Contacts of the helix formed by residues 81 - 91 (chain B) in PDB entry 3L73
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 SER 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B THR* 3.8 12.6 - - - -
77B THR 4.8 0.4 - - - -
80B ALA* 1.3 74.2 - - - +
82B SER* 1.3 67.9 + - - +
83B PHE* 2.9 4.6 + - - -
84B ARG* 3.0 16.3 + - - +
85B ILE* 2.8 26.5 + - - +
100S GLU* 5.9 6.5 - - - -
103S GLU* 2.6 35.9 + - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A HIS* 3.8 24.2 + - - -
74B PRO* 3.1 28.0 + - - +
75B LEU* 4.1 5.5 - - - +
76B THR* 3.0 30.2 - - - +
81B SER* 1.3 71.9 - - - +
83B PHE* 1.3 63.9 + - - +
85B ILE* 3.8 1.4 + - - +
86B THR* 3.5 21.8 + - - -
136B GLU* 4.1 6.8 + - - -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A HIS* 3.4 34.9 + + + +
81B SER* 2.9 8.2 + - - +
82B SER* 1.3 77.1 - - - +
84B ARG* 1.3 64.4 + - - +
85B ILE 3.1 0.9 + - - -
86B THR* 3.2 4.0 + - - -
87B ARG* 2.9 82.2 + - + +
103S GLU* 4.2 16.2 - - + +
104S ARG* 3.6 50.0 - - + +
107S TRP* 3.6 26.5 - + + -
108S ASN* 4.0 5.4 - - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY 3.2 13.5 + - - -
80B ALA* 3.1 42.0 - - - +
81B SER* 3.0 15.8 + - - +
83B PHE* 1.3 84.0 - - + +
85B ILE* 1.3 58.0 + - - +
87B ARG* 4.5 1.8 - - - -
88B GLY* 2.6 33.2 + - - +
121B GLU* 2.8 32.5 + - - -
122B TYR* 3.6 17.2 + - - +
103S GLU* 3.9 18.3 + - - +
107S TRP* 3.4 34.8 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER 4.4 4.3 - - - +
74B PRO* 4.0 18.2 - - + +
75B LEU 3.5 24.2 - - - +
77B THR* 4.1 20.2 - - + +
80B ALA* 3.8 15.3 - - + +
81B SER 2.8 27.8 + - - +
82B SER 3.9 4.5 - - - +
84B ARG* 1.3 72.5 - - - +
86B THR* 1.3 61.3 + - - +
89B ILE* 3.0 37.7 + - + +
96B LEU* 4.3 19.1 - - + -
122B TYR* 3.6 25.0 - - + -
125B ASN* 6.0 0.2 - - + -
126B VAL* 4.5 7.9 - - + -
70I LEU* 5.5 1.3 - - + -
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLY* 3.7 33.4 + - - -
289A HIS* 4.0 16.4 - - - +
290A LEU* 3.9 10.1 - - + -
74B PRO* 4.5 10.2 - - - +
82B SER 3.5 11.4 + - - -
83B PHE 3.2 6.0 + - - -
85B ILE* 1.3 74.9 - - - +
87B ARG* 1.3 66.5 + - - +
89B ILE* 4.1 0.3 - - - +
90B GLU* 3.1 48.0 + - - +
70I LEU* 4.1 17.2 - - + +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LYS 5.4 1.6 + - - -
289A HIS* 2.8 25.9 + - - +
290A LEU 3.7 12.8 + - - -
291A SER* 3.4 25.2 + - - +
83B PHE* 2.9 56.6 + - + +
84B ARG* 4.3 0.9 - - - +
86B THR* 1.3 71.6 - - - +
88B GLY* 1.3 59.1 + - - +
90B GLU* 3.2 3.6 + - - +
91B ALA* 2.9 30.1 + - - +
107S TRP* 3.6 33.0 + - + +
108S ASN* 2.9 29.7 + - - +
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG 2.6 24.0 + - - -
87B ARG* 1.3 74.1 - - - +
89B ILE* 1.3 59.6 + - - +
91B ALA* 3.3 16.5 - - - +
92B VAL* 4.0 8.7 + - - +
118B THR* 5.0 4.9 - - - +
122B TYR* 3.7 21.7 - - - -
107S TRP* 3.7 15.7 - - - -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 3.0 24.7 + - + +
86B THR 4.1 2.0 - - - +
88B GLY* 1.3 74.6 - - - +
90B GLU* 1.3 64.5 + - + +
92B VAL* 3.1 14.2 - - - +
94B GLY* 3.0 49.3 + - - +
95B SER* 3.5 11.9 - - - +
96B LEU* 3.4 39.7 - - + -
109B VAL* 5.1 1.6 - - + -
119B VAL* 4.6 15.5 - - + +
122B TYR* 3.7 28.5 - - + -
70I LEU* 4.3 12.3 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A HIS 4.3 0.5 - - - +
290A LEU* 3.6 19.6 - - - +
291A SER* 2.8 47.7 + - - +
292A SER 5.5 0.5 + - - -
356A ARG* 3.2 20.2 - - - +
360A HIS* 5.7 0.9 - - - +
86B THR* 3.1 29.6 + - + +
87B ARG 3.7 3.1 - - - +
89B ILE* 1.3 74.0 - - + +
91B ALA* 1.3 63.4 + - - +
92B VAL 3.1 3.1 - - - -
93B GLY* 3.1 14.4 + - - +
94B GLY 4.4 3.8 - - - +
70I LEU* 4.9 7.0 - - + -
71I ASN* 3.8 22.5 - - - +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS* 5.1 4.7 - - - +
356A ARG* 4.1 18.0 - - - +
359A ASN* 3.0 17.2 + - - -
87B ARG 2.9 12.6 + - - +
88B GLY* 3.3 17.7 - - - +
89B ILE 3.1 0.4 - - - -
90B GLU* 1.3 77.1 - - - +
92B VAL* 1.3 62.5 + - + +
93B GLY 3.5 0.2 - - - -
107S TRP* 4.9 9.0 - - + +
110S LYS* 5.4 6.3 - - - +
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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