Contacts of the helix formed by residues 76 - 95 (chain A) in PDB entry 2DAT
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 7.8 - - - +
18A MET* 4.3 6.1 - - - +
74A TYR* 3.6 5.4 - - - +
75A ARG* 1.3 78.8 - - - +
77A LEU* 1.3 73.6 + - - +
78A GLY 3.2 5.7 + - - -
79A ASP* 2.9 29.0 + - - +
80A LEU 3.8 1.4 + - - -
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Residues in contact with LEU 77 (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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14A LEU* 5.0 5.9 - - + +
17A GLN* 3.3 36.1 - - + +
18A MET* 4.3 12.7 - - + +
21A ILE* 3.4 30.5 - - + -
76A SER* 1.3 76.6 + - - +
78A GLY* 1.3 67.3 + - - +
80A LEU* 2.7 37.6 + - + +
81A GLU* 3.3 3.9 + - + +
112A PHE* 5.5 3.4 - - + -
116A ARG* 4.0 34.1 - - + +
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 3.2 6.3 + - - -
77A LEU* 1.3 78.3 - - - +
79A ASP* 1.3 54.7 + - - +
81A GLU* 2.7 37.1 + - - +
82A LYS* 3.1 18.7 + - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.7 23.8 - - + -
75A ARG* 4.0 13.4 + - - +
76A SER* 2.9 38.4 + - - +
78A GLY* 1.3 71.9 - - - +
80A LEU* 1.3 63.2 + - - +
82A LYS* 3.1 27.6 + - - +
83A ASP* 3.4 8.8 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.9 45.8 - - + +
21A ILE* 4.4 2.0 - - + -
22A ILE* 4.3 6.3 - - + -
65A ILE* 3.4 33.4 - - + -
69A ILE* 4.2 10.1 - - + -
74A TYR* 3.7 22.3 - - + -
76A SER 3.8 1.0 + - - -
77A LEU* 2.7 29.5 + - + +
79A ASP* 1.3 74.8 - - - +
81A GLU* 1.3 53.9 + - - +
83A ASP* 3.3 3.5 + - - +
84A VAL* 2.9 39.8 + - + +
112A PHE* 4.2 16.6 - - + -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.3 4.1 + - + +
78A GLY* 2.7 24.4 + - - +
80A LEU* 1.3 71.9 - - - +
82A LYS* 1.3 79.7 + - - +
84A VAL* 4.3 0.7 - - - -
85A MET* 2.9 48.2 + - + +
112A PHE* 4.0 29.7 - - + -
113A LYS* 6.1 0.7 - - - +
116A ARG* 5.1 8.5 + - - +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY* 3.1 16.5 + - - +
79A ASP* 3.1 17.0 + - - +
81A GLU* 1.3 96.8 + - - +
83A ASP* 1.3 65.3 + - - +
85A MET* 4.3 2.2 - - - +
86A LEU* 3.2 21.3 + - - +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 5.4 8.3 + - - -
60A VAL* 3.9 22.6 - - + +
65A ILE* 4.2 11.7 - - + +
68A ARG* 5.4 7.8 + - - -
74A TYR* 3.3 30.7 + - - +
79A ASP 3.4 6.6 + - - +
80A LEU 3.3 6.5 + - - +
82A LYS* 1.3 80.0 - - - +
84A VAL* 1.3 58.6 + - - +
85A MET 3.1 1.1 - - - -
86A LEU* 2.5 30.7 + - - +
87A LEU* 2.8 15.3 + - - -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.8 20.2 - - + -
25A VAL* 5.7 4.3 - - + -
62A PHE* 5.4 6.3 - - + -
65A ILE* 4.5 12.5 - - + +
80A LEU* 2.9 44.1 + - + +
81A GLU 4.0 1.3 - - - +
83A ASP* 1.3 73.2 - - - +
85A MET* 1.3 84.4 + - + +
87A LEU* 3.4 5.6 + - - +
88A CYS* 3.3 25.0 + - - +
108A LEU 5.9 0.4 - - - +
109A GLN* 6.3 0.2 - - - -
112A PHE* 3.5 37.0 - - + -
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 2.9 37.1 + - + +
82A LYS* 4.4 3.4 - - - +
84A VAL* 1.3 99.7 - - + +
86A LEU* 1.3 57.8 + - - +
88A CYS* 3.4 6.0 + - - +
89A HIS* 2.9 29.0 + - - +
109A GLN* 4.5 29.6 + - + +
112A PHE* 3.3 40.6 - - + -
113A LYS* 4.8 11.0 - - + -
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Residues in contact with LEU 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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57A ARG* 6.1 2.5 - - + -
58A LYS* 2.8 55.6 - - + +
60A VAL* 4.2 5.4 - - + -
82A LYS 3.2 15.6 + - - +
83A ASP* 2.5 27.1 + - - +
85A MET* 1.3 69.7 - - - +
87A LEU* 1.3 63.7 + - - +
88A CYS 2.9 3.2 + - - -
89A HIS* 3.1 12.1 + - + +
90A ASN* 2.9 50.0 + - - +
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Residues in contact with LEU 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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40A PHE* 3.9 25.5 - - + +
60A VAL* 3.8 25.7 - - + +
61A ASP* 3.4 36.3 - - - +
62A PHE* 3.5 47.6 - - + +
65A ILE* 3.8 4.9 - - + -
83A ASP 2.8 10.4 + - - +
84A VAL 3.7 8.3 - - - +
86A LEU* 1.3 73.6 - - - +
88A CYS* 1.3 78.1 + - - +
90A ASN* 3.9 14.1 - - - +
91A ALA* 4.1 2.6 + - - +
108A LEU* 5.0 0.2 - - + -
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Residues in contact with CYS 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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40A PHE* 5.2 1.1 - - - -
62A PHE* 5.7 0.9 - - - -
84A VAL* 3.3 13.3 + - - +
85A MET 3.5 8.5 - - - +
86A LEU 2.9 0.6 - - - -
87A LEU* 1.3 92.5 - - - +
89A HIS* 1.3 67.6 + - - +
91A ALA* 2.8 24.7 + - - +
92A GLN* 3.4 3.4 + - - +
105A SER* 3.7 28.8 - - - +
108A LEU* 3.9 24.5 - - - -
109A GLN* 4.0 27.1 - - + +
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Residues in contact with HIS 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 MET 2.9 17.6 + - - +
86A LEU* 3.7 14.1 - - + +
88A CYS* 1.3 74.1 - - - +
90A ASN* 1.3 73.5 + - - +
91A ALA 2.8 1.7 + - - -
92A GLN* 3.0 25.0 + - + +
93A THR* 3.0 31.2 + - - -
109A GLN* 5.1 2.2 - - - +
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Residues in contact with ASN 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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52A TYR* 4.3 11.8 + - - +
56A ILE* 3.3 36.9 - - + +
57A ARG* 4.5 3.1 + - - +
58A LYS 2.7 28.8 + - - -
59A PRO* 3.4 11.5 - - - +
60A VAL 3.7 4.8 + - - +
86A LEU* 2.9 34.0 + - - +
87A LEU* 3.9 10.1 - - - +
89A HIS* 1.3 83.2 - - - +
91A ALA* 1.3 60.6 + - - +
93A THR* 3.4 4.9 - - - -
94A PHE* 3.1 18.8 + - - +
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Residues in contact with ALA 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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40A PHE* 3.9 26.7 - - + -
52A TYR* 6.5 0.2 - - - -
87A LEU 4.1 2.4 + - - +
88A CYS 2.8 12.5 + - - +
89A HIS 2.8 0.8 + - - -
90A ASN* 1.3 74.8 - - - +
92A GLN* 1.3 52.3 + - - +
93A THR 2.5 5.7 + - - -
94A PHE* 2.5 27.7 + - - +
95A ASN* 2.7 35.5 + - + +
101A ILE* 4.4 3.4 - - + +
102A TYR* 6.1 0.2 - - - -
105A SER* 4.4 8.1 - - - -
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Residues in contact with GLN 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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88A CYS 3.4 2.4 + - - +
89A HIS* 3.0 19.1 + - + +
91A ALA* 1.3 74.5 - - - +
93A THR* 1.3 58.4 + - - +
95A ASN* 3.3 18.6 - - - +
97A GLU* 5.5 1.7 - - - +
102A TYR* 3.5 40.2 + - + +
105A SER* 3.1 30.9 + - - +
106A ILE* 3.3 22.2 - - - +
109A GLN* 3.8 16.3 - - - +
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Residues in contact with THR 93 (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 LEU* 5.0 12.8 - - + +
56A ILE* 4.1 17.5 - - + -
89A HIS* 3.0 34.6 + - - -
90A ASN* 3.4 11.2 - - - -
91A ALA 2.5 5.1 + - - -
92A GLN* 1.3 78.1 - - - +
94A PHE* 1.3 62.0 + - - +
95A ASN 4.7 0.3 - - - +
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Residues in contact with PHE 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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49A LEU* 3.8 31.2 - - + -
51A GLU* 3.7 23.8 - - - -
52A TYR* 4.2 24.0 - + + -
55A LEU* 3.2 31.6 - - + -
56A ILE* 4.7 4.5 - - + -
90A ASN 3.1 11.7 + - - +
91A ALA* 2.5 12.9 + - - +
93A THR* 1.3 74.6 - - - +
95A ASN* 1.3 71.4 + - - +
96A LEU* 3.5 3.5 + - - +
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Residues in contact with ASN 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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91A ALA* 2.7 25.2 + - - +
92A GLN* 3.3 22.2 - - - +
93A THR 4.5 0.2 - - - -
94A PHE* 1.3 83.9 - - - +
96A LEU* 1.3 69.6 + - - +
99A SER* 5.1 4.0 + - - -
101A ILE* 2.7 53.6 - - + +
102A TYR* 4.1 7.1 - - - +
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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
------------------------------------------------------------
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