Contacts of the helix formed by residues 81 - 100 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLY 3.5 0.4 - - - -
80C ASN* 1.3 83.9 - - + +
82C GLU* 1.3 59.1 + - - +
83C MET* 3.5 6.1 + - - +
84C GLU* 3.0 41.2 + - + +
85C GLN* 2.9 35.2 + - - +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.5 30.7 - - + +
73B LYS* 4.8 19.1 + - + +
74B ASN* 3.3 26.4 + - - -
81C THR* 1.3 73.5 - - - +
83C MET* 1.3 61.9 + - - +
85C GLN* 3.3 15.4 + - - +
86C CYS 3.2 15.2 + - - -
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Residues in contact with MET 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.9 24.2 - - + +
59B LEU* 3.6 35.7 - - + -
61B LEU* 4.0 20.9 - - + -
70B TYR* 3.4 32.9 - - + +
81C THR* 3.2 5.6 + - - +
82C GLU* 1.3 75.6 - - - +
84C GLU* 1.3 64.6 + - + +
86C CYS* 3.0 6.4 + - - +
87C HIS* 2.9 37.9 + - + +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLY* 4.7 0.9 - - - -
80C ASN* 3.5 36.2 + - - +
81C THR* 3.0 37.2 + - + +
83C MET* 1.3 78.5 - - + +
85C GLN* 1.3 57.9 + - - +
87C HIS* 3.1 10.9 + - + +
88C VAL* 2.8 33.0 + - - +
142C ILE* 3.6 16.3 - - + +
143C GLY* 3.5 26.5 + - - -
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Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 3.2 34.2 + - + +
78C ALA* 3.3 35.5 - - + +
79C GLY 3.5 18.1 + - - +
80C ASN 5.1 0.2 - - - -
81C THR* 2.9 22.3 + - - +
82C GLU* 3.5 13.0 - - - +
83C MET 3.2 0.2 - - - -
84C GLU* 1.3 76.5 - - - +
86C CYS* 1.3 61.6 + - - +
88C VAL* 3.3 3.0 + - - +
89C ASP* 3.1 28.4 + - - +
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Residues in contact with CYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.9 29.8 - - + -
62B HIS 4.8 2.7 - - - -
66B ALA* 3.7 30.2 - - - +
67B ILE* 4.1 4.7 - - - -
70B TYR* 3.9 23.6 - - + -
82C GLU 3.2 11.5 + - - +
83C MET* 3.0 12.0 + - - +
85C GLN* 1.3 77.9 - - - +
87C HIS* 1.3 57.2 + - - +
89C ASP* 3.2 9.7 + - - +
90C ALA* 2.8 27.1 + - - +
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 6.2 1.4 - - - +
60B THR 3.5 24.4 + - - -
61B LEU* 3.6 21.5 - - + +
62B HIS* 4.9 12.7 + + - -
83C MET* 2.9 32.7 + - + +
84C GLU* 3.1 15.0 + - + +
86C CYS* 1.3 76.0 - - - +
88C VAL* 1.3 64.4 + - - +
90C ALA* 3.7 4.9 - - - +
91C ILE* 2.9 29.3 + - - +
134C TYR* 3.8 26.1 + + - +
142C ILE* 3.9 11.0 - - + -
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA 3.6 16.4 - - - +
79C GLY* 4.3 0.7 - - - -
84C GLU 2.8 20.0 + - - +
85C GLN 3.5 8.1 - - - +
87C HIS* 1.3 76.8 - - - +
89C ASP* 1.3 65.5 + - - +
91C ILE* 3.4 1.7 + - - +
92C VAL* 3.0 28.1 + - - +
142C ILE* 4.1 17.3 - - + -
147C THR* 3.9 26.2 - - + +
148C TRP* 3.4 40.4 - - + +
149C ALA* 4.0 13.4 - - + +
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Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.6 17.5 - - + +
69B ARG* 3.0 37.3 + - - +
69C ARG* 2.9 30.7 + - - +
85C GLN* 3.1 17.2 + - - +
86C CYS* 3.2 10.4 + - - +
88C VAL* 1.3 78.8 - - - +
90C ALA* 1.3 57.5 + - - +
92C VAL* 3.4 7.1 + - - +
93C ASP* 3.0 32.8 + - - +
148C TRP* 3.9 10.6 + - - -
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 3.4 49.4 - - + +
63B GLN* 3.3 14.1 - - + +
66B ALA* 3.7 1.1 - - + +
86C CYS* 2.8 17.7 + - - +
87C HIS* 3.7 8.1 - - - +
88C VAL 3.2 0.2 - - - -
89C ASP* 1.3 74.9 - - - +
91C ILE* 1.3 59.5 + - - +
93C ASP 3.3 0.2 + - - -
94C THR* 2.9 32.6 + - - -
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.5 38.4 - - + -
62B HIS* 4.3 7.0 - - + +
87C HIS 2.9 19.9 + - - +
88C VAL 3.9 2.9 - - - +
90C ALA* 1.3 75.4 - - - +
92C VAL* 1.3 63.3 + - - +
94C THR* 3.2 4.2 + - - -
95C LEU* 3.0 37.3 + - + +
131C LEU* 4.6 7.4 - - + -
134C TYR* 3.7 32.3 - - + +
141C LEU* 4.1 24.5 - - + -
142C ILE* 3.9 11.0 - - + -
149C ALA* 4.3 7.4 - - + -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.5 30.1 - - + -
69C ARG* 5.5 1.8 - - - +
88C VAL* 3.0 19.0 + - + +
89C ASP* 3.7 4.9 - - - +
91C ILE* 1.3 77.2 - - - +
93C ASP* 1.3 58.1 - - - +
95C LEU* 3.3 3.7 + - - +
96C ASP* 2.8 27.2 + - - +
148C TRP* 3.8 39.3 - - + -
149C ALA* 3.9 24.0 - - - -
152C TYR* 3.8 18.6 - - + -
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 3.6 26.7 - - + +
65B LEU* 4.2 23.6 - - - +
66B ALA* 4.5 6.6 + - - +
69B ARG* 5.3 4.0 + - - -
93B ASP* 5.1 6.7 - - - +
4002B MG 4.2 14.0 - - - -
65C LEU* 4.0 17.2 - - - +
69C ARG* 4.9 7.7 + - - -
89C ASP* 3.0 19.6 + - - +
90C ALA 3.8 0.7 - - - +
92C VAL* 1.3 75.8 - - - +
94C THR* 1.3 61.2 + - - +
96C ASP* 3.9 3.5 - - - +
97C ASP* 2.8 37.3 + - - +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.8 23.1 - - + +
62B HIS* 3.3 16.7 + - - -
63B GLN* 3.1 19.3 + - - +
90C ALA 2.9 17.2 + - - -
91C ILE* 3.2 8.5 + - - -
93C ASP* 1.3 78.0 - - - +
95C LEU* 1.3 64.5 + - - +
97C ASP* 3.5 5.3 + - - +
98C PHE* 3.4 17.2 + - - +
127C LEU* 3.7 27.9 - - + +
131C LEU* 5.4 2.5 - - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ILE* 3.0 36.2 + - + +
92C VAL* 3.7 4.0 - - - +
94C THR* 1.3 77.3 - - + +
96C ASP* 1.3 62.2 + - - +
98C PHE* 3.2 8.2 + - - +
99C MET* 3.1 26.8 + - - +
127C LEU* 4.6 10.1 - - + -
128C MET* 5.7 0.2 - - + -
131C LEU* 3.7 32.8 - - + -
149C ALA 4.4 0.9 - - - +
152C TYR* 4.0 21.3 - - + +
153C TRP* 3.7 47.6 - - + +
156C CYS* 4.3 10.1 - - + -
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Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 5.0 1.2 - - - +
4002B MG 3.9 13.0 - - - -
14C ARG* 2.9 27.3 + - - -
65C LEU* 3.7 22.3 - - + +
92C VAL 2.8 17.6 + - - +
93C ASP* 3.9 5.6 - - - +
95C LEU* 1.3 74.9 - - - +
97C ASP* 1.3 65.0 + - - +
99C MET* 3.3 3.3 + - - +
100C SER* 2.8 37.7 + - - -
152C TYR* 2.7 28.5 + - + -
2003C GSH 4.7 6.4 + - - -
2601C HQL 4.0 1.9 - - - -
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLN* 3.1 15.8 + - - +
96B ASP* 5.1 2.8 - - - +
100B SER* 5.2 5.5 + - - -
2002B GSH 2.8 35.6 + - - +
4002B MG 4.1 14.2 - - - -
93C ASP* 2.8 26.6 + - - +
94C THR* 3.6 6.9 - - - +
95C LEU 3.2 0.2 - - - -
96C ASP* 1.3 74.0 - - - +
98C PHE* 1.3 63.5 + - - +
100C SER* 3.4 10.5 + - - -
101C CYS* 3.4 20.3 + - - -
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR 3.4 4.1 + - - +
95C LEU 3.2 8.9 + - - +
97C ASP* 1.3 77.7 - - - +
99C MET* 1.3 69.8 + - - +
101C CYS* 3.0 27.0 + - + +
102C PHE* 3.5 36.9 - + - -
119C LEU* 3.8 16.2 - - + -
120C LEU* 4.6 0.2 - - + -
123C ASN* 3.9 24.7 - - + -
124C ALA* 3.7 32.1 - - + -
127C LEU* 3.7 31.6 - - + -
128C MET* 5.3 0.7 - - + -
160C LEU* 4.1 25.4 - - + -
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Residues in contact with MET 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 4.6 1.5 + - - -
95C LEU 3.1 16.4 + - - +
96C ASP* 3.8 6.5 - - - +
98C PHE* 1.3 78.6 - - - +
100C SER* 1.3 61.1 + - - +
101C CYS 3.1 1.8 + - - -
102C PHE* 3.5 7.1 + - - +
104C TRP* 5.1 0.9 + - - -
156C CYS* 3.6 45.5 - - - +
159C THR* 4.8 2.2 - - - -
160C LEU* 3.9 28.7 - - + -
2601C HQL 3.2 93.2 - - + -
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 5.3 4.5 + - - -
100B SER* 6.3 2.9 - - - -
14C ARG* 3.0 23.7 + - - +
96C ASP* 2.8 28.9 + - - -
97C ASP* 3.8 7.6 - - - -
98C PHE 3.1 0.4 - - - -
99C MET* 1.3 74.7 - - - +
101C CYS* 1.3 59.5 + - - +
102C PHE 3.3 5.3 + - - +
2003C GSH 5.5 0.9 + - - -
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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
------------------------------------------------------------
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