Contacts of the helix formed by residues 90 - 98 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E SER* 3.9 0.9 - - - -
45E GLN* 3.8 1.3 - - - +
102E GLU* 3.4 25.4 - - + -
103E VAL 3.2 32.5 - - - +
104E LEU* 4.4 4.4 - - + +
89G SER* 1.3 85.0 - - - +
91G LEU* 1.3 65.8 + - - +
92G LYS* 3.8 8.4 + - - +
93G GLU* 2.8 45.2 + - - +
94G PHE* 3.0 19.4 + - - -
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Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E SER* 4.8 3.4 - - - +
38E VAL* 4.1 17.9 - - + +
41E SER* 3.7 22.7 - - - +
91E LEU* 4.0 24.5 - - + +
94E PHE* 3.7 36.1 - - + -
95E SER* 4.0 20.2 - - - +
102E GLU* 2.9 21.3 + - - +
90G THR* 1.3 71.5 - - - +
92G LYS* 1.3 57.0 + - - +
94G PHE* 3.6 20.2 - - + +
95G SER* 2.9 33.8 + - - -
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Residues in contact with LYS 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E SER* 5.1 6.7 + - - +
102E GLU* 4.5 1.2 + - - -
90G THR* 3.0 8.6 - - - +
91G LEU* 1.3 79.2 - - - +
93G GLU* 1.3 65.0 + - + +
95G SER* 4.1 2.9 - - - -
96G GLU* 2.8 74.1 + - - +
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Residues in contact with GLU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 3.5 27.3 - - + +
105E GLY 5.1 0.3 + - - -
87G PRO 5.2 0.3 - - - +
88G PHE* 3.5 34.7 - - + -
89G SER* 3.1 22.4 + - - -
90G THR* 2.8 33.7 + - - +
92G LYS* 1.3 77.4 - - + +
94G PHE* 1.3 66.4 - - - +
96G GLU* 4.9 1.8 - - - -
97G ASN* 3.0 37.3 + - - +
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Residues in contact with PHE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 4.0 17.9 - - - -
44E HIS* 6.2 2.7 - + + -
48E TRP* 4.4 11.7 - + - -
91E LEU* 3.8 11.9 - - + -
33G VAL* 3.9 6.1 - - + -
34G ALA* 3.8 14.0 - - - +
37G SER* 3.5 39.0 - - - -
38G VAL* 4.1 2.9 - - - -
73G LEU* 6.2 0.2 - - + -
88G PHE* 3.2 41.1 - - + -
89G SER* 3.8 13.7 - - - -
90G THR 3.0 15.9 + - - -
91G LEU* 3.6 22.9 - - + +
92G LYS 3.3 0.2 - - - -
93G GLU* 1.3 77.1 - - - +
95G SER* 1.3 57.6 + - - +
98G SER* 2.9 34.3 + - - -
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Residues in contact with SER 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E LEU* 4.1 18.2 - - - +
92E LYS* 5.0 7.7 + - - +
38G VAL* 4.2 10.7 - - - +
91G LEU 2.9 17.7 + - - -
92G LYS* 4.1 3.1 - - - -
94G PHE* 1.3 78.7 - - - +
96G GLU* 1.3 63.9 + - - +
98G SER* 3.8 12.8 + - - +
100G LEU 5.3 2.4 - - - +
102G GLU* 4.8 4.0 + - - -
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Residues in contact with GLU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LYS* 2.8 62.1 + - + +
93G GLU* 4.3 2.0 - - - +
95G SER* 1.3 80.2 - - - +
97G ASN* 1.3 64.9 + - - +
98G SER 4.2 2.9 - - - +
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Residues in contact with ASN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G PRO* 6.2 0.2 - - - +
31G GLN* 2.9 27.3 + - - +
34G ALA* 3.7 6.7 - - + -
88G PHE* 3.0 46.8 - - + -
93G GLU* 3.0 34.5 + - - +
96G GLU* 1.3 83.5 + - - +
98G SER* 1.3 60.9 + - - +
99G GLN* 4.3 3.8 + - - +
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Residues in contact with SER 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G GLN* 3.9 0.9 - - - +
34G ALA* 3.8 8.9 - - - +
35G ASP* 2.8 21.9 + - - -
38G VAL* 3.3 24.4 - - - +
94G PHE 2.9 17.9 + - - -
95G SER 3.8 10.8 + - - +
96G GLU 3.5 3.3 - - - +
97G ASN* 1.3 80.1 - - - +
99G GLN* 1.3 60.5 + - - +
100G LEU* 3.0 26.3 + - - +
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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