Contacts of the helix formed by residues 81 - 100 (chain D) in PDB entry 2CVD
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 THR 81 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D GLY 3.5 0.2 - - - -
80D ASN* 1.3 84.6 - - + +
82D GLU* 1.3 58.8 + - - +
83D MET* 3.4 7.2 + - - +
84D GLU* 2.9 39.8 + - + +
85D GLN* 2.9 36.0 + - - +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.5 32.5 - - + +
73A LYS* 4.7 18.4 + - + +
74A ASN* 3.1 28.5 + - - -
81D THR* 1.3 74.5 - - - +
83D MET* 1.3 62.1 + - - +
85D GLN* 3.3 15.3 + - - +
86D CYS 3.2 15.1 + - - -
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Residues in contact with MET 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.5 17.7 - - + -
59A LEU* 3.8 31.4 - - + -
61A LEU* 3.7 31.4 - - + -
70A TYR* 3.5 31.3 - - + +
81D THR* 3.2 7.5 + - - +
82D GLU* 1.3 77.6 - - - +
84D GLU* 1.3 66.0 + - + +
86D CYS* 3.1 6.4 + - - +
87D HIS* 3.0 34.7 + - + +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY* 4.7 0.7 - - - -
80D ASN* 3.5 37.2 + - - +
81D THR* 2.9 35.9 + - + +
83D MET* 1.3 74.6 - - + +
85D GLN* 1.3 61.5 + - - +
87D HIS* 3.2 10.7 + - + +
88D VAL* 2.9 32.8 + - - +
142D ILE* 3.6 16.4 - - + +
143D GLY* 3.5 26.3 + - - -
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Residues in contact with GLN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS* 2.6 35.9 + - - +
78D ALA* 3.4 35.1 - - + +
79D GLY 3.5 18.0 + - - +
80D ASN 5.0 0.8 - - - -
81D THR* 2.9 26.4 + - - +
82D GLU* 3.5 12.4 - - - +
83D MET 3.2 0.2 - - - -
84D GLU* 1.3 77.4 - - - +
86D CYS* 1.3 61.1 + - - +
88D VAL* 3.4 2.6 + - - +
89D ASP* 3.1 28.8 + - - +
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Residues in contact with CYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.1 29.4 - - + -
62A HIS 4.7 2.7 - - - -
66A ALA* 3.6 30.5 - - - +
67A ILE* 4.1 4.7 - - - -
70A TYR* 3.9 23.3 - - + -
82D GLU 3.2 12.0 + - - +
83D MET* 3.1 11.8 + - - +
85D GLN* 1.3 78.2 - - - +
87D HIS* 1.3 56.6 + - - +
89D ASP* 3.2 9.5 + - - +
90D ALA* 2.8 29.7 + - - +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.2 1.6 - - - +
60A THR 3.4 24.6 + - - -
61A LEU* 3.6 21.5 - - + +
62A HIS* 4.8 13.8 + + - -
83D MET* 3.0 35.4 + - + +
84D GLU* 3.2 13.2 + - + +
86D CYS* 1.3 78.3 - - - +
88D VAL* 1.3 56.5 + - - +
90D ALA* 3.7 4.7 - - - +
91D ILE* 2.9 34.9 + - - +
134D TYR* 3.7 27.7 + + - +
142D ILE* 3.9 11.9 - - + -
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ALA 3.7 16.4 - - - +
79D GLY* 4.4 0.7 - - - -
84D GLU 2.9 19.8 + - - +
85D GLN 3.6 8.1 - - - +
87D HIS* 1.3 76.6 - - - +
89D ASP* 1.3 63.9 + - - +
91D ILE* 3.9 1.2 - - - +
92D VAL* 3.0 29.2 + - + +
142D ILE* 4.0 17.5 - - + -
147D THR* 3.9 26.9 - - + +
148D TRP* 3.4 40.8 - - + +
149D ALA* 4.0 12.9 - - + +
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA* 3.7 17.0 - - + +
69A ARG* 2.9 33.5 + - - +
73A LYS* 6.0 0.3 + - - -
69D ARG* 2.9 35.9 + - - +
85D GLN* 3.1 14.7 + - - +
86D CYS* 3.2 8.8 + - - +
88D VAL* 1.3 80.8 - - - +
90D ALA* 1.3 58.0 + - - +
92D VAL* 3.4 7.1 + - - +
93D ASP* 2.9 33.7 + - - +
148D TRP* 3.8 10.6 + - - -
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.4 49.1 - - + +
63A GLN* 3.3 13.7 - - + +
66A ALA* 3.9 1.1 - - + -
86D CYS* 2.8 17.7 + - - +
87D HIS* 3.7 7.9 - - - +
88D VAL 3.2 0.2 - - - -
89D ASP* 1.3 74.7 - - - +
91D ILE* 1.3 59.5 + - - +
93D ASP 3.4 0.2 + - - -
94D THR* 2.9 32.4 + - - -
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.5 36.8 - - + -
62A HIS* 4.3 5.4 - - + +
87D HIS 2.9 19.9 + - - +
88D VAL 3.9 2.9 - - - +
90D ALA* 1.3 75.6 - - - +
92D VAL* 1.3 63.7 + - - +
94D THR* 3.2 4.8 + - - -
95D LEU* 3.0 38.1 + - + +
131D LEU* 4.7 7.9 - - + -
134D TYR* 3.6 33.0 - - + +
141D LEU* 4.1 24.2 - - + -
142D ILE* 3.9 7.4 - - + -
149D ALA* 4.3 11.2 - - + -
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 3.6 36.3 - - + -
69D ARG* 5.5 1.3 - - - +
88D VAL* 3.0 19.4 + - + +
89D ASP* 3.7 5.2 - - - +
91D ILE* 1.3 76.9 - - - +
93D ASP* 1.3 58.7 - - - +
95D LEU* 3.3 3.8 + - - +
96D ASP* 2.8 26.3 + - - +
148D TRP* 3.8 30.7 - - + -
149D ALA* 3.9 24.7 - - - -
152D TYR* 3.7 19.3 - - + -
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Residues in contact with ASP 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.6 27.1 - - + +
65A LEU* 4.2 23.7 - - - +
66A ALA* 4.6 6.2 + - - +
69A ARG* 5.4 3.7 + - - -
93A ASP* 5.1 6.6 - - - +
4001A MG 4.2 13.0 - - - -
65D LEU* 4.0 17.5 - - - +
69D ARG* 4.9 8.1 + - - -
89D ASP 2.9 19.6 + - - +
90D ALA 3.9 0.7 - - - +
91D ILE 3.3 0.2 - - - -
92D VAL* 1.3 75.6 - - - +
94D THR* 1.3 61.2 + - - +
96D ASP* 3.9 3.7 - - - +
97D ASP* 2.8 37.0 + - - +
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Residues in contact with THR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.9 23.9 - - + +
62A HIS* 3.4 16.6 + - - -
63A GLN* 3.1 18.1 + - - +
90D ALA 2.9 19.2 + - - -
91D ILE* 3.2 8.7 + - - +
93D ASP* 1.3 76.7 - - - +
95D LEU* 1.3 64.7 + - - +
97D ASP* 3.5 4.9 + - - +
98D PHE* 3.4 17.0 + - - +
127D LEU* 3.7 27.6 - - + +
131D LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ILE* 3.0 32.7 + - + +
92D VAL* 3.6 6.7 - - - +
94D THR* 1.3 77.7 - - - +
96D ASP* 1.3 62.3 + - - +
98D PHE* 3.1 8.3 + - - +
99D MET* 3.1 26.4 + - - +
127D LEU* 4.6 10.1 - - + -
128D MET* 5.8 0.2 - - + -
131D LEU* 3.8 32.3 - - + -
141D LEU* 5.5 0.2 - - + -
149D ALA 4.5 1.1 - - - +
152D TYR* 4.0 21.1 - - + +
153D TRP* 3.7 48.7 - - + +
156D CYS* 4.3 9.9 - - + -
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.0 1.2 - - - +
4001A MG 3.9 12.1 - - - -
14D ARG* 2.9 25.3 + - - -
65D LEU* 3.6 24.4 - - + +
92D VAL 2.8 17.8 + - - +
93D ASP* 3.9 5.4 - - - +
95D LEU* 1.3 77.1 - - - +
97D ASP* 1.3 62.4 + - - +
99D MET* 3.8 3.3 - - - +
100D SER* 2.8 39.7 + - - -
152D TYR* 2.6 29.1 + - + -
2004D GSH 4.7 6.9 + - - +
2801D HQL 3.9 2.3 - - - -
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 3.0 15.7 + - - +
96A ASP* 5.1 2.3 - - - +
100A SER* 5.2 5.5 + - - -
2001A GSH 2.8 35.3 + - - +
4001A MG 4.1 14.2 - - - -
93D ASP* 2.8 25.8 + - - +
94D THR* 3.6 7.0 - - - +
95D LEU 3.2 0.2 - - - -
96D ASP* 1.3 74.4 - - - +
98D PHE* 1.3 63.7 + - - +
100D SER* 3.5 10.1 + - - -
101D CYS* 3.3 20.0 + - - -
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR 3.4 3.8 + - - +
95D LEU 3.1 8.3 + - - +
97D ASP* 1.3 77.7 - - - +
99D MET* 1.3 70.0 + - - +
101D CYS* 3.0 28.1 + - - +
102D PHE* 3.5 36.5 - + - -
119D LEU* 3.8 16.6 - - + -
120D LEU* 4.7 0.4 - - + -
123D ASN* 4.0 24.5 - - + -
124D ALA* 3.7 32.5 - - + -
127D LEU* 3.7 31.9 - - + -
128D MET* 5.3 0.7 - - + -
160D LEU* 4.1 25.1 - - + -
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Residues in contact with MET 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 4.6 1.9 + - - +
95D LEU 3.1 16.2 + - - +
96D ASP* 3.8 6.5 - - - +
98D PHE* 1.3 79.3 - - - +
100D SER* 1.3 61.4 + - - +
101D CYS 3.1 1.4 + - - -
102D PHE* 3.4 7.8 + - - +
104D TRP* 5.4 0.5 - - - -
156D CYS* 3.6 46.4 - - + +
159D THR* 4.8 2.0 - - - -
160D LEU* 3.9 26.5 - - + -
2801D HQL 3.2 95.5 - - + -
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Residues in contact with SER 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.2 4.5 + - - -
100A SER* 6.4 2.2 - - - -
14D ARG* 3.1 24.0 + - - +
96D ASP* 2.8 29.8 + - - -
97D ASP* 3.8 7.4 - - - -
98D PHE 3.1 0.4 - - - -
99D MET* 1.3 76.8 - - - +
101D CYS* 1.3 60.4 + - - +
102D PHE 3.3 6.3 + - - +
2004D GSH 5.5 0.7 + - - -
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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