Contacts of the helix formed by residues 90 - 98 (chain I) in PDB entry 1UMN
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 THR 90 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I SER* 1.3 82.8 - - - +
91I LEU* 1.3 65.7 + - - +
92I LYS* 3.8 6.6 + - - +
93I GLU* 2.9 38.3 + - - +
94I PHE* 3.1 25.8 + - - -
41K SER* 3.8 0.9 - - - -
45K GLN* 3.9 2.7 - - - +
102K GLU* 3.4 27.8 - - + -
103K VAL 3.1 31.6 - - - +
104K LEU* 4.4 3.9 - - + +
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Residues in contact with LEU 91 (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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90I THR* 1.3 71.0 - - - +
92I LYS* 1.3 55.0 + - - +
94I PHE* 3.3 20.8 + - + +
95I SER* 2.8 32.0 + - - -
37K SER* 4.6 4.0 - - - +
38K VAL* 3.8 21.1 - - + +
41K SER* 3.7 21.3 - - - +
91K LEU* 4.0 24.2 - - + +
94K PHE* 3.7 32.5 - - + -
95K SER* 3.1 26.9 - - - +
102K GLU* 2.8 21.8 + - - +
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Residues in contact with LYS 92 (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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90I THR* 3.2 6.8 + - - +
91I LEU* 1.3 79.6 - - - +
93I GLU* 1.3 60.7 + - + +
95I SER* 4.5 4.0 - - - -
96I GLU* 2.8 71.0 + - + +
95K SER* 4.4 5.4 + - - +
102K GLU* 4.5 1.0 + - - -
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Residues in contact with GLU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I PRO 4.9 0.7 - - - +
88I PHE* 3.3 36.6 - - + -
89I SER* 3.1 24.0 + - - -
90I THR* 2.9 35.5 + - - +
92I LYS* 1.3 80.4 - - + +
94I PHE* 1.3 65.6 + - - +
96I GLU* 4.8 2.0 - - - -
97I ASN* 2.7 36.1 + - - +
104K LEU* 3.6 26.8 - - + +
105K GLY 5.0 0.7 + - - -
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Residues in contact with PHE 94 (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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33I VAL* 3.9 7.9 - - + -
34I ALA* 3.7 14.6 - - - +
37I SER* 3.5 37.5 - - - -
38I VAL* 4.2 2.0 - - - -
73I LEU* 6.0 0.9 - - + -
88I PHE* 3.3 35.2 - - + -
89I SER* 3.9 17.5 - - - -
90I THR 3.1 13.0 + - - -
91I LEU* 3.5 22.9 - - + +
93I GLU* 1.3 77.5 - - - +
95I SER* 1.3 57.9 + - - +
98I SER* 3.0 35.5 + - - -
41K SER* 4.0 17.7 - - - -
44K HIS* 6.2 2.9 - + + -
48K TRP* 4.6 10.5 - + - -
91K LEU* 3.7 12.8 - - + -
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Residues in contact with SER 95 (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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38I VAL* 4.4 9.8 - - - +
91I LEU 2.8 17.1 + - - -
92I LYS* 3.8 5.2 - - - -
94I PHE* 1.3 79.5 - - - +
96I GLU* 1.3 63.4 + - - +
97I ASN 3.5 0.2 + - - -
98I SER* 3.8 12.6 + - - +
100I LEU 5.2 2.4 - - - +
102I GLU* 4.8 4.5 + - - -
91K LEU* 4.1 16.9 - - - +
92K LYS* 4.9 8.4 + - - +
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Residues in contact with GLU 96 (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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92I LYS* 2.8 64.5 + - + +
93I GLU* 4.3 2.5 - - - +
95I SER* 1.3 75.5 - - - +
97I ASN* 1.3 66.1 + - - +
98I SER 4.4 2.6 - - - +
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Residues in contact with ASN 97 (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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31I GLN* 2.9 26.2 + - - +
34I ALA* 3.9 5.4 - - + -
88I PHE* 3.3 44.8 - - + -
93I GLU* 2.7 38.0 + - - +
96I GLU* 1.3 81.1 - - - +
98I SER* 1.3 64.7 + - - +
99I GLN* 3.7 3.3 + - - +
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Residues in contact with SER 98 (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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31I GLN* 3.9 1.1 - - - +
34I ALA* 3.9 8.4 - - - +
35I ASP* 2.7 23.2 + - - -
38I VAL* 3.5 22.3 - - - +
94I PHE 3.0 19.2 + - - -
95I SER 3.9 11.0 - - - +
96I GLU 3.6 3.0 - - - +
97I ASN* 1.3 80.8 - - - +
99I GLN* 1.3 60.4 + - - +
100I LEU* 3.0 25.9 + - - +
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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