Contacts of the helix formed by residues 80 - 90 (chain B) in PDB entry 1ATH
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 PRO 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ASN 5.2 2.5 - - - +
58B PHE* 5.0 4.9 - - + -
59B ALA* 3.6 38.8 - - + +
62B PHE* 6.2 0.4 - - + -
78B LEU* 3.8 22.2 - - + +
79B SER* 1.3 82.4 - - - +
81B LEU* 1.3 65.7 + - - +
83B ILE* 3.2 12.9 + - + +
84B SER* 2.9 27.1 + - - -
420B ILE* 4.4 8.3 - - + +
421B ILE 3.6 11.9 - - - +
422B PHE 4.5 0.2 - - - -
423B MET* 4.2 21.1 - - + -
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Residues in contact with LEU 81 (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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55B ASN* 4.9 9.0 - - + +
79B SER* 3.4 3.7 - - - +
80B PRO* 1.3 78.8 - - - +
82B SER* 1.3 50.6 + - - +
84B SER* 3.2 4.0 + - - -
85B THR* 2.8 52.6 + - - +
123B PHE* 4.2 17.3 - - + -
126B LEU* 4.7 6.3 - - + -
130B LEU* 4.0 15.5 - - + -
131B TYR* 3.3 27.1 - - + +
140B LEU* 6.3 0.4 - - + -
219B ILE* 3.6 15.3 - - + -
419B THR* 4.0 18.6 - - + -
420B ILE 4.0 11.0 + - - +
421B ILE* 4.0 19.0 + - + -
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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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79B SER* 3.2 25.0 + - - -
81B LEU* 1.3 74.8 - - - +
83B ILE* 1.3 63.6 + - - +
85B THR* 2.9 13.0 + - - -
86B ALA* 2.9 12.5 + - - +
217B ASN* 3.1 27.6 + - - +
219B ILE* 3.4 9.6 - - - +
369B HIS* 3.6 3.3 + - - -
384B ALA* 4.4 4.9 - - - -
385B SER* 3.5 7.6 - - - -
386B THR* 2.6 33.2 + - - -
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Residues in contact with ILE 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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58B PHE* 4.3 9.6 - - + -
62B PHE* 4.3 9.2 - - + -
78B LEU* 4.0 23.3 - - + -
79B SER 3.3 16.2 - - - +
80B PRO* 3.2 8.8 + - + +
82B SER* 1.3 72.6 - - - +
84B SER* 1.3 63.3 + - - +
86B ALA 3.5 0.2 + - - -
87B PHE* 3.1 43.7 + - + +
106B PHE* 4.0 13.2 - - + -
329B PHE* 5.1 0.2 - - + -
331B LEU* 4.0 28.0 - - + -
335B LEU* 5.0 1.6 - - + -
369B HIS* 3.3 28.9 - - + +
386B THR* 3.2 9.2 + - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.3 33.5 + - - +
58B PHE* 3.4 26.7 - - - +
80B PRO 2.9 16.4 + - - -
81B LEU* 3.8 4.5 - - - -
83B ILE* 1.3 76.6 - - - +
85B THR* 1.3 57.8 + - - +
88B ALA* 3.0 31.0 + - - +
106B PHE* 3.8 15.7 - - - -
108B PHE* 4.4 2.6 - - - -
123B PHE* 3.8 5.7 - - - -
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Residues in contact with THR 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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81B LEU* 2.8 25.3 + - - +
82B SER 2.9 5.4 + - - -
84B SER* 1.3 74.1 - - - +
86B ALA* 1.3 64.9 + - - +
88B ALA* 3.0 13.4 + - - +
89B MET* 3.1 16.1 + - - +
123B PHE* 3.4 26.9 - - + -
127B ASN* 4.8 6.8 + - - +
131B TYR* 5.0 3.4 + - - +
142B SER* 5.1 1.6 - - - +
144B ASN* 3.7 18.2 - - - +
166B TYR* 5.1 9.5 - - + -
217B ASN* 3.2 28.0 - - - +
219B ILE* 5.5 0.8 - - - +
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Residues in contact with ALA 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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82B SER 2.9 7.4 + - - +
83B ILE 4.0 0.4 - - - +
85B THR* 1.3 74.9 - - - +
87B PHE* 1.3 63.6 + - - +
89B MET* 3.0 25.4 - - + +
90B THR* 3.0 23.0 + - - -
215B LEU 5.4 1.1 - - - +
216B VAL 5.1 0.7 - - - -
217B ASN* 4.0 9.8 - - + +
386B THR* 3.7 39.9 - - + +
388B VAL* 4.3 10.5 - - + +
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Residues in contact with PHE 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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83B ILE* 3.1 34.5 + - + +
86B ALA* 1.3 73.4 - - + +
88B ALA* 1.3 57.0 + - - +
89B MET 2.9 4.7 - - - -
90B THR* 3.1 10.7 + - - -
91B LYS* 2.9 30.2 + - - +
102B LEU* 3.8 23.9 - - + +
106B PHE* 3.6 29.8 - + + -
108B PHE* 5.6 1.1 - - + -
331B LEU* 4.5 0.9 - - + -
335B LEU* 3.4 31.0 - - + -
340B LEU* 4.1 2.9 - - + -
343B LEU* 3.8 21.5 - - + -
344B PHE* 4.3 5.4 - + - -
364B VAL* 5.6 0.2 - - + -
367B ALA* 3.7 23.8 - - + -
386B THR* 4.2 4.7 - - + -
388B VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 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 SER 3.0 22.0 + - - +
85B THR 3.0 3.6 + - - +
87B PHE* 1.3 75.2 - - - +
89B MET* 1.3 56.9 + - - +
91B LYS* 3.7 8.4 - - - +
108B PHE* 3.6 27.7 - - + -
119B ILE* 5.2 1.6 - - + -
120B HIS* 2.9 36.2 + - + -
123B PHE* 3.7 12.3 - - + -
166B TYR* 3.2 15.3 + - + +
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Residues in contact with MET 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 THR* 3.1 8.6 + - - +
86B ALA* 3.0 31.9 - - - +
88B ALA* 1.3 75.4 - - - +
90B THR* 1.3 62.0 + - - +
91B LYS 3.0 1.9 + - - -
92B LEU* 3.1 21.6 + - + +
93B GLY 4.7 0.2 + - - -
144B ASN* 3.6 31.0 - - - +
145B ARG 5.0 2.0 - - - +
146B LEU* 5.0 7.6 - - + -
158B TYR* 4.4 5.5 + - - +
162B SER* 5.6 4.0 - - - +
166B TYR* 4.1 33.9 - - + -
168B ALA* 4.6 7.0 - - + -
215B LEU* 4.0 19.5 - - + +
216B VAL 3.3 35.4 - - - +
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Residues in contact with THR 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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86B ALA 3.0 14.7 + - - -
87B PHE* 3.1 13.3 + - - -
89B MET* 1.3 73.7 - - - +
91B LYS* 1.3 62.1 + - - +
93B GLY* 3.1 14.7 + - - -
94B ALA 3.8 4.9 + - - -
102B LEU* 5.1 2.7 - - + -
158B TYR* 5.4 1.1 - - - -
215B LEU* 3.7 25.1 - - + +
343B LEU* 4.6 10.5 - - + -
351B LEU* 4.1 15.7 - - + +
364B VAL* 4.2 24.7 - - + -
388B VAL* 3.8 21.9 - - + +
390B ILE* 5.0 2.9 - - + -
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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