Contacts of the helix formed by residues 80 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 1.3 75.7 - - - +
81A PRO* 1.3 61.0 - - - +
83A SER* 2.6 39.3 + - - -
84A ILE* 3.1 8.5 + - - +
220A ILE* 3.3 14.2 - - - +
370A HIS* 3.1 9.3 + - - -
385A ALA* 3.3 29.1 - - - +
422A ILE 2.7 21.6 + - - -
423A PHE* 3.6 6.5 - - - -
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 5.3 1.6 - - - +
59A PHE* 4.3 5.6 - - + -
60A ALA* 3.4 40.6 - - + +
63A PHE* 6.0 2.2 - - + -
79A LEU* 3.5 25.9 - - + +
80A SER* 1.3 85.7 - - - +
82A LEU* 1.3 56.5 + - - +
84A ILE* 3.4 11.3 + - + +
85A SER* 2.8 33.9 + - - -
421A ILE* 3.8 12.3 - - + +
422A ILE 3.8 7.9 - - - +
423A PHE* 3.9 7.2 - - - -
424A MET* 4.2 10.8 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 4.6 11.4 - - + +
80A SER* 3.0 2.9 - - - +
81A PRO* 1.3 76.2 - - - +
83A SER* 1.4 62.6 + - - +
85A SER* 3.3 3.7 + - - +
86A THR* 2.8 40.8 + - - +
124A PHE* 4.0 19.3 - - + -
127A LEU* 4.8 8.3 - - + -
128A ASN* 5.3 0.7 - - - +
131A LEU* 3.5 21.3 - - + -
132A TYR* 3.2 24.7 - - + +
220A ILE* 3.7 15.7 - - + -
420A THR* 4.9 8.5 - - + -
421A ILE 4.0 13.6 + - - +
422A ILE* 4.2 18.2 - - + +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 2.6 35.1 + - - -
82A LEU* 1.4 71.0 - - - +
84A ILE* 1.3 60.6 + - - -
86A THR* 3.2 1.9 + - - -
87A ALA* 3.0 24.1 + - - +
218A ASN* 2.6 34.3 + - - +
220A ILE* 3.7 6.0 - - - +
370A HIS* 4.1 5.4 - - - -
385A ALA* 4.4 5.8 - - - -
386A SER* 3.8 1.4 - - - -
387A THR* 3.2 24.2 + - - -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.4 32.1 - - + -
63A PHE* 3.9 21.5 - - + -
79A LEU* 4.8 2.9 - - + -
80A SER 3.1 4.1 + - - +
81A PRO* 3.7 9.4 - - + +
83A SER* 1.3 77.8 - - - +
85A SER* 1.3 60.6 + - - +
87A ALA 3.4 0.2 + - - -
88A PHE* 3.2 31.9 + - + -
107A PHE* 4.1 4.9 - - + -
330A PHE* 4.3 1.8 - - + -
332A VAL* 3.9 29.8 - - + -
370A HIS* 3.2 41.5 - - + +
387A THR* 3.5 9.6 - - + +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 3.3 36.8 + - - +
59A PHE* 3.5 19.4 - - - -
81A PRO 2.8 21.6 + - - -
82A LEU* 3.3 4.7 + - - -
84A ILE* 1.3 72.2 - - - +
86A THR* 1.3 56.2 + - - +
88A PHE* 4.5 0.2 - - - +
89A ALA* 2.9 31.4 + - - +
107A PHE* 4.4 14.0 - - - +
109A PHE* 4.1 5.2 - - - -
124A PHE* 4.2 5.8 - - - -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 2.8 24.9 + - - +
83A SER* 3.6 1.1 - - - -
85A SER* 1.3 76.4 - - - +
87A ALA* 1.3 64.2 + - - +
89A ALA* 3.0 4.8 + - - +
90A MET* 3.0 27.6 + - + +
124A PHE* 3.3 30.0 - - + -
128A ASN* 4.4 7.3 + - - +
132A TYR* 5.2 1.6 + - - -
143A SER* 6.4 0.4 - - - -
145A ASN* 3.6 19.7 - - - +
167A TYR* 4.5 9.4 - - + -
218A ASN* 3.1 24.2 - - - +
220A ILE* 5.6 0.5 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER 3.0 12.2 + - - +
84A ILE 4.1 0.9 - - - +
86A THR* 1.3 75.9 - - - +
88A PHE* 1.3 63.3 + - + +
90A MET* 3.2 26.4 - - + +
91A THR* 3.3 6.2 + - - -
216A LEU* 3.6 12.5 - - + +
217A VAL 5.5 0.2 - - - -
218A ASN* 4.0 14.3 + - + +
387A THR* 3.5 33.4 - - + +
389A ILE* 3.8 10.5 - - + +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.2 22.9 + - + +
85A SER 4.5 0.7 - - - +
86A THR 3.2 0.4 - - - -
87A ALA* 1.3 76.2 - - + +
89A ALA* 1.3 65.8 + - - +
90A MET 3.0 1.6 - - - -
91A THR* 2.9 17.6 + - - +
92A LYS* 2.9 12.7 + - - +
103A LEU* 4.2 13.3 - - + +
107A PHE* 3.3 39.7 - + + -
109A PHE* 5.2 0.7 - - - -
332A VAL* 3.6 23.1 - - + -
336A LEU* 3.4 27.4 - - + -
341A LEU* 4.2 0.7 - - + -
344A LEU* 4.1 20.4 - - + -
345A PHE* 4.5 4.3 - + - -
368A ALA* 4.1 10.1 - - + -
387A THR* 4.4 15.9 - - + -
389A ILE* 4.3 16.6 - - + -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 2.9 24.3 + - - +
86A THR* 3.7 2.7 - - - +
88A PHE* 1.3 71.1 - - - +
90A MET* 1.3 61.0 + - - +
92A LYS* 3.5 9.5 + - - +
109A PHE* 3.4 33.7 - - + -
120A ILE* 5.5 1.8 - - + -
121A HIS* 2.9 28.5 + - - +
124A PHE* 4.3 9.9 - - + -
167A TYR* 3.7 15.9 - - + +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR* 3.0 22.4 + - + +
87A ALA* 3.2 18.2 - - + +
89A ALA* 1.3 76.3 - - - +
91A THR* 1.4 55.5 + - - +
93A LEU* 3.2 26.0 - - - +
145A ASN* 3.6 44.6 - - - +
147A LEU* 3.6 31.6 - - + -
159A TYR* 3.4 11.7 + - - +
163A SER* 5.0 4.9 - - - +
167A TYR* 4.0 29.1 + - + -
169A ALA* 4.0 4.9 - - - -
216A LEU* 4.4 10.3 - - + -
217A VAL 4.8 3.8 - - - +
218A ASN* 4.6 2.9 - - + +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 3.3 4.0 + - - -
88A PHE* 2.9 14.0 + - + +
90A MET* 1.4 73.2 - - - +
92A LYS* 1.3 54.4 + - - +
93A LEU 2.8 11.3 + - - -
94A GLY* 2.8 15.2 + - - -
95A ALA* 3.4 6.4 + - - +
103A LEU* 4.8 3.4 - - + -
159A TYR* 4.4 6.2 + - - -
216A LEU* 3.4 15.2 - - - +
344A LEU* 4.2 31.9 - - + -
352A LEU* 4.9 10.2 - - + +
355A ILE* 4.9 4.6 - - + +
365A VAL* 4.6 2.7 - - + -
389A ILE* 3.2 33.7 - - + +
391A ILE* 5.4 1.1 - - + -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 5.6 1.6 - - - +
88A PHE 2.9 11.4 + - - +
89A ALA* 3.7 8.1 - - - +
90A MET 3.5 0.6 - - - -
91A THR* 1.3 73.0 - - - +
93A LEU* 1.3 63.4 + - - +
94A GLY 3.2 0.4 - - - -
95A ALA* 3.8 15.5 + - - +
100A LEU* 3.8 22.0 - - + +
103A LEU* 3.7 30.9 - - + +
104A MET* 3.4 30.2 - - - -
109A PHE* 3.7 27.8 - - + -
117A SER* 3.7 17.0 + - - -
120A ILE* 4.6 6.9 - - - +
121A HIS* 3.0 33.7 - - - -
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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