Contacts of the helix formed by residues 26 - 34 (chain J) in PDB entry 6ALG
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 26 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J LEU 3.7 4.8 + - - -
25J ALA* 1.3 75.4 - - - +
27J PRO* 1.3 71.4 - - - +
28J ASP* 3.3 14.5 + - - +
29J MET* 3.1 19.2 + - - +
30J ILE* 2.9 26.7 + - - +
236J TRP* 3.3 43.8 + - - -
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Residues in contact with PRO 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ALA 4.1 3.1 - - - +
26J SER* 1.3 90.5 - - - +
28J ASP* 1.3 58.2 + - - +
30J ILE* 3.3 11.7 + - + +
31J ARG* 3.0 48.8 + - - +
235J GLU 6.1 0.2 - - - +
236J TRP* 3.9 22.0 - - + +
238J ILE 5.5 2.7 - - - +
240J THR* 4.0 34.5 - - + +
241J VAL* 4.7 7.6 - - + +
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Residues in contact with ASP 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J SER* 3.3 10.0 + - - +
27J PRO* 1.3 79.6 - - - +
29J MET* 1.3 57.2 + - - +
31J ARG* 3.3 23.0 + - - +
32J SER* 2.9 30.1 + - - -
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Residues in contact with MET 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336I ASN* 4.1 25.1 - - - +
1338I GLU* 5.3 2.9 - - - +
24J LEU 5.7 0.2 - - - +
25J ALA* 5.2 0.2 - - - -
26J SER* 3.1 27.4 + - - +
28J ASP* 1.3 76.7 - - - +
30J ILE* 1.3 59.7 + - - +
32J SER* 3.0 15.7 + - - -
33J TRP* 3.0 49.0 + - + -
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Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334I GLY* 5.3 0.4 - - - -
25J ALA* 3.8 24.0 - - + +
26J SER 2.9 18.1 + - - +
27J PRO* 3.7 11.4 - - + +
29J MET* 1.3 75.6 - - - +
31J ARG* 1.3 62.9 + - - +
33J TRP* 3.1 39.0 + - + +
34J SER* 3.2 13.0 + - - -
103J GLY 5.3 0.4 - - - +
104J HIS* 4.4 6.5 - - + -
239J LEU* 4.9 7.9 - - + -
241J VAL* 3.5 39.7 - - + +
243J PRO* 3.7 31.2 - - + -
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Residues in contact with ARG 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PRO* 3.0 37.1 + - - +
28J ASP* 3.6 24.0 + - - +
30J ILE* 1.3 77.2 - - - +
32J SER* 1.3 60.6 + - - +
34J SER* 3.7 17.2 + - - +
104J HIS* 4.8 11.4 - - + +
106J GLU* 3.2 38.2 + - - +
240J THR* 4.6 8.1 - - - +
241J VAL* 3.4 17.8 - - + +
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Residues in contact with SER 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ASP 2.9 17.6 + - - -
29J MET* 3.0 21.4 + - - -
31J ARG* 1.3 76.6 - - - +
33J TRP* 1.3 64.8 + - - +
34J SER 4.1 3.6 - - - +
35J PHE* 5.9 1.2 - - - -
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Residues in contact with TRP 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331I ARG* 3.6 61.4 - - + +
1333I LEU 4.9 0.4 - - - -
1336I ASN* 3.2 49.4 + - + -
25J ALA* 4.1 11.2 - - + -
29J MET* 3.0 30.5 + - + +
30J ILE* 3.1 39.2 + - + +
32J SER* 1.3 79.8 - - - +
34J SER* 1.3 65.1 + - - +
35J PHE* 3.7 15.2 - - - -
102J MET* 4.4 24.4 + - + +
243J PRO* 4.9 3.4 - - + -
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Residues in contact with SER 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE 3.2 14.2 + - - -
31J ARG* 3.7 11.4 + - - +
32J SER 3.3 6.7 - - - +
33J TRP* 1.3 82.9 - - - +
35J PHE* 1.3 82.6 + - - +
36J GLY 3.2 4.7 + - - -
102J MET 4.2 7.0 - - - -
103J GLY* 3.3 18.4 - - - +
104J HIS* 2.6 39.8 + - - -
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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