Contacts of the helix formed by residues 82 - 91 (chain F) in PDB entry 4LSZ
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 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F HIS* 3.8 3.1 - - - -
73F VAL 4.7 3.8 - - - -
74F ASN* 4.3 16.6 - - + +
75F ALA 3.3 4.5 - - - +
76F THR* 3.8 24.0 - - + -
80F GLY 4.5 0.4 - - - +
81F MET* 1.3 74.0 - - - +
83F PRO* 1.3 75.2 - - - +
84F LEU* 3.4 11.0 + - - +
85F HIS* 2.9 50.3 + - + +
86F LEU* 3.3 8.8 + - - +
105F ASP 5.3 1.4 + - - +
108F ALA* 4.4 15.2 - - + +
116F PRO* 5.5 0.7 - - - +
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Residues in contact with PRO 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F LEU* 3.8 44.4 - - + +
52F HIS* 3.7 25.8 - - + +
55F ALA* 3.8 6.5 - - + +
72F ASP 4.7 1.8 - - - +
73F VAL 3.5 13.7 - - - +
75F ALA 3.3 15.9 - - - +
82F THR* 1.3 86.5 - - - +
84F LEU* 1.3 55.9 + - - +
86F LEU* 3.3 6.7 + - + +
87F ALA* 3.0 28.4 + - - +
99F LEU* 3.6 15.6 - - + +
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Residues in contact with LEU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F VAL 5.1 0.8 + - - +
74F ASN* 6.1 0.2 - - - +
82F THR* 3.1 9.9 + - - +
83F PRO* 1.3 77.5 - - - +
85F HIS* 1.3 66.5 + - - +
88F ALA* 2.9 26.1 + - + +
96F VAL* 3.9 43.5 - - + +
99F LEU* 3.5 14.2 - - + +
100F LEU* 4.1 8.1 - - + -
104F ALA* 3.9 23.1 - - + -
105F ASP 3.7 22.7 - - - +
106F VAL* 4.0 10.5 - - - -
116F PRO* 3.8 21.1 - - + -
132F LEU* 4.3 7.9 - - + -
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Residues in contact with HIS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F GLY 4.0 5.8 - - - -
81F MET* 3.6 19.3 - - + -
82F THR* 2.9 37.9 + - + +
84F LEU* 1.3 79.4 - - - +
86F LEU* 1.3 63.3 + - + +
88F ALA* 4.8 0.9 - - - -
89F ASP* 3.1 20.4 + - - +
108F ALA* 2.8 40.4 + - + -
109F TYR 4.0 0.2 - - - -
110F ASP* 3.6 23.1 + - + +
114F ASN 3.1 17.7 + - - -
116F PRO* 3.7 16.1 - - + +
119F LEU* 3.3 29.7 - - + +
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C TYR* 6.0 2.9 - - + -
48F GLN* 4.0 15.0 - - - +
52F HIS* 3.4 49.1 - - + +
53F LEU* 6.3 0.2 - - + -
56F GLN* 3.6 41.1 + - + +
81F MET* 3.8 35.9 - - + -
82F THR 3.6 9.2 - - - +
83F PRO* 3.3 6.0 + - + +
84F LEU 3.3 0.4 - - - -
85F HIS* 1.3 76.6 - - - +
87F ALA* 1.3 62.0 + - - +
89F ASP* 3.4 6.8 + - + +
90F ASP* 3.1 26.7 + - - +
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Residues in contact with ALA 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ALA* 4.2 12.7 + - + +
83F PRO 3.0 16.8 + - - +
84F LEU 3.3 3.8 + - - +
86F LEU* 1.3 74.7 - - - +
88F ALA* 1.3 64.5 + - - +
90F ASP 3.2 1.2 + - - -
91F GLY 3.1 19.1 + - - -
92F HIS* 3.2 14.5 + - + +
95F ILE* 3.7 31.0 - - + -
96F VAL* 3.8 15.4 - - + +
99F LEU* 3.9 5.4 - - + -
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Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F LEU* 2.9 18.6 + - + +
85F HIS 3.9 2.9 - - - +
87F ALA* 1.3 76.0 - - - +
89F ASP* 1.3 64.1 + - - +
90F ASP 3.4 0.2 + - - -
91F GLY* 3.5 7.6 + - - -
96F VAL* 3.8 14.2 - - + +
116F PRO* 3.7 35.4 - - + +
119F LEU* 4.4 3.3 - - + -
120F ALA* 4.2 6.7 - - - +
125F HIS* 3.6 15.4 - - - -
128F ILE* 4.3 14.3 - - + +
132F LEU* 4.9 0.2 - - + -
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Residues in contact with ASP 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN 5.8 0.5 - - - +
118C LYS* 3.7 22.9 + - - -
56F GLN* 6.3 0.4 - - - +
85F HIS 3.1 19.2 + - - +
86F LEU* 3.6 8.5 - - - +
87F ALA 3.2 0.2 - - - -
88F ALA* 1.3 79.8 - - - +
90F ASP* 1.3 60.5 + - - +
91F GLY 3.6 0.2 + - - -
119F LEU* 4.2 28.8 - - + +
123F ASP* 3.3 27.2 - - - +
125F HIS* 3.9 4.2 + - - -
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Residues in contact with ASP 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN* 5.2 8.5 + - - +
56F GLN* 3.6 30.7 + - - +
86F LEU 3.1 15.9 + - - +
89F ASP* 1.3 78.2 - - - +
91F GLY* 1.3 61.6 + - - +
92F HIS* 3.5 30.5 + - + +
125F HIS* 4.4 3.6 + - - -
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Residues in contact with GLY 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ALA 3.1 3.4 + - - -
88F ALA 3.5 1.2 + - - -
89F ASP 3.3 3.6 + - - -
90F ASP* 1.3 80.8 - - - +
92F HIS* 1.3 60.1 + - - +
93F LEU* 3.2 9.3 + - - +
125F HIS* 3.6 22.0 + - - -
128F ILE* 3.5 20.9 - - - +
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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