Contacts of the strand formed by residues 22 - 28 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.6 2.5 - - + -
11D VAL* 3.3 43.3 - - + -
14D LEU* 3.3 26.0 - - + -
15D LEU* 3.5 29.6 - - + -
19D PRO* 2.8 29.8 + - + +
20D GLU 4.1 1.9 - - - +
21D ARG* 1.3 78.2 - - - +
23D GLN* 1.3 60.5 + - - +
25D VAL* 3.9 18.6 - - + -
43D LEU* 4.2 10.5 - - + -
46D GLN* 5.1 0.2 - - - -
48D VAL* 3.6 30.5 - - + +
72D ALA* 4.0 20.2 - - + -
74D VAL* 4.2 7.4 - - + -
75D LYS* 3.8 10.0 + - - -
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1D HIS* 6.1 0.6 + - - -
1D MSE 4.9 2.0 + - - -
2D SER* 2.5 35.5 + - - -
22D PHE* 1.3 73.5 - - - +
24D GLU* 1.3 65.1 + - - +
48D VAL* 4.4 7.3 - - - +
49D VAL* 4.7 9.2 + - - +
73D ARG* 2.9 38.3 + - - +
74D VAL 3.4 3.8 - - - +
75D LYS* 3.5 52.1 - - + +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLN* 1.3 83.9 - - - +
25D VAL* 1.3 64.6 + - - +
26D PHE* 3.5 30.8 - - + -
48D VAL* 4.4 1.2 - - - +
49D VAL* 3.8 15.1 - - + +
51D GLN* 3.6 28.2 - - + +
72D ALA* 3.3 3.8 - - - -
73D ARG* 2.8 70.2 + - + +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 5.5 0.2 - - + -
22D PHE* 3.9 17.3 - - + -
24D GLU* 1.3 77.7 - - - +
26D PHE* 1.3 64.8 + - - +
27D ILE* 4.6 6.5 - - + -
40D ILE* 5.9 0.4 - - + -
43D LEU* 3.6 34.1 - - + -
48D VAL* 3.8 17.0 - - + -
49D VAL 3.0 13.2 + - - +
50D ILE* 3.4 11.3 - - + -
51D GLN* 2.7 34.7 + - - +
70D ILE* 4.0 17.0 - - + -
71D ILE 3.6 8.7 - - - +
72D ALA* 4.1 6.7 - - + -
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D MSE 4.1 23.8 - - + -
24D GLU* 3.5 42.4 - - + -
25D VAL* 1.3 74.9 - - - +
27D ILE* 1.3 63.5 + - - +
51D GLN* 3.5 28.5 - - + +
53D ALA* 4.3 7.0 - - + -
57D TYR* 3.0 47.1 - + + -
58D LEU* 3.4 20.5 - - + +
70D ILE* 3.2 6.8 - - - +
71D ILE* 3.0 38.1 + - + +
73D ARG* 4.7 4.3 - - + -
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 4.6 6.1 - - + -
26D PHE* 1.3 77.6 - - - +
28D LEU* 1.3 60.4 + - - +
29D LYS 3.3 0.2 + - - -
31D ARG 6.0 1.8 - - - +
36D LEU* 4.4 6.3 - - + -
40D ILE* 3.3 42.0 - - + -
50D ILE* 4.1 13.9 - - + -
51D GLN 2.9 12.5 + - - +
52D LEU* 3.2 34.1 - - + -
53D ALA* 2.8 30.3 + - - +
58D LEU* 3.5 6.0 - - - +
69D GLY 3.3 16.2 - - - +
70D ILE* 4.3 13.7 - - + -
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ILE* 1.3 73.7 - - - +
29D LYS* 1.3 67.9 + - - +
31D ARG* 3.2 67.5 + - + +
33D ASP* 5.6 1.1 - - - +
36D LEU* 5.6 0.8 - - - +
52D LEU* 5.0 1.0 - - - +
53D ALA 3.6 0.7 - - - -
54D ASN* 3.6 0.9 - - - -
55D ARG* 3.2 50.0 - - + +
58D LEU* 3.1 27.5 - - + +
67D HIS* 4.7 3.4 - - + -
69D GLY* 3.6 20.6 + - - -
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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