Contacts of the helix formed by residues 90 - 98 (chain H) in PDB entry 1LNU
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 GLN 90 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86H TYR* 3.3 34.7 + - + +
87H TRP 4.0 0.4 + - - -
88H ASN 3.7 0.4 - - - -
89H SER* 1.3 84.8 + - - +
91H PRO* 1.4 65.9 - - - +
92H GLU* 3.2 27.3 - - - +
93H ILE* 2.7 32.3 + - + +
94H LEU* 2.7 30.7 + - - +
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Residues in contact with PRO 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H SER 3.2 11.0 - - - +
90H GLN* 1.4 88.5 - - - +
92H GLU* 1.3 62.9 + - + +
94H LEU* 5.0 2.5 - - + -
95H GLU* 2.8 50.0 + - + +
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Residues in contact with GLU 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H GLN* 3.0 24.0 - - + +
91H PRO* 1.3 83.5 - - + +
93H ILE* 1.3 61.3 + - + +
96H ARG* 3.5 31.3 + - - +
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Residues in contact with ILE 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ASN* 3.4 38.2 - - + +
10H LYS 5.9 1.1 - - - +
86H TYR* 4.0 18.2 - - + +
87H TRP* 3.6 36.6 - - + +
90H GLN* 2.7 27.2 + - + +
92H GLU* 1.3 79.7 - - + +
94H LEU* 1.3 63.7 + - - +
95H GLU 3.3 1.6 - - - -
96H ARG* 3.4 16.7 + - - +
97H THR* 3.1 26.7 + - - -
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Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H TYR* 5.1 2.3 - - + -
71H GLY 4.3 1.3 - - - +
72H GLU* 4.2 9.4 - - + -
73H HIS* 3.1 26.5 - - + +
87H TRP 3.0 9.9 - - - +
88H ASN* 2.4 51.1 - - - +
90H GLN 2.7 15.3 + - - +
91H PRO* 5.0 1.6 - - + -
93H ILE* 1.3 76.1 - - - +
95H GLU* 1.3 60.4 + - + +
96H ARG 3.3 0.2 - - - -
97H THR* 4.0 1.8 - - - -
98H ARG* 2.8 60.6 + - - +
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Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H PRO* 2.8 34.6 + - + +
94H LEU* 1.3 79.6 - - + +
96H ARG* 1.3 64.3 + - - +
98H ARG* 3.4 43.1 + - - +
99H ALA* 3.2 21.8 + - - +
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Residues in contact with ARG 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LYS* 4.0 45.2 - - + +
8H ALA 5.5 3.4 + - - -
9H ASN* 4.4 16.2 + - - +
91H PRO 4.0 1.0 + - - -
92H GLU 3.5 23.6 + - - +
93H ILE* 3.4 16.9 + - - +
95H GLU* 1.3 77.6 - - - +
97H THR* 1.3 66.8 + - - +
99H ALA* 3.1 20.3 + - - +
100H GLU* 3.3 16.0 + - + +
103H THR* 5.0 0.5 + - - -
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Residues in contact with THR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LYS 5.4 1.4 + - - -
9H ASN* 3.7 19.8 + - - +
52H TYR* 4.1 8.1 - - + -
54H THR* 4.3 6.7 - - + +
56H TYR* 5.6 1.6 - - - +
66H TYR* 4.0 22.6 - - + -
73H HIS* 3.7 24.2 - - + -
93H ILE 3.1 15.9 + - - -
94H LEU 4.0 4.5 - - - -
96H ARG* 1.3 75.9 + - - +
98H ARG* 1.3 57.7 + - - +
99H ALA 2.8 10.7 + - - -
100H GLU* 2.8 41.3 + - - +
101H LEU 4.3 0.3 + - - -
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Residues in contact with ARG 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H TYR* 3.0 31.9 + - - -
68H SER 6.1 0.2 - - - -
71H GLY* 3.0 28.8 + - - -
94H LEU* 2.8 47.6 + - - +
95H GLU* 3.4 31.6 + - - +
96H ARG 3.3 0.2 - - - -
97H THR* 1.3 79.4 - - - +
99H ALA* 1.3 57.1 + - - +
101H LEU* 4.3 11.4 + - - +
102H ASP* 4.7 2.8 - - - +
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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