Contacts of the helix formed by residues 88 - 99 (chain C) in PDB entry 2VM8
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C PHE* 3.7 3.1 - - - +
77C GLN* 3.2 28.9 - - + +
84C THR* 5.8 2.7 - - + -
85C SER 5.0 1.3 - - - +
86C ALA 3.4 7.5 + - - +
87C ASP* 1.3 75.5 - - - +
89C PHE* 1.3 59.9 + - - +
90C PHE* 3.2 9.2 + - - +
91C GLN* 3.0 25.0 + - - +
92C GLY* 2.8 25.5 + - - -
130C LYS* 3.1 25.2 + - - +
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Residues in contact with PHE 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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76C PHE* 3.8 29.2 - + + -
77C GLN* 2.7 40.4 + - + +
88C ASP* 1.3 71.1 - - - +
90C PHE* 1.3 51.5 + - - +
92C GLY 4.1 0.7 - - - -
93C THR* 2.5 40.6 + - + +
104C ILE* 4.3 10.1 - - + -
106C ASP* 3.8 32.3 - - + -
123C TRP* 3.7 29.4 - + - -
126C TRP* 3.8 24.7 - + + -
127C ALA* 3.7 29.6 - - + -
130C LYS* 3.7 15.7 - - + -
131C SER* 3.8 6.2 - - - +
135C TYR* 5.1 1.8 - + - -
137C LEU* 4.9 0.7 - - + -
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Residues in contact with PHE 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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88C ASP* 3.2 9.2 + - - +
89C PHE* 1.3 77.5 - - - +
91C GLN* 1.3 83.6 + - + +
93C THR* 3.3 3.0 + - - -
94C LYS* 3.1 44.3 + - + +
130C LYS* 3.3 29.1 - - + +
132C CYS* 3.5 27.6 - - - -
461C VAL* 3.9 19.5 - - + -
463C GLU* 3.5 37.7 - - + -
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Residues in contact with GLN 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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86C ALA 5.4 0.7 - - - +
87C ASP* 3.7 21.3 - - - +
88C ASP* 3.0 20.0 + - - +
90C PHE* 1.3 99.9 - - + +
92C GLY* 1.3 63.1 + - - +
94C LYS* 3.8 17.6 + - - +
95C ALA* 3.2 23.7 + - - +
426C ASN* 3.0 32.5 + - - +
427C SER* 4.2 5.0 - - - +
428C SER* 4.8 6.3 - - - +
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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
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76C PHE* 3.3 39.0 - - - -
87C ASP* 4.1 7.2 - - - +
88C ASP 2.8 16.2 + - - -
91C GLN* 1.3 77.2 - - - +
93C THR* 1.3 55.2 + - - +
95C ALA* 3.5 6.6 + - - +
96C ALA* 3.1 21.7 + - - +
333C HIS* 5.4 0.9 - - - -
358C THR* 3.7 2.4 - - - +
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Residues in contact with THR 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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76C PHE* 3.7 20.6 - - + -
89C PHE* 2.5 26.9 + - + +
90C PHE 3.3 5.2 + - - -
92C GLY* 1.3 72.7 - - - +
94C LYS* 1.3 59.1 + - - +
96C ALA* 3.6 9.0 - - - +
97C LEU* 3.2 32.6 + - - +
104C ILE* 3.9 17.7 - - + -
131C SER* 3.6 16.4 - - - +
132C CYS* 2.9 27.1 + - - +
133C CYS* 3.9 9.3 - - - -
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Residues in contact with LYS 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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90C PHE* 3.1 36.6 + - + +
91C GLN* 3.8 23.6 + - - +
93C THR* 1.3 74.7 + - - +
95C ALA* 1.3 65.2 + - - +
96C ALA 3.1 1.3 - - - -
97C LEU* 3.3 3.5 + - - +
98C ALA* 3.0 22.2 + - - +
132C CYS* 4.3 6.2 - - - -
426C ASN* 4.3 7.9 - - - +
459C LEU* 3.6 38.8 + - + +
461C VAL* 3.9 32.1 - - + +
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Residues in contact with ALA 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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87C ASP* 6.3 0.9 - - - -
91C GLN 3.2 11.0 + - - +
92C GLY* 3.6 6.1 - - - +
94C LYS* 1.3 76.3 - - - +
96C ALA* 1.3 68.9 + - - +
98C ALA* 3.2 3.4 + - - +
99C GLY 3.1 13.9 + - - -
333C HIS* 5.4 4.3 - - + -
358C THR* 4.0 12.6 - - + -
359C GLU* 3.5 22.8 - - + +
426C ASN* 3.5 36.9 - - + +
427C SER* 5.6 1.3 - - - -
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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
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92C GLY 3.1 11.8 + - - +
93C THR* 3.6 14.1 - - - +
94C LYS 3.1 0.2 - - - -
95C ALA* 1.3 77.9 - - - +
97C LEU* 1.3 55.5 + - - +
99C GLY* 2.6 31.2 + - - -
101C THR* 3.2 32.7 + - + +
104C ILE* 4.1 9.9 - - + -
133C CYS* 5.1 0.7 - - - -
358C THR* 3.7 26.9 - - - +
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Residues in contact with LEU 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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93C THR 3.2 21.5 + - - +
94C LYS 3.8 4.0 - - - +
95C ALA 3.3 0.2 - - - -
96C ALA* 1.3 79.8 - - - +
98C ALA* 1.3 56.6 + - - +
100C GLY* 3.0 15.8 + - - -
101C THR 3.3 20.0 - - - +
102C THR* 3.9 9.0 - - + -
132C CYS* 3.6 23.3 - - + +
133C CYS* 3.9 12.3 - - + -
446C VAL* 3.5 19.2 - - + +
448C SER* 3.7 29.6 - - - +
453C VAL* 4.1 20.4 - - + -
454C LEU* 4.4 2.5 - - + +
459C LEU* 6.3 0.2 - - + -
461C VAL* 3.5 31.2 - - + -
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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
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94C LYS 3.0 7.8 + - - +
95C ALA 3.6 7.4 - - - +
96C ALA 3.0 0.6 + - - -
97C LEU* 1.3 75.8 - - - +
99C GLY* 1.3 57.1 + - - +
100C GLY 3.4 0.2 - - - -
359C GLU* 3.7 7.5 - - - +
426C ASN* 3.6 27.8 - - - +
443C PRO* 3.5 17.2 - - - +
454C LEU* 3.9 18.0 - - + +
459C LEU* 3.6 21.9 - - + +
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Residues in contact with GLY 99 (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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95C ALA 3.1 6.2 + - - -
96C ALA 2.6 15.5 + - - -
98C ALA* 1.3 70.0 - - - +
100C GLY* 1.3 58.0 + - - -
101C THR* 3.4 4.5 - - - -
358C THR 4.7 1.6 - - - -
359C GLU* 3.1 28.3 + - - +
362C MET* 3.7 22.7 + - - +
363C SER* 4.8 1.5 + - - -
412C TRP* 4.0 2.3 - - - -
443C PRO* 3.5 15.0 - - - +
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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