Contacts of the strand formed by residues 29 - 35 (chain C) in PDB entry 4GG6
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 ASP 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.0 6.8 - - - -
26C PHE 2.9 30.9 + - - +
27C ASP 4.4 1.8 - - - +
28C GLY* 1.3 77.6 - - - +
30C GLU* 1.3 61.5 + - - +
31C GLU 3.7 0.2 + - - -
138C LEU* 4.0 7.0 - - - +
123D TYR* 4.1 11.1 + - - -
149D ARG* 3.1 41.1 + - - +
151D GLY* 4.1 10.8 - - - +
153D TRP* 3.7 52.0 - - + +
154D THR 5.1 0.2 + - - -
155D PHE* 4.4 4.9 - - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 4.3 8.2 - - - +
24C HIS 3.7 5.4 - - - +
25C GLU* 4.3 1.1 - - + -
29C ASP* 1.3 73.3 - - - +
31C GLU* 1.3 60.5 + - - +
32C PHE 4.0 14.4 - - - +
33C TYR* 3.5 17.1 - - - +
44C GLN* 3.2 34.3 + - + +
135C THR* 3.9 10.8 - - + +
136C SER* 2.7 45.2 + - - -
138C LEU* 3.7 22.4 - - + +
151D GLY 5.1 6.7 + - - +
153D TRP* 2.7 27.0 + - - +
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TYR* 4.2 5.2 - - - -
24C HIS* 2.9 28.8 + - - +
25C GLU 4.6 2.0 - - - -
26C PHE* 3.4 18.8 - - - +
29C ASP 3.7 0.4 + - - -
30C GLU* 1.3 72.4 - - - +
32C PHE* 1.3 63.3 + - + +
43C TRP* 3.4 21.7 - - + -
44C GLN* 2.8 25.8 + - - +
48C PHE* 3.9 8.7 - - + -
52C ARG* 2.9 20.6 + - - -
86D GLU* 2.7 39.5 - - - +
90D THR* 3.8 2.4 + - - -
153D TRP* 3.6 21.8 - - + -
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.2 8.7 - + - -
23C SER* 3.1 5.7 - - - -
24C HIS* 3.0 72.1 + + + +
30C GLU* 3.6 5.1 - - - +
31C GLU* 1.3 81.9 - - - +
33C TYR* 1.3 72.5 + - - +
34C VAL* 3.8 7.2 - - + -
41C THR* 3.6 10.5 - - + -
42C VAL 3.1 18.8 - - - +
43C TRP* 3.3 49.1 - + + -
44C GLN* 4.3 3.8 - - - -
54C PHE* 3.4 39.5 - + + -
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 5.2 4.7 - - + -
22C TYR 3.2 11.7 - - - +
23C SER* 3.9 4.3 - - - -
30C GLU* 3.5 22.2 - - - +
32C PHE* 1.3 76.9 - - - +
34C VAL* 1.3 74.4 + - - +
35C ASP* 3.8 24.7 + - + -
42C VAL* 2.8 68.7 + - + +
44C GLN* 3.8 17.7 - - - -
136C SER* 3.6 15.3 - - - +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 5.7 0.5 - - - -
22C TYR* 2.9 18.4 + - + +
32C PHE* 3.8 21.5 - - + -
33C TYR* 1.3 83.9 - - - +
35C ASP* 1.3 73.1 + - - +
36C LEU* 3.0 24.7 + - + +
39C LYS* 4.9 1.1 - - - -
40C GLU 3.6 8.7 - - - +
41C THR* 4.0 9.9 - - - +
54C PHE* 3.8 17.5 - - + -
56C PRO* 4.0 21.8 - - + +
59C ALA* 3.8 21.5 - - + -
60C LEU* 5.6 0.9 - - + -
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Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR* 3.7 22.4 + - + +
34C VAL* 1.3 69.8 - - - +
36C LEU* 1.3 52.2 + - - +
37C GLU* 3.0 11.1 + - - +
38C ARG* 2.7 56.3 + - + +
39C LYS* 2.7 35.2 + - - -
40C GLU* 3.1 16.3 + - + +
42C VAL* 4.5 5.4 - - + -
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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