Contacts of the helix formed by residues 81 - 95 (chain A) in PDB entry 2A4X
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 ASP 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE 3.4 0.8 - - - -
80A PRO* 1.3 87.2 - - - +
82A THR* 1.3 64.5 + - - +
83A ALA* 3.5 10.5 + - - +
84A SER* 2.8 55.2 + - - -
85A VAL 3.3 6.1 + - - -
127A ALA* 3.3 17.1 - - - +
128A PRO 5.1 2.9 - - - -
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Residues in contact with THR 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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81A ASP* 1.3 75.3 - - - +
83A ALA* 1.3 65.4 + - - +
85A VAL* 3.1 2.4 + - - +
86A ASP* 3.0 29.5 + - - +
105A ASN* 5.1 0.4 + - - +
111A ARG* 3.5 45.9 - - - +
127A ALA* 4.0 1.4 - - - +
128A PRO 5.1 1.5 + - - -
129A LEU* 3.6 26.3 - - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 3.3 11.7 + - - +
82A THR* 1.3 80.0 - - - +
84A SER* 1.3 57.5 + - - +
86A ASP* 3.6 4.1 + - - +
87A LYS* 3.0 32.3 + - - +
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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
----------------------------------------------------------
79A PHE* 3.3 18.2 - - - +
80A PRO* 3.3 3.8 - - - +
81A ASP* 2.8 42.0 + - - -
83A ALA* 1.3 73.0 - - - +
85A VAL* 1.3 64.7 + - - +
87A LYS* 3.9 7.4 - - - +
88A LYS* 3.0 24.9 + - - +
202B SER* 3.9 19.1 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.6 17.5 - - + -
81A ASP 3.4 2.2 - - - +
82A THR 3.1 7.7 + - - +
84A SER* 1.3 76.2 + - - +
86A ASP* 1.3 72.8 + - - +
88A LYS* 3.2 4.8 + - - +
89A TYR* 3.0 21.7 + - - +
103A PRO* 4.8 0.9 - - + -
111A ARG* 4.1 15.5 - - + +
113A ALA* 4.4 13.0 - - + -
125A LEU* 4.2 26.2 - - + +
126A PHE 3.6 15.0 - - - -
127A ALA* 3.4 34.3 - - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 3.0 20.3 + - - +
83A ALA* 4.0 4.3 - - - +
85A VAL* 1.3 75.5 - - - +
87A LYS* 1.3 63.2 + - - +
89A TYR* 3.4 3.5 + - - +
90A ALA* 3.1 23.8 + - - +
103A PRO* 3.3 21.5 - - + +
111A ARG* 2.7 48.5 + - - +
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Residues in contact with LYS 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 ALA 3.0 21.0 + - - +
84A SER* 3.9 6.3 - - - +
86A ASP* 1.3 77.4 - - - +
88A LYS* 1.3 58.3 + - - +
90A ALA* 3.5 5.0 + - - +
91A GLU* 2.9 37.1 + - + +
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Residues in contact with LYS 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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24A LYS 2.7 28.6 + - - +
25A LEU* 3.9 17.9 - - + +
79A PHE* 3.6 32.8 - - + -
84A SER 3.0 19.0 + - - +
85A VAL 3.6 3.8 - - - +
87A LYS* 1.3 73.3 - - - +
89A TYR* 1.3 61.6 + - - +
91A GLU* 2.6 32.3 + - - +
92A LEU* 2.8 44.6 + - + +
125A LEU* 4.3 2.7 - - + -
203B ALA* 5.5 1.6 - - - -
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Residues in contact with TYR 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 VAL 3.0 12.9 + - - +
86A ASP 3.6 8.5 - - - +
87A LYS 3.4 0.2 - - - -
88A LYS* 1.3 78.7 - - - +
90A ALA* 1.3 60.6 + - + +
92A LEU* 3.2 3.5 + - - +
93A VAL* 2.9 41.6 + - + +
99A GLY* 3.2 29.5 + - - -
101A LEU 3.4 16.4 - - - -
102A LYS* 3.4 29.0 + - + +
103A PRO* 3.7 20.0 - - + -
113A ALA* 3.8 16.8 - - + -
114A ILE 3.5 13.2 - - - -
115A VAL* 3.6 19.3 - - + -
125A LEU* 4.1 10.5 - - + +
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Residues in contact with ALA 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 ASP 3.1 13.8 + - - +
87A LYS* 3.8 6.1 - - - +
89A TYR* 1.3 85.8 - - + +
91A GLU* 1.3 58.4 + - - +
93A VAL* 3.9 4.2 - - - +
94A ASP* 2.8 44.6 + - - +
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Residues in contact with GLU 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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24A LYS* 3.7 24.6 - - + +
87A LYS* 2.9 26.5 + - + +
88A LYS* 2.6 43.2 + - - +
90A ALA* 1.3 77.4 - - - +
92A LEU* 1.3 56.3 + - - +
94A ASP* 3.4 7.5 + - - +
95A ALA* 3.0 28.0 + - + +
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Residues in contact with LEU 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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21A PHE* 4.3 13.2 - - + +
24A LYS* 3.8 31.9 - - + +
25A LEU* 4.3 12.8 - - + -
88A LYS* 2.8 41.7 + - + +
89A TYR 3.7 3.6 - - - +
91A GLU* 1.3 71.5 - - - +
93A VAL* 1.3 66.8 + - - +
95A ALA* 3.0 9.6 + - - -
97A TYR* 3.1 48.8 + - + -
115A VAL* 4.0 34.3 - - + -
125A LEU* 4.4 4.5 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 2.9 35.1 + - + +
90A ALA* 3.9 5.8 - - - +
92A LEU* 1.3 76.7 - - - +
94A ASP* 1.3 64.0 - - - +
96A GLY* 3.0 19.6 + - - -
97A TYR 3.5 9.7 + - - +
98A GLU 4.6 0.2 - - - -
99A GLY* 3.5 34.3 - - - +
115A VAL* 5.2 2.0 - - + -
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Residues in contact with ASP 94 (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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90A ALA* 2.8 31.1 + - - +
91A GLU* 3.7 7.5 - - - +
92A LEU 3.2 0.2 - - - -
93A VAL* 1.3 83.4 - - - +
95A ALA* 1.3 57.8 + - - +
96A GLY 3.2 1.4 + - - -
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Residues in contact with ALA 95 (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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24A LYS* 4.4 17.7 - - + +
91A GLU* 3.0 16.7 + - + +
92A LEU* 3.0 8.4 + - - +
94A ASP* 1.3 76.6 - - - +
96A GLY* 1.3 58.1 + - - +
97A TYR* 3.5 25.1 - - + -
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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