Contacts of the strand formed by residues 22 - 28 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H ILE* 4.8 1.3 - - + -
11H VAL* 3.2 34.3 - - + -
14H LEU* 3.9 17.7 - - + -
15H LEU* 3.2 41.1 - - + -
19H PRO* 3.1 30.3 + - + +
20H GLU 3.8 7.3 - - - +
21H ARG* 1.3 79.7 - - - +
23H GLN* 1.3 62.4 + - - +
25H VAL* 4.0 20.4 - - + -
43H LEU* 4.0 8.3 - - + -
48H VAL* 3.9 22.7 - - + -
72H ALA* 3.9 20.0 - - + -
74H VAL* 3.9 11.7 - - + -
75H LYS* 4.7 2.8 - - - -
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Residues in contact with GLN 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1H HIS 5.9 1.0 + - - -
2H SER* 2.2 36.7 + - - -
21H ARG 4.0 0.7 - - - +
22H PHE* 1.3 79.6 - - - +
24H GLU* 1.3 65.2 + - - +
48H VAL* 4.9 2.0 - - - +
49H VAL* 3.6 20.1 + - - +
73H ARG* 3.0 33.1 + - - +
74H VAL* 3.4 10.4 - - - -
75H LYS* 3.6 37.8 + - + +
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Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLN* 1.3 83.6 - - - +
25H VAL* 1.3 65.4 + - - +
26H PHE* 3.2 24.0 - - + -
48H VAL* 5.0 0.4 - - - +
49H VAL* 3.6 18.1 - - + +
51H GLN* 2.9 32.7 + - - +
72H ALA* 3.4 1.7 - - - -
73H ARG* 2.6 77.2 + - + +
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 5.2 0.9 - - + -
22H PHE* 4.0 7.9 - - + -
24H GLU* 1.3 77.9 - - - +
26H PHE* 1.3 68.4 + - - +
27H ILE* 4.4 6.7 - - + -
43H LEU* 3.8 19.7 - - + -
48H VAL* 3.7 21.8 - - + -
49H VAL 2.8 14.1 + - - +
50H ILE* 4.3 8.3 - - + -
51H GLN* 2.8 34.4 + - - +
70H ILE* 3.8 27.4 - - + -
71H ILE 3.4 10.1 - - - +
72H ALA* 3.9 16.2 - - + -
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Residues in contact with PHE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H MSE 3.9 30.7 - - + -
24H GLU* 3.2 41.7 - - + -
25H VAL* 1.3 76.1 - - - +
27H ILE* 1.3 62.1 + - - +
51H GLN* 3.2 35.0 - - + +
53H ALA* 4.4 18.6 - - + -
57H TYR* 5.8 4.0 - + - -
58H LEU* 4.6 18.4 - - + +
61H LYS* 4.2 15.9 - - + -
69H GLY 3.9 0.3 - - - +
70H ILE* 3.4 7.1 - - - +
71H ILE* 2.7 42.6 + - + +
73H ARG* 4.7 1.3 - - + -
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Residues in contact with ILE 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H VAL* 4.4 7.9 - - + -
26H PHE* 1.3 78.6 - - - +
28H LEU* 1.3 70.0 + - + +
29H LYS 2.9 9.7 + - - -
36H LEU* 5.3 0.7 - - + -
40H ILE* 3.7 36.3 - - + -
50H ILE* 3.7 18.4 - - + -
51H GLN 2.9 13.6 + - - +
52H LEU* 3.4 30.8 - - + -
53H ALA 3.2 19.1 + - - +
58H LEU* 4.9 4.9 - - - -
69H GLY 3.5 6.5 - - - +
70H ILE* 4.4 14.6 - - + -
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 1.3 78.9 - - + +
29H LYS* 1.3 66.1 + - - +
30H GLY 3.0 4.7 + - - -
31H ARG* 3.1 58.0 + - + +
32H GLU 4.8 1.1 - - - +
33H ASP* 4.2 11.0 - - + +
36H LEU* 4.0 25.1 - - + -
40H ILE* 5.6 2.5 - - + -
52H LEU* 5.0 0.2 - - - +
53H ALA 4.5 2.9 - - - -
54H ASN 6.2 0.4 - - - -
55H ARG* 6.2 4.3 - - - +
58H LEU* 4.5 10.9 - - + +
68H GLN 5.0 0.4 - - - +
69H GLY* 3.3 27.1 + - - +
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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