Contacts of the helix formed by residues 87 - 103 (chain C) in PDB entry 2VUU
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 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 3.8 15.8 - - + +
86C GLY* 1.3 68.3 - - - -
88C GLU* 1.3 57.2 + - - +
89C ILE* 2.9 22.8 + - - +
90C ALA* 3.0 27.8 + - + +
91C ILE* 3.0 31.7 + - - +
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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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81C THR* 2.8 24.7 + - - +
82C THR* 3.5 25.1 - - - +
83C SER* 3.2 25.3 + - - -
86C GLY 2.9 7.9 + - - +
87C ASP* 1.3 72.2 + - - +
89C ILE* 1.3 57.3 + - - +
91C ILE* 4.0 7.1 - - + +
92C GLY* 2.9 24.6 + - - -
110C TYR* 5.2 1.4 + - - +
126C PRO 5.4 0.5 - - - +
127C MET* 4.9 11.0 - - - +
130C PRO* 4.8 18.4 - - + +
131C LYS* 2.6 41.7 + - - +
134C VAL* 3.7 6.5 - - + +
1353C NAP 4.7 2.2 + - - -
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP* 2.9 9.7 + - - +
88C GLU* 1.3 74.3 - - - +
90C ALA* 1.3 66.9 + - - +
92C GLY 4.0 0.2 - - - -
93C LYS* 3.0 49.5 + - + +
130C PRO* 3.7 43.7 - - + +
133C THR* 4.2 21.5 - - + +
134C VAL* 3.8 7.6 - - + +
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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
----------------------------------------------------------
61C LEU* 4.8 8.3 - - + -
62C ASN* 5.4 5.4 - - - +
87C ASP* 3.0 34.1 + - + +
89C ILE* 1.3 78.2 - - - +
91C ILE* 1.3 57.9 + - - +
93C LYS* 3.9 4.7 - - - +
94C ASP* 3.1 38.2 + - - +
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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
----------------------------------------------------------
60C LEU* 3.8 23.3 - - + +
61C LEU* 4.0 28.7 - - + +
62C ASN 5.3 0.2 - - - +
67C MET* 5.3 0.7 - - - -
81C THR* 4.1 11.7 - - + -
82C THR 5.3 0.9 - - - +
85C ALA* 3.8 39.9 - - + +
86C GLY 4.3 1.3 - - - -
87C ASP 3.0 26.4 + - - +
88C GLU* 4.0 8.1 - - + +
90C ALA* 1.3 73.6 - - - +
92C GLY* 1.3 61.7 + - - +
94C ASP* 3.0 9.5 + - - +
95C LEU* 2.9 50.0 + - + +
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C THR* 5.1 3.5 - - - +
88C GLU 2.9 19.7 + - - -
89C ILE 4.0 0.2 - - - -
90C ALA 3.5 0.2 - - - -
91C ILE* 1.3 76.5 - - - +
93C LYS* 1.3 60.2 + - - +
95C LEU* 3.8 13.3 - - - +
96C ALA* 3.2 22.5 + - - +
108C TYR* 4.5 2.5 + - - -
110C TYR* 5.2 3.6 - - - -
134C VAL* 3.8 26.5 - - - +
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.0 39.5 + - + +
90C ALA* 3.9 4.9 - - - +
92C GLY* 1.3 74.8 - - - +
94C ASP* 1.3 62.0 + - - +
96C ALA* 3.3 2.3 + - - +
97C ASP* 2.9 37.6 + - - +
133C THR* 4.8 10.8 - - - +
134C VAL* 5.0 3.1 - - + -
137C TYR* 3.6 55.9 - - + +
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Residues in contact with ASP 94 (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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62C ASN* 4.6 14.2 + - - +
64C VAL* 4.2 16.6 - - + +
67C MET* 3.4 30.5 - - + +
90C ALA* 3.1 21.8 + - - +
91C ILE* 3.0 9.3 + - - +
93C LYS* 1.3 78.7 - - - +
95C LEU* 1.3 57.6 + - - +
97C ASP* 3.3 11.8 + - - +
98C ALA* 2.8 28.4 + - - +
101C ARG* 4.2 3.7 + - - +
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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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11C VAL* 4.1 24.0 - - + -
60C LEU* 4.1 6.5 - - + -
67C MET* 3.4 30.7 - - + -
70C LEU* 5.1 1.1 - - + -
71C PHE* 3.4 16.8 - - + -
79C ILE* 3.4 29.8 - - + -
81C THR* 4.1 9.6 - - + -
91C ILE* 2.9 35.0 + - + +
92C GLY* 3.8 7.2 - - - +
94C ASP* 1.3 73.8 - - - +
96C ALA* 1.3 60.3 + - - +
98C ALA* 3.0 5.8 + - - +
99C ALA* 2.8 28.2 + - - +
108C TYR* 3.8 12.1 - - - +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLY 3.2 15.6 + - - +
93C LYS 3.6 4.7 - - - +
95C LEU* 1.3 79.7 - - - +
97C ASP* 1.3 62.1 + - - +
99C ALA 3.4 0.2 + - - -
100C LYS* 3.0 17.7 + - - +
108C TYR* 3.7 9.1 + - - +
137C TYR* 3.9 20.9 - - + -
138C VAL* 4.1 20.4 - - + -
141C LEU* 3.4 15.3 - - + +
143C LEU* 3.5 12.4 - - + +
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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
----------------------------------------------------------
93C LYS* 2.9 18.7 + - - +
94C ASP* 3.4 15.0 - - - +
96C ALA* 1.3 74.9 - - - +
98C ALA* 1.3 61.3 + - - +
100C LYS* 3.1 4.6 + - - +
101C ARG* 2.8 50.9 + - - +
137C TYR* 2.5 32.0 + - - -
141C LEU* 3.5 11.9 - - - +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C MET* 3.7 19.1 - - + +
68C ASP* 4.0 8.0 - - - +
71C PHE* 3.2 26.9 - - + +
94C ASP 2.8 14.1 + - - +
95C LEU 3.3 6.7 - - - +
97C ASP* 1.3 75.1 - - - +
99C ALA* 1.3 63.5 + - - +
101C ARG* 3.0 22.5 + - - +
102C ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 3.6 25.0 - - + -
95C LEU 2.8 10.1 + - - +
96C ALA 3.6 3.6 - - - +
98C ALA* 1.3 77.3 - - - +
100C LYS* 1.3 65.9 + - - +
102C ALA* 3.2 11.3 + - - +
103C GLY* 3.3 8.0 + - - -
105C ILE* 3.9 16.3 + - + +
108C TYR* 3.5 37.7 - - + -
143C LEU* 4.2 6.5 - - + +
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Residues in contact with LYS 100 (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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96C ALA 3.0 14.6 + - - +
97C ASP* 3.4 8.7 - - - +
99C ALA* 1.3 74.9 - - - +
101C ARG* 1.3 65.2 + - - +
103C GLY* 2.9 16.8 + - - -
141C LEU* 3.6 57.1 + - + +
143C LEU* 3.9 17.9 - - + +
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Residues in contact with ARG 101 (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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64C VAL* 3.2 32.0 - - - +
68C ASP* 3.2 24.9 + - - +
94C ASP* 4.2 4.6 + - - +
97C ASP* 2.8 28.9 + - - +
98C ALA* 3.3 31.2 - - - +
100C LYS* 1.3 78.0 - - - +
102C ALA* 1.3 63.5 + - - +
103C GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 102 (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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71C PHE* 3.7 35.0 - - + +
72C GLU* 5.6 1.1 - - - -
98C ALA 2.9 11.8 + - - +
99C ALA* 3.4 11.4 - - - +
100C LYS 3.2 0.2 - - - -
101C ARG* 1.3 76.4 - - - +
103C GLY* 1.3 57.5 + - - +
104C THR* 3.0 25.8 + - - +
105C ILE* 4.8 3.1 - - + -
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Residues in contact with GLY 103 (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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99C ALA 3.3 3.6 + - - -
100C LYS* 2.9 16.8 + - - -
101C ARG 3.1 1.5 - - - -
102C ALA* 1.3 76.7 - - - +
104C THR* 1.3 61.2 + - - +
105C ILE 3.6 3.7 - - - +
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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