Contacts of the helix formed by residues 17 - 28 (chain U) 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 SER 17 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1338A G 3.4 19.3 + - - -
1339A G 3.1 26.9 + - - -
1392A A 5.7 0.3 + - - -
15U HIS* 4.3 3.1 - - - -
16U VAL* 1.3 77.6 - - - +
18U GLU* 1.3 60.7 + - - +
19U LYS* 2.5 29.6 + - - +
20U ALA* 3.7 11.4 - - - +
21U SER* 3.0 26.4 + - - -
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Residues in contact with GLU 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1338A G 5.8 1.4 - - - -
1392A A 3.7 35.9 + - - +
1393A A 5.3 0.6 + - - +
17U SER* 1.3 74.4 + - - +
19U LYS* 1.3 64.6 + - - +
21U SER* 3.2 6.6 + - - -
22U THR* 2.8 38.1 + - - +
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Residues in contact with LYS 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339A G 3.6 30.2 + - - +
1340A U 2.6 24.2 + - - +
1341A G 3.2 26.3 + - - -
1393A A 4.7 14.2 - - + +
1394A U 3.2 27.2 + - - +
17U SER* 2.5 20.3 + - - +
18U GLU* 1.3 72.6 - - - +
20U ALA* 1.3 64.8 + - - +
22U THR* 3.3 5.2 + - - -
23U ALA* 2.9 24.4 + - + +
84U TYR* 3.4 23.1 - - + +
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Residues in contact with ALA 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A G 4.7 0.6 + - - +
15U HIS* 3.7 20.2 - - + +
16U VAL* 4.3 1.1 - - - -
17U SER* 3.3 20.8 + - - +
19U LYS* 1.3 79.7 - - - +
21U SER* 1.3 63.5 + - - +
23U ALA* 3.1 6.1 + - - +
24U MET* 2.9 22.3 + - - +
29U THR 4.5 1.6 - - - +
31U VAL* 3.6 32.8 - - + +
84U TYR* 5.5 0.2 - - - -
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Residues in contact with SER 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U SER 3.0 14.5 + - - -
18U GLU* 3.2 12.0 + - - -
20U ALA* 1.3 77.2 - - - +
22U THR* 1.3 60.7 + - - +
24U MET* 2.8 37.5 + - - +
25U GLU* 3.0 19.7 + - - +
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Residues in contact with THR 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18U GLU* 2.8 30.9 + - - +
19U LYS* 3.8 4.9 - - - -
21U SER* 1.3 76.9 - - - +
23U ALA* 1.3 57.7 + - - +
25U GLU* 4.0 6.0 - - + +
26U LYS* 2.9 51.9 + - + +
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Residues in contact with ALA 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341A G 5.5 10.1 - - - +
19U LYS* 2.9 16.4 + - + +
20U ALA* 3.4 11.0 - - - +
22U THR* 1.3 77.8 - - - +
24U MET* 1.3 57.9 + - - +
26U LYS* 5.1 0.4 - - - -
27U SER* 2.9 34.3 + - - +
28U ASN 3.1 6.4 + - - -
29U THR* 3.4 22.0 + - + +
31U VAL* 5.1 4.5 - - + -
84U TYR* 5.3 6.5 - - + -
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Residues in contact with MET 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ALA 2.9 10.1 + - - +
21U SER* 2.8 31.0 + - - +
23U ALA* 1.3 76.5 - - - +
25U GLU* 1.3 86.9 + - + +
28U ASN* 3.1 23.6 + - - +
29U THR 3.1 19.0 + - - +
30U ILE* 5.5 0.4 - - + -
93U LEU* 4.2 20.9 - - + -
95U PHE* 4.7 20.0 - - - -
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Residues in contact with GLU 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U SER* 3.0 19.3 + - - +
22U THR* 4.0 5.8 - - + +
24U MET* 1.3 99.3 - - + +
26U LYS* 1.3 65.7 + - + +
28U ASN* 4.3 1.7 + - - +
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Residues in contact with LYS 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390A U 5.3 10.0 + - - -
22U THR* 2.9 34.3 + - + +
23U ALA* 5.1 0.4 - - - -
25U GLU* 1.3 84.1 - - + +
27U SER* 1.3 61.9 + - - +
28U ASN* 3.8 0.3 + - - +
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Residues in contact with SER 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341A G 5.1 3.3 + - - -
1398A C 4.1 19.2 + - - -
1399A C 4.1 18.8 + - - -
23U ALA* 2.9 21.6 + - - -
26U LYS* 1.3 75.3 - - - +
28U ASN* 1.3 70.1 + - - +
29U THR* 3.3 15.7 + - - -
86U THR* 4.6 9.4 - - - +
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Residues in contact with ASN 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U ALA 3.1 2.8 + - - -
24U MET 3.1 16.0 + - - +
25U GLU 4.3 1.5 + - - +
26U LYS 3.5 2.6 + - - +
27U SER* 1.3 81.1 - - - +
29U THR* 1.3 58.9 + - - +
86U THR* 4.2 0.2 - - - -
87U LEU* 3.2 38.1 + - - +
88U LYS 3.5 23.2 + - - -
89U GLU* 3.7 16.8 + - - +
91U GLN 3.7 18.1 + - - +
93U LEU* 4.2 15.3 - - - +
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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