Contacts of the helix formed by residues 90 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A PHE 3.9 0.2 - - - -
89A SER* 1.3 83.5 - - - +
91A LEU* 1.3 65.7 + - - +
92A LYS* 4.0 8.1 + - - +
93A GLU* 2.7 41.7 + - - +
94A PHE* 3.1 27.6 + - - -
41C SER* 3.8 0.9 - - - -
45C GLN* 3.8 1.3 - - - +
102C GLU* 3.5 27.6 - - + -
103C VAL 3.1 34.5 - - - +
104C LEU* 4.4 2.1 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 1.3 70.7 - - - +
92A LYS* 1.3 56.8 + - - +
94A PHE* 3.1 20.0 + - + +
95A SER* 2.8 34.3 + - - -
37C SER 4.7 5.2 - - - +
38C VAL* 4.0 15.0 - - + -
41C SER* 3.9 21.1 - - - +
91C LEU* 3.8 29.1 - - + +
94C PHE* 3.6 36.8 - - + -
95C SER* 3.9 17.5 - - - +
102C GLU* 2.9 23.2 + - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 3.2 7.4 - - - +
91A LEU* 1.3 78.6 - - - +
93A GLU* 1.3 62.3 + - + +
95A SER* 3.4 4.3 + - - -
96A GLU* 2.9 75.6 + - + +
95C SER* 4.9 7.5 + - - +
102C GLU* 4.6 0.6 + - - -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 4.5 0.2 - - - +
87A PRO 5.1 0.3 - - - +
88A PHE* 3.5 37.0 - - + -
89A SER* 3.1 24.6 + - - -
90A THR* 2.7 35.4 + - - +
92A LYS* 1.3 81.2 - - + +
94A PHE* 1.3 64.8 + - - +
96A GLU* 4.8 2.7 - - - +
97A ASN* 2.7 37.8 + - - +
104C LEU* 3.5 28.2 - - + +
105C GLY 5.0 0.5 + - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.7 9.4 - - + -
34A ALA* 3.8 14.3 - - - +
37A SER* 3.5 36.1 - - - -
38A VAL* 3.7 2.4 - - - +
73A LEU* 6.0 0.2 - - + -
88A PHE* 3.3 39.0 - - + -
89A SER* 3.8 11.9 - - - -
90A THR 3.1 15.2 + - - -
91A LEU* 3.4 23.1 - - + +
93A GLU* 1.3 74.8 - - - +
95A SER* 1.3 63.0 + - - +
98A SER* 3.0 30.0 + - - -
41C SER* 4.0 18.4 - - - -
44C HIS* 6.2 1.8 - + + -
48C TRP* 4.4 11.9 - + - -
91C LEU* 3.6 13.2 - - + -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.5 7.6 - - - -
91A LEU 2.8 23.0 + - - -
92A LYS* 3.9 4.5 - - - -
94A PHE* 1.3 75.2 - - - +
96A GLU* 1.3 64.7 + - - +
98A SER* 3.8 13.0 + - - +
100A LEU 5.3 2.1 - - - +
102A GLU* 4.9 1.7 + - - -
91C LEU* 3.3 27.9 - - - +
92C LYS* 4.6 3.4 + - - +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 2.9 62.7 + - + +
93A GLU* 4.2 3.6 - - - +
95A SER* 1.3 78.9 - - - +
97A ASN* 1.3 65.8 + - - +
98A SER 4.5 1.9 - - - +
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 2.9 27.6 + - - +
34A ALA* 3.8 5.6 - - + -
88A PHE* 3.2 46.5 - - + -
93A GLU* 2.7 38.4 + - - +
96A GLU* 1.3 82.8 + - - +
98A SER* 1.3 63.0 + - - +
99A GLN* 3.7 3.8 + - - +
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.9 1.6 - - - +
34A ALA* 3.8 7.7 - - - +
35A ASP* 2.8 22.2 + - - -
38A VAL* 3.4 22.2 - - - +
94A PHE 3.0 19.9 + - - -
95A SER 3.8 11.2 + - - +
96A GLU 3.6 2.5 - - - +
97A ASN* 1.3 80.1 - - - +
99A GLN* 1.3 59.0 + - - +
100A LEU* 3.0 27.6 + - - +
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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