Contacts of the helix formed by residues 80 - 92 (chain B) in PDB entry 1ATT
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 1.3 76.3 - - - +
81B PRO* 1.3 64.5 - - - +
82B LEU 3.6 0.3 + - - -
83B SER* 3.1 20.4 + - - -
84B ILE* 3.5 1.7 + - - +
220B ILE* 3.8 11.4 - - - +
370B HIS* 3.3 25.4 + - - -
372B ALA* 5.0 0.4 - - - +
385B ALA* 3.5 27.8 - - - -
422B ILE 2.8 18.9 + - - -
423B PHE* 3.7 10.3 - - - -
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASN 4.9 4.0 - - - +
59B PHE* 4.7 6.4 - - + -
60B ALA* 3.4 40.2 - - + +
63B PHE* 6.0 2.5 - - + -
79B LEU* 3.9 17.0 - - + +
80B SER* 1.3 84.2 - - - +
82B LEU* 1.3 56.9 + - - +
84B ILE* 3.2 9.7 + - + +
85B SER* 2.9 31.6 + - - -
421B ILE* 4.1 13.0 - - + +
422B ILE 3.2 20.2 - - - +
423B PHE* 4.1 3.6 - - - -
424B MET* 4.3 11.7 - - + +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASN* 5.2 9.0 - - - +
80B SER 3.2 0.2 - - - -
81B PRO* 1.3 80.5 - - - +
83B SER* 1.3 61.5 + - - +
85B SER* 4.7 2.5 - - - +
86B THR* 3.0 41.1 + - - +
124B PHE* 4.7 10.8 - - + -
127B LEU* 5.4 3.6 - - + -
128B ASN* 5.2 2.0 - - - +
131B LEU* 3.5 21.5 - - + -
132B TYR* 2.9 29.6 - - + +
141B LEU* 5.8 0.4 - - + -
218B ASN* 4.5 0.2 - - - +
220B ILE* 3.5 18.2 - - + -
420B THR* 4.2 19.1 - - + -
421B ILE 4.0 6.3 + - - +
422B ILE* 3.9 21.1 - - + +
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Residues in contact with SER 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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80B SER* 3.1 21.6 + - - -
82B LEU* 1.3 78.6 - - - +
84B ILE* 1.3 62.2 + - - +
86B THR* 3.7 1.4 - - - -
87B ALA* 3.0 20.8 + - - +
218B ASN* 3.0 26.8 + - - +
220B ILE* 3.9 3.5 - - - +
370B HIS* 3.8 5.2 - - - -
385B ALA* 4.4 8.5 - - - -
386B SER* 3.3 4.2 - - - -
387B THR* 2.7 38.0 + - - -
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 4.2 10.8 - - + -
63B PHE* 3.8 35.2 - - + -
79B LEU* 3.8 7.4 - - + -
80B SER 3.7 5.2 - - - +
81B PRO* 3.2 5.8 + - + +
83B SER* 1.3 74.5 - - - +
85B SER* 1.3 65.4 + - - +
87B ALA 3.1 10.7 + - - -
88B PHE* 3.3 28.8 + - + -
107B PHE* 4.3 9.9 - - + -
330B PHE* 4.5 0.4 - - + -
332B VAL* 3.8 28.3 - - + -
370B HIS* 3.3 34.5 - - + +
387B THR* 3.5 8.1 - - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASN* 3.1 40.7 + - - +
59B PHE* 4.2 7.3 - - - -
81B PRO 2.9 20.0 + - - -
82B LEU* 4.3 4.7 - - - -
84B ILE* 1.3 70.7 - - - +
86B THR* 1.3 58.9 + - - +
88B PHE* 3.6 1.0 + - - +
89B ALA* 2.9 30.5 + - - +
107B PHE* 3.8 23.7 + - - -
109B PHE* 4.1 9.7 - - - -
124B PHE* 4.3 2.7 - - - -
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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
----------------------------------------------------------
82B LEU* 3.0 25.9 + - - +
83B SER 3.7 3.1 - - - -
85B SER* 1.3 76.2 - - - +
87B ALA* 1.3 63.5 + - - +
89B ALA* 3.2 2.5 + - - +
90B MET* 2.9 28.4 + - + +
124B PHE* 3.1 28.2 - - + -
128B ASN* 5.0 6.1 + - - +
132B TYR* 5.5 0.8 + - - +
143B SER* 5.3 1.1 - - - +
145B ASN* 3.7 28.9 - - - +
167B TYR* 4.6 12.5 - - + -
218B ASN* 4.0 11.9 - - - +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER 3.0 15.3 + - - +
84B ILE 3.1 2.0 + - - +
86B THR* 1.3 72.7 - - - +
88B PHE* 1.3 61.6 + - + +
90B MET* 3.4 19.6 - - + +
91B THR* 3.1 23.7 + - - -
216B LEU* 4.4 5.8 - - + +
218B ASN* 4.5 8.7 - - + +
387B THR* 3.5 35.2 - - + -
389B ILE* 3.7 13.1 - - + +
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Residues in contact with PHE 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 ILE* 3.3 29.0 + - + -
86B THR 3.2 0.4 - - - -
87B ALA* 1.3 80.0 - - + +
89B ALA* 1.3 59.8 + - - +
91B THR* 2.9 10.5 + - - -
92B LYS* 2.9 29.0 + - - +
103B LEU* 4.0 8.5 - - + +
107B PHE* 3.2 41.1 - + + -
109B PHE* 5.1 1.1 - - - -
332B VAL* 4.6 4.0 - - + -
336B LEU* 3.5 11.9 - - + -
341B LEU* 3.5 24.0 - - + -
344B LEU* 3.6 20.9 - - + -
345B PHE* 4.2 4.9 - + - -
365B VAL* 5.5 0.7 - - + -
368B ALA* 4.0 19.7 - - + -
387B THR* 4.5 4.7 - - + -
389B ILE* 3.4 28.9 - - + -
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Residues in contact with ALA 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 SER 2.9 19.6 + - - +
86B THR* 3.6 5.8 - - - +
88B PHE* 1.3 75.7 - - - +
90B MET* 1.4 56.5 + - - +
92B LYS* 3.4 6.4 - - - +
109B PHE* 3.5 28.8 - - + -
120B ILE* 5.6 1.1 - - + -
121B HIS* 3.0 31.2 + - + -
124B PHE* 3.8 17.7 - - + -
167B TYR* 3.9 13.5 - - + +
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 2.9 14.7 + - + +
87B ALA* 3.4 24.0 - - - +
89B ALA* 1.4 72.4 - - - +
91B THR* 1.3 65.2 + - - +
93B LEU* 2.8 26.3 + - + +
145B ASN* 3.5 21.5 - - + +
147B LEU* 4.4 15.0 - - + -
159B TYR* 4.4 3.8 - - - +
163B SER* 5.6 4.0 - - - +
167B TYR* 3.5 47.8 - - + -
169B ALA* 4.5 2.5 - - - -
216B LEU* 3.9 24.9 - - + -
217B VAL 3.5 30.5 - - - +
218B ASN* 4.6 0.4 - - + -
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Residues in contact with THR 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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87B ALA 3.1 11.9 + - - -
88B PHE* 2.9 15.7 + - - -
90B MET* 1.3 71.2 - - - +
92B LYS* 1.3 60.9 + - - +
93B LEU 2.9 1.7 + - - -
94B GLY* 3.0 14.1 + - - +
95B ALA* 3.1 8.8 + - - +
103B LEU* 4.3 1.8 - - + -
159B TYR* 5.4 2.5 - - - -
216B LEU* 3.7 18.9 - - - +
344B LEU* 3.9 22.2 - - + -
352B LEU* 3.8 28.6 - - + +
355B ILE* 5.4 2.2 - - + +
365B VAL* 4.8 6.7 - - + -
389B ILE* 4.0 12.3 - - + +
391B ILE* 4.6 8.3 - - + -
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Residues in contact with LYS 92 (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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20B PRO* 5.4 1.6 - - - +
88B PHE 2.9 14.5 + - - +
89B ALA* 3.4 16.2 - - - +
90B MET 2.9 0.2 + - - -
91B THR* 1.3 71.5 - - - +
93B LEU* 1.3 60.9 + - - +
95B ALA* 3.5 10.6 + - - +
100B LEU* 3.7 24.1 - - + +
103B LEU* 3.6 34.9 - - + +
104B MET* 2.9 33.0 - - - -
109B PHE* 3.5 19.5 - - + -
117B SER* 3.2 25.6 + - - +
120B ILE* 3.3 16.6 - - - +
121B HIS* 3.6 14.0 + - - +
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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