Contacts of the strand formed by residues 18 - 24 (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 ILE 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E HIS* 3.8 25.9 + - + -
152E GLN* 4.9 4.7 - - - +
4I LEU* 5.5 4.9 - - + -
5I SER* 5.1 14.9 - - - +
8I ILE* 3.7 30.1 - - + -
16I LEU 3.9 3.7 + - - +
17I VAL* 1.3 76.5 - - - +
19I GLN* 1.3 60.9 + - - +
20I GLU 3.3 26.5 - - - +
21I SER* 3.9 5.4 - - - +
44I HIS* 3.7 29.6 - - + -
45I THR 3.6 1.8 - - - +
46I ALA* 4.2 7.4 - - + -
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Residues in contact with GLN 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E TYR* 3.3 11.1 - - - -
148E HIS* 5.7 0.9 - - - -
152E GLN* 3.1 35.3 + - - +
164E VAL* 5.5 2.6 - - - +
165E PRO* 4.1 30.9 + - - +
166E PRO 4.7 2.6 + - - -
167E PRO* 4.1 9.8 - - + +
168E PRO* 3.5 27.8 - - + -
17I VAL* 3.8 26.5 - - - +
18I ILE* 1.3 73.3 - - - +
20I GLU* 1.3 62.7 + - - +
45I THR 2.8 9.1 + - - +
46I ALA* 4.6 4.7 - - - -
47I TYR* 4.7 7.2 - - + +
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Residues in contact with GLU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E TYR* 3.8 18.7 + - + -
148E HIS* 5.1 3.8 - - - -
167E PRO* 3.3 16.3 - - - +
168E PRO* 3.5 15.5 - - + +
169E SER* 3.0 50.8 + - - -
270E SER* 4.6 0.7 - - - -
271E PRO* 4.2 4.7 - - - +
18I ILE* 3.3 11.2 - - - +
19I GLN* 1.3 81.2 - - - +
21I SER* 1.3 60.5 + - - +
22I ILE* 4.0 18.5 - - + +
45I THR* 2.8 46.2 + - - +
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Residues in contact with SER 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLN* 4.2 3.6 - - - +
145E ASP* 4.5 11.6 - - - +
148E HIS* 2.8 26.3 + - - -
214E ALA* 3.4 24.4 - - - +
18I ILE* 3.9 0.7 - - - +
20I GLU* 1.3 76.0 + - - +
22I ILE* 1.3 66.7 + - - +
23I LEU 4.0 1.0 + - - -
42I LEU* 4.4 9.2 - - - +
43I VAL 3.3 6.7 - - - -
44I HIS* 3.0 28.3 - - - -
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Residues in contact with ILE 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLN* 3.7 11.7 - - - +
147E TYR* 6.1 2.0 - - + -
158E PHE* 5.4 3.6 - - + -
169E SER* 4.3 5.2 - - - +
268E HIS* 3.4 51.8 - - + +
270E SER* 4.3 4.9 - - - +
20I GLU* 4.0 28.0 - - + +
21I SER* 1.3 79.7 - - - +
23I LEU* 1.3 71.2 + - - +
24I MET* 4.0 16.4 - - + -
41I ILE 3.4 1.6 - - - +
42I LEU* 4.3 1.3 - - - -
43I VAL* 2.8 42.6 + - + +
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Residues in contact with LEU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLN* 2.9 37.2 + - + +
215E ASN* 3.6 22.2 - - - +
248E TYR* 3.7 37.9 - - + +
21I SER 4.0 0.2 + - - -
22I ILE* 1.3 71.6 - - - +
24I MET* 1.3 73.6 + - - +
25I LEU* 5.5 2.0 - - + -
28I GLU* 4.8 0.5 - - - +
40I ASP* 3.5 41.3 - - + +
41I ILE 3.4 9.6 - - - +
42I LEU* 4.0 15.8 - - + +
61I ASP* 4.2 16.2 - - - +
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Residues in contact with MET 24 (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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268E HIS* 4.7 3.6 - - + -
270E SER* 3.7 24.7 - - - +
272E LEU* 4.4 15.9 - - + -
273E SER* 3.7 26.7 - - - +
22I ILE* 4.0 14.4 - - + +
23I LEU* 1.3 82.3 - - - +
25I LEU* 1.3 67.5 + - - +
28I GLU* 3.5 33.4 - - - +
29I VAL* 3.9 17.3 - - + -
32I VAL* 6.1 0.7 - - - -
40I ASP* 3.5 4.7 - - - +
41I ILE* 2.7 38.0 + - - +
43I VAL* 3.7 25.1 - - + -
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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
------------------------------------------------------------
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