Contacts of the helix formed by residues 80 - 91 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASN* 5.1 2.0 - - - +
58A PHE* 5.0 6.7 - - + -
59A ALA* 3.6 31.0 - - + +
62A PHE* 5.7 2.2 - - + -
78A LEU* 3.1 28.7 - - + +
79A SER* 1.3 80.5 - - - +
81A LEU* 1.3 56.7 + - - +
83A ILE* 3.2 12.4 + - + +
84A SER* 2.8 33.3 + - - +
420A ILE* 4.9 4.9 - - + +
421A ILE 4.2 5.8 - - - +
422A PHE 4.4 1.1 - - - -
423A MET* 3.6 31.4 - - + +
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Residues in contact with LEU 81 (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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55A ASN* 4.1 21.1 - - + +
79A SER* 3.2 3.4 + - - +
80A PRO* 1.3 76.7 - - - +
82A SER* 1.3 61.5 + - - +
84A SER* 4.6 2.0 - - - +
85A THR* 2.7 47.7 + - - +
123A PHE* 4.9 1.6 - - + -
126A LEU* 4.4 8.5 - - + -
127A ASN* 5.2 2.0 - - - +
130A LEU* 3.8 19.1 - - + -
131A TYR* 3.4 26.2 - - - +
219A ILE* 3.6 16.4 - - + -
419A THR* 4.0 24.5 - - + -
420A ILE 3.7 18.5 + - - +
421A ILE* 4.3 9.2 + - + -
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Residues in contact with SER 82 (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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79A SER* 2.8 30.1 + - - -
81A LEU* 1.3 73.2 - - - +
83A ILE* 1.3 51.5 + - - +
85A THR* 3.6 4.8 - - - -
86A ALA* 2.7 37.8 + - - +
144A ASN* 3.9 7.7 + - - +
217A ASN* 3.7 11.0 - - - -
218A THR* 3.9 16.3 - - - -
219A ILE* 3.7 21.3 - - - +
369A HIS* 3.1 17.8 + - - -
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Residues in contact with ILE 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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58A PHE* 3.8 21.3 - - + -
62A PHE* 3.9 28.5 - - + -
78A LEU* 4.0 18.4 - - + -
79A SER 3.7 9.0 - - - +
80A PRO* 3.2 10.4 + - + +
82A SER* 1.3 78.4 + - - +
84A SER* 1.3 62.9 + - - +
86A ALA* 3.0 7.6 + - - +
87A PHE* 3.1 37.7 + - + -
106A PHE* 4.1 4.9 - - + -
217A ASN* 3.8 16.6 + - - +
329A PHE* 5.0 0.2 - - + -
331A LEU* 4.1 20.0 - - + -
335A LEU* 5.4 1.6 - - + -
369A HIS* 4.3 13.5 - - + +
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Residues in contact with SER 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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55A ASN* 4.0 31.4 + - - +
58A PHE* 3.6 25.6 - - - +
80A PRO* 2.8 20.7 + - - +
81A LEU* 4.1 4.5 - - - -
83A ILE* 1.3 72.2 - - - +
85A THR* 1.3 57.0 + - - +
87A PHE* 3.6 1.0 + - - +
88A ALA* 3.0 29.8 + - - +
106A PHE* 4.5 11.8 + - - +
108A PHE* 3.7 12.2 - - - -
123A PHE* 4.1 4.0 - - - -
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Residues in contact with THR 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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81A LEU* 2.7 38.7 + - + +
82A SER* 3.6 5.4 - - - -
84A SER* 1.3 74.9 - - - +
86A ALA* 1.3 64.3 + - - +
88A ALA* 3.2 2.6 + - - +
89A MET* 3.0 23.4 + - + +
123A PHE* 3.1 29.8 - - + -
127A ASN* 4.4 11.6 + - - +
131A TYR* 5.4 3.1 - - + +
144A ASN* 5.0 8.1 - - - +
166A TYR* 3.7 23.5 - - + +
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Residues in contact with ALA 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 SER 2.7 20.3 + - - +
83A ILE 3.0 2.7 + - - +
85A THR* 1.3 71.6 - - - +
87A PHE* 1.3 59.2 + - + +
89A MET* 3.2 12.1 + - - +
90A THR* 3.0 29.1 + - - -
144A ASN* 3.1 28.2 - - - +
215A LEU* 3.9 11.9 - - + -
217A ASN* 3.4 23.3 - - - +
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Residues in contact with PHE 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 ILE* 3.1 34.0 + - + +
84A SER 4.2 2.2 - - - +
86A ALA* 1.3 78.9 - - + +
88A ALA* 1.3 58.3 + - - +
90A THR* 3.1 8.2 + - + -
91A LYS* 2.8 28.6 + - - +
102A LEU* 4.4 6.2 - - + +
106A PHE* 3.4 41.1 - + + -
108A PHE* 5.3 1.1 - - - -
215A LEU* 3.7 21.1 - - + -
217A ASN* 5.1 1.3 - - - -
331A LEU* 4.5 9.6 - - + -
335A LEU* 3.4 32.3 - - + -
340A LEU* 4.5 2.5 - - + -
343A LEU* 4.3 25.8 - - + -
344A PHE* 4.7 4.5 - + - -
364A VAL* 5.6 2.5 - - + -
367A ALA* 3.9 22.2 - - + -
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Residues in contact with ALA 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 SER 3.0 19.8 + - - +
85A THR 3.2 4.5 + - - +
87A PHE* 1.3 74.8 - - - +
89A MET* 1.3 60.6 + - - +
91A LYS* 3.6 10.8 - - - +
108A PHE* 3.8 16.7 - - + -
119A ILE* 5.1 1.8 - - + -
120A HIS* 2.9 30.6 - - + -
123A PHE* 3.7 21.3 - - + -
166A TYR* 3.3 17.7 - - + +
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Residues in contact with MET 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 THR* 3.0 10.5 + - + +
86A ALA* 3.3 14.4 - - - +
88A ALA* 1.3 77.5 - - - +
90A THR* 1.3 61.1 + - - +
92A LEU* 3.0 27.4 - - - +
144A ASN* 3.4 33.9 - - + +
145A ARG 4.7 0.4 - - - +
146A LEU* 5.0 4.9 - - - -
158A TYR* 3.6 5.4 - - - -
162A SER* 4.1 12.6 - - - +
166A TYR* 3.7 40.3 - - + -
168A ALA* 3.6 26.9 - - + -
170A LEU* 4.6 15.3 - - - -
215A LEU* 4.5 11.0 - - + -
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Residues in contact with THR 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 ALA 3.0 13.4 + - - -
87A PHE* 3.1 15.5 + - + +
89A MET* 1.3 73.5 - - - +
91A LYS* 1.3 62.1 + - - +
92A LEU 3.0 4.7 - - - -
93A GLY* 2.9 16.3 + - - -
94A ALA* 3.9 3.3 + - - +
102A LEU* 4.7 1.1 - - + -
146A LEU* 4.4 7.8 - - + +
158A TYR* 3.6 16.8 + - - +
213A LEU* 6.3 0.7 - - + -
215A LEU* 3.6 24.2 - - + +
343A LEU* 4.2 32.5 - - + -
351A LEU* 5.0 5.8 - - + +
364A VAL* 4.5 11.4 - - + -
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Residues in contact with LYS 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 PHE 2.8 19.0 + - - +
88A ALA* 3.6 7.7 + - - +
89A MET 3.3 0.2 - - - -
90A THR* 1.3 71.3 - - - +
92A LEU* 1.3 62.6 + - - +
93A GLY 3.0 1.7 + - - -
94A ALA* 3.0 16.1 + - - +
99A LEU* 4.0 20.6 - - + +
102A LEU* 3.5 35.0 - - + +
103A MET* 4.0 25.2 - - + +
108A PHE* 5.0 8.8 - - + -
116A SER* 3.0 27.6 + - - -
119A ILE* 3.7 17.6 - - - +
120A HIS* 2.8 34.6 + - - -
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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