Contacts of the helix formed by residues 26 - 33 (chain I) in PDB entry 1UGH
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 PRO 26 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24I MET 3.9 0.4 - - - -
25I LEU* 1.3 85.8 - - + +
27I GLU* 1.3 65.8 + - - +
29I VAL 3.2 1.6 + - - -
30I GLU* 2.7 30.5 + - - +
36I LYS* 3.6 12.3 - - - +
37I PRO* 3.2 46.5 - - + +
38I GLU 4.6 6.5 - - - +
39I SER* 3.9 15.2 - - - +
40I ASP* 3.1 20.0 - - - +
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Residues in contact with GLU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 3.4 28.2 - - + +
26I PRO* 1.3 79.9 - - - +
28I GLU* 1.3 66.8 + - - +
30I GLU* 3.6 21.6 - - - +
31I GLU* 3.1 30.8 + - + +
36I LYS* 3.1 28.0 + - - +
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E GLY* 3.4 10.9 - - - -
247E SER* 3.1 47.0 + - - +
248E TYR 4.5 0.9 + - - -
267E ALA* 5.6 0.9 - - - -
268E HIS* 4.7 4.9 + - - +
273E SER* 5.2 5.8 + - - -
23I LEU 4.8 0.6 - - - +
24I MET* 3.5 32.5 - - + +
25I LEU* 2.8 32.9 + - + +
27I GLU* 1.3 81.0 - - + +
29I VAL* 1.3 58.9 + - - +
31I GLU* 3.8 7.8 + - - +
32I VAL* 3.4 20.4 - - - +
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Residues in contact with VAL 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LEU* 5.0 7.6 - - + -
24I MET* 3.9 21.8 - - + -
25I LEU 3.0 14.6 + - - +
26I PRO 3.4 7.6 - - - +
28I GLU* 1.3 76.5 - - - +
30I GLU* 1.3 55.2 + - - +
32I VAL* 2.9 7.1 + - - +
33I ILE* 2.7 40.6 + - + +
37I PRO* 3.7 7.2 - - + -
41I ILE* 3.7 27.6 - - + -
58I LEU* 4.6 2.9 - - + -
68I TRP* 3.4 39.0 - - + -
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Residues in contact with GLU 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I PRO 2.7 19.4 + - - +
27I GLU* 3.6 16.4 - - - +
29I VAL* 1.3 71.8 - - - +
31I GLU* 1.3 73.6 + - - +
32I VAL 2.9 0.2 + - - -
34I GLY* 2.7 36.4 + - - +
35I ASN 4.0 12.6 - - - -
36I LYS* 3.6 44.0 - - + +
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E ARG* 3.0 51.0 + - - +
27I GLU* 3.1 19.0 + - + +
28I GLU* 3.9 7.0 - - - +
29I VAL 3.3 0.2 - - - -
30I GLU* 1.3 92.9 - - - +
32I VAL* 1.3 60.0 + - - +
34I GLY* 4.7 0.6 + - - -
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LEU* 3.3 46.7 - - + +
273E SER* 4.7 8.5 - - - -
276E ARG* 3.8 28.3 - - + +
24I MET* 6.1 0.9 - - - -
28I GLU 3.4 17.3 - - - +
29I VAL* 2.9 6.4 + - - +
30I GLU 2.9 0.8 + - - -
31I GLU* 1.3 82.0 - - - +
33I ILE* 1.3 64.9 + - + +
34I GLY 3.5 0.6 + - - -
79I ASN* 4.2 15.9 + - - +
81I ILE* 4.6 5.4 - - - +
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Residues in contact with ILE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LEU* 4.4 11.4 - - + -
29I VAL* 2.7 36.9 + - + +
32I VAL* 1.3 78.5 - - + +
34I GLY* 1.3 56.4 + - - +
35I ASN* 3.5 10.0 + - + +
58I LEU* 4.0 9.4 - - + -
68I TRP* 3.6 28.3 - - + -
69I ALA* 5.4 0.2 - - + -
71I VAL* 3.6 31.6 - - + -
79I ASN* 6.3 0.2 - - - +
81I ILE* 3.2 37.0 - - + +
83I MET* 4.1 15.0 - - + -
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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