Contacts of the strand formed by residues 23 - 28 (chain G) in PDB entry 5GAG
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 VAL 23 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G LYS 3.7 1.0 - - - +
20G ASN* 2.9 48.3 + - + +
21G GLY 3.4 0.2 - - - -
22G GLN* 1.3 80.3 - - + +
24G ILE* 1.3 65.7 + - - +
25G THR* 4.1 3.9 + - - +
34G THR* 3.8 24.0 - - + -
35G ARG 4.0 2.7 - - - +
36G THR* 3.3 30.7 - - + +
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Residues in contact with ILE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL* 4.7 8.3 - - + -
18G LYS 3.4 9.4 - - - +
19G ILE* 3.9 30.3 - - + -
22G GLN 4.2 5.6 - - - +
23G VAL* 1.3 83.2 - - - +
25G THR* 1.3 63.6 + - - +
26G ILE* 3.7 26.0 + - + -
33G LEU 3.9 0.5 - - - +
34G THR* 3.3 4.5 - - - +
35G ARG* 2.9 43.0 + - + +
37G LEU* 3.9 17.5 - - + -
43G VAL* 4.2 16.8 - - + -
72G LEU* 4.0 24.5 - - + -
75G MET* 4.5 1.7 - - + +
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ASP 3.6 1.9 - - - +
18G LYS* 2.9 53.1 + - + +
23G VAL* 4.1 4.4 + - - +
24G ILE* 1.3 72.4 - - - +
26G ILE* 1.3 64.2 + - - +
27G LYS* 4.2 5.3 + - + -
32G GLU* 3.2 32.3 - - + +
33G LEU 3.4 5.6 - - - +
34G THR* 3.1 22.4 + - - +
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 3.6 23.6 - - + -
16G ASP 3.1 11.7 - - - +
17G VAL* 4.8 8.3 - - + -
24G ILE* 3.7 23.1 - - + -
25G THR* 1.3 78.1 - - - +
27G LYS* 1.3 63.3 + - - +
32G GLU* 3.6 1.4 - - - +
33G LEU* 2.9 35.5 + - + +
50G LEU* 4.8 7.9 - - + -
72G LEU* 4.2 24.0 - - + +
75G MET* 4.2 33.4 - - + +
76G VAL* 4.7 9.2 - - + -
79G VAL* 3.8 15.0 - - + +
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Residues in contact with LYS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G VAL* 3.3 11.8 - - - +
16G ASP* 2.9 55.5 + - + +
25G THR* 4.2 6.0 + - + -
26G ILE* 1.3 72.8 - - - +
28G GLY* 1.3 77.5 + - - +
31G GLY* 3.7 4.7 - - - -
32G GLU* 3.6 42.8 - - + +
79G VAL* 4.1 4.3 - - - -
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Residues in contact with GLY 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLY 3.6 13.9 - - - -
15G VAL* 4.8 1.3 - - - -
16G ASP* 4.6 0.7 - - - -
27G LYS* 1.3 90.3 + - - +
29G LYS* 1.3 61.3 + - - -
30G ASN 3.1 3.4 - - - -
31G GLY* 2.9 28.1 + - - +
79G VAL* 3.5 11.4 - - - +
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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