - + -
48F VAL* 3.7 27.0 - - + +
72F ALA* 4.0 17.0 - - + -
73F ARG 4.9 0.4 - - - -
74F VAL* 4.0 11.9 - - + -
75F LYS* 5.4 1.4 - - - -
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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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2F SER* 2.5 30.4 + - - -
21F ARG 3.9 0.9 - - - +
22F PHE* 1.3 78.9 - - - +
24F GLU* 1.3 62.5 + - + +
48F VAL* 4.6 4.4 - - - +
49F VAL* 4.1 19.1 + - - +
73F ARG* 2.9 28.4 + - + +
74F VAL* 3.2 17.7 + - - +
75F LYS* 3.4 36.5 + - + +
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Residues in contact with GLU 24 (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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23F GLN* 1.3 80.8 - - - +
25F VAL* 1.3 68.3 - - - +
26F PHE* 3.0 25.9 - - + -
48F VAL* 4.7 0.2 - - - +
49F VAL* 4.1 13.7 - - + -
51F GLN* 2.7 37.4 + - - +
72F ALA* 3.4 1.9 - - - +
73F ARG* 2.6 76.4 + - + +
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Residues in contact with VAL 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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11F VAL* 5.0 4.9 - - + -
22F PHE* 3.6 33.4 - - + -
24F GLU* 1.3 81.9 - - - +
26F PHE* 1.3 70.2 + - - +
27F ILE* 4.8 4.5 - - + -
43F LEU* 3.7 26.7 - - + -
48F VAL* 3.7 13.0 - - + -
49F VAL 3.0 13.6 + - - +
50F ILE* 3.3 11.4 - - + +
51F GLN* 2.6 33.4 + - - +
70F ILE* 6.1 0.4 - - + -
71F ILE 3.7 12.6 - - - +
72F ALA* 4.3 2.5 - - + +
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Residues in contact with PHE 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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4F MSE 5.2 4.0 - - - -
24F GLU* 3.0 47.3 - - + -
25F VAL* 1.3 79.1 - - - +
27F ILE* 1.3 72.6 + - - +
51F GLN* 3.0 28.9 - - + +
53F ALA* 5.0 5.6 - - + -
57F TYR* 4.3 31.2 - + - -
58F LEU* 4.6 5.4 - - + -
61F LYS* 5.2 11.7 - - + -
69F GLY 3.7 0.2 - - - +
70F ILE* 3.5 1.7 - - - -
71F ILE* 2.9 72.3 + - + +
72F ALA 4.5 1.8 - - - -
73F ARG* 4.9 13.9 - - + -
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Residues in contact with ILE 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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25F VAL* 4.8 5.4 - - + -
26F PHE* 1.3 79.9 - - - +
28F LEU* 1.3 58.9 + - + +
36F LEU* 4.5 6.5 - - + -
39F LEU* 6.2 0.2 - - + -
40F ILE* 3.2 42.6 - - + -
43F LEU* 6.2 0.2 - - + -
50F ILE* 3.9 20.4 - - + -
51F GLN 2.8 10.5 + - - +
52F LEU* 3.0 32.0 - - + -
53F ALA* 2.7 33.8 + - - +
58F LEU* 5.1 5.8 - - - -
69F GLY 3.4 15.5 - - - +
70F ILE* 4.4 11.4 - - + -
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Residues in contact with LEU 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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242E ARG 5.5 0.7 - - - +
243E SER 5.3 4.5 - - - +
27F ILE* 1.3 75.2 - - + +
29F LYS* 1.3 64.0 + - - +
30F GLY 3.5 1.0 + - - -
31F ARG* 2.8 58.8 + - + +
32F GLU 4.6 1.8 - - - +
33F ASP* 3.8 19.5 - - - +
36F LEU* 3.5 23.1 - - + -
52F LEU* 3.3 14.3 - - - +
53F ALA 3.7 7.4 - - - +
58F LEU* 5.2 4.0 - - + +
69F GLY* 4.1 11.3 + - - +
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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