Contacts of the helix formed by residues 82 - 94 (chain C) in PDB entry 2CVL
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ILE* 3.5 36.5 + - + +
77C LEU* 4.2 7.9 - - + -
79C ASP* 3.0 26.8 + - + +
81C GLU* 1.3 81.5 - - - +
83C PHE* 1.3 62.2 + - - +
84C PRO* 3.4 2.5 - - - -
85C GLY 3.4 3.0 + - - +
86C PHE* 2.9 22.9 + - - +
114C ARG* 2.9 45.2 + - - +
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Residues in contact with PHE 83 (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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108B ALA 5.5 0.2 - - - -
109B LEU 4.8 3.8 - - - -
110B PRO* 4.0 32.8 - - + -
77C LEU* 3.3 21.5 - - + -
79C ASP 4.2 0.7 - - - -
80C MSE 2.9 42.8 + - + +
82C ASP* 1.3 76.7 - - - +
84C PRO* 1.3 65.6 - - + +
86C PHE* 3.2 3.6 + + - +
87C ASN* 2.8 47.4 + - - +
101C ARG* 6.1 1.6 - - - -
103C THR* 3.5 32.5 - - + -
104C VAL* 4.4 14.1 - - - -
105C ALA* 4.3 10.1 - - + -
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Residues in contact with PRO 84 (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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46C ARG* 4.6 6.0 + - - +
80C MSE 4.4 1.1 - - - +
81C GLU 3.5 17.5 - - - +
82C ASP 3.5 0.9 - - - -
83C PHE* 1.3 94.8 - - + +
85C GLY* 1.3 60.7 + - - +
87C ASN* 3.3 7.5 + - + +
88C GLU* 3.1 22.5 + - - +
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Residues in contact with GLY 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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45C ILE* 3.8 15.7 - - - +
46C ARG* 3.7 32.9 - - - +
81C GLU 5.3 0.2 + - - -
82C ASP* 3.4 4.2 + - - +
84C PRO* 1.3 77.3 - - - +
86C PHE* 1.3 66.2 + - - +
88C GLU* 3.3 3.2 + - - +
89C VAL* 3.3 26.5 + - - +
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Residues in contact with PHE 86 (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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45C ILE* 3.6 13.1 - - + +
49C THR* 3.5 29.2 - - + -
53C MSE 4.5 0.2 - - + -
75C CYS* 3.6 31.2 - - + -
77C LEU* 4.0 20.9 - - + -
82C ASP 2.9 17.5 + - - +
83C PHE* 3.5 5.6 - + - +
85C GLY* 1.3 78.5 - - - +
87C ASN* 1.3 66.6 + - - +
89C VAL* 3.3 2.1 + - - +
90C TYR* 2.9 52.0 + + - +
101C ARG* 3.7 22.9 - - - -
103C THR* 4.5 6.1 - - + -
115C VAL* 3.7 24.2 - - + -
117C VAL* 3.8 9.2 - - + -
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Residues in contact with ASN 87 (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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13B ILE 5.1 3.2 + - - -
14B GLY* 5.1 4.0 - - - -
15B PRO* 3.6 16.7 - - + +
83C PHE* 2.8 35.8 + - - +
84C PRO* 3.6 6.9 - - + +
86C PHE* 1.3 82.6 - - - +
88C GLU* 1.3 56.7 + - - +
90C TYR* 3.5 5.1 - - - +
91C ALA* 2.9 31.2 + - - +
101C ARG* 2.7 43.7 + - - +
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Residues in contact with GLU 88 (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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46C ARG* 2.7 40.8 + - - -
84C PRO 3.1 13.3 + - - +
85C GLY 3.6 8.5 - - - +
86C PHE 3.3 0.4 - - - -
87C ASN* 1.3 78.5 - - - +
89C VAL* 1.3 63.4 + - + +
91C ALA* 3.4 10.9 + - - +
92C ARG* 2.9 44.4 + - + +
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Residues in contact with VAL 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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46C ARG* 3.6 36.1 - - + +
49C THR* 3.6 26.5 - - + +
50C GLU* 3.7 24.5 - - + +
53C MSE 4.2 0.7 - - + -
85C GLY 3.3 14.1 + - - +
86C PHE 4.0 0.9 - - - +
88C GLU* 1.3 73.3 - - - +
90C TYR* 1.3 68.1 + - - +
92C ARG* 2.8 43.7 + - - +
93C TYR* 3.3 19.7 - - + -
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Residues in contact with TYR 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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15B PRO* 3.3 38.5 + - + -
49C THR* 4.4 0.8 - - - +
53C MSE 4.0 23.1 - - + -
73C THR* 2.7 36.1 + - + +
75C CYS* 4.0 9.0 - - - -
86C PHE* 2.9 38.2 + + + +
87C ASN* 3.5 8.7 - - - +
89C VAL* 1.3 75.3 - - - +
91C ALA* 1.3 59.1 + - - +
93C TYR* 3.2 3.3 + - - +
94C PHE* 2.9 59.5 + + + +
99C PRO* 4.2 10.1 - - + +
101C ARG* 3.5 25.1 - - - +
117C VAL* 5.1 0.9 - - + -
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Residues in contact with ALA 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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15B PRO* 4.1 18.4 - - + -
87C ASN 2.9 17.9 + - - +
88C GLU* 3.7 8.1 - - - +
89C VAL 3.1 0.2 - - - -
90C TYR* 1.3 76.5 - - - +
92C ARG* 1.3 58.8 + - - +
93C TYR 3.3 0.2 - - - -
94C PHE 3.3 19.2 - - - +
95C THR* 4.3 7.1 - - - +
98C TYR* 4.4 8.4 + - - +
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Residues in contact with ARG 92 (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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46C ARG* 4.3 15.2 + - - +
50C GLU* 4.2 17.0 + - - +
88C GLU* 2.9 47.5 + - + +
89C VAL* 2.8 34.6 + - - +
91C ALA* 1.3 78.6 - - - +
93C TYR* 1.3 70.5 + - + +
95C THR* 4.9 6.0 - - - +
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Residues in contact with TYR 93 (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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50C GLU* 3.4 23.4 - - + +
53C MSE 3.5 47.8 - - + -
54C GLU* 2.6 34.1 + - - -
57C LYS* 4.8 8.7 - - + -
67C LEU* 3.6 42.0 - - + +
89C VAL* 3.3 27.6 - - + -
90C TYR 3.2 5.0 + - - +
92C ARG* 1.3 91.9 - - + +
94C PHE* 1.3 62.7 + - + +
95C THR* 3.9 5.9 + - - +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MSE 3.7 24.9 - - + -
56C LEU* 4.6 8.7 - - + -
60C LEU* 5.4 0.4 - - + -
67C LEU* 3.5 44.4 - - + -
70C VAL* 3.5 24.7 - - + -
73C THR* 4.1 12.8 - - + -
90C TYR* 2.9 55.1 + + + +
91C ALA* 3.3 16.6 - - - +
93C TYR* 1.3 78.5 - - - +
95C THR* 1.3 60.9 + - - +
98C TYR* 2.9 25.4 - - + -
99C PRO* 3.6 17.0 - - + -
119C CYS* 5.6 1.1 - - - -
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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