Contacts of the helix formed by residues 83 - 99 (chain C) in PDB entry 2VZE
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 PHE 83 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 4.0 19.0 - - + +
54C TRP* 3.8 28.9 - + + -
55C ALA* 3.7 9.3 - - - +
58C GLU* 3.1 16.8 + - - +
63C ARG* 3.9 13.5 - - - -
66C SER* 3.4 19.0 + - - -
67C PRO 3.5 15.9 - - - -
68C ALA* 3.5 18.8 - - + -
82C ASN* 1.3 76.6 - - - +
84C ARG* 1.3 56.5 + - - +
86C LEU* 3.8 3.1 - - - +
87C SER* 2.9 28.2 + - - -
277C TRP* 3.6 22.4 - + + -
280C GLY* 3.2 31.2 - - - -
281C ALA 3.3 22.7 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 4.1 12.1 - - - +
58C GLU* 3.3 24.9 + - + +
59C LYS* 3.8 48.2 + - - +
82C ASN* 3.7 6.3 - - - +
83C PHE* 1.3 77.5 - - - +
85C GLU* 1.3 58.9 + - + +
87C SER* 3.2 2.9 + - - -
88C GLU* 2.8 56.7 + - - +
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Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C MET* 3.6 9.2 - - - +
81C TRP* 3.5 27.2 - - + -
82C ASN* 2.8 49.2 + - - +
84C ARG* 1.3 71.7 - - + +
86C LEU* 1.3 60.9 + - - +
88C GLU* 4.5 12.1 - - - +
89C ASN* 2.9 39.2 + - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.5 26.2 - - + -
68C ALA* 3.8 13.5 - - + -
69C LEU* 4.7 13.9 - - + -
81C TRP* 4.2 10.5 - - + +
82C ASN 2.9 16.1 + - - +
83C PHE* 3.8 4.5 - - + +
85C GLU* 1.3 74.9 - - - +
87C SER* 1.3 65.5 + - - +
89C ASN* 4.8 2.5 - - - -
90C SER* 3.0 27.9 + - - -
120C TRP* 5.4 0.9 - - + -
121C LEU* 4.0 16.4 - - + -
124C LEU* 3.9 14.4 - - + -
277C TRP* 3.3 47.6 - - + -
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.4 4.9 - - - +
52C ASP* 3.1 22.0 + - - -
55C ALA* 3.7 14.6 - - - +
59C LYS* 5.0 5.8 + - - -
83C PHE 2.9 19.2 + - - -
84C ARG 3.2 4.7 + - - -
86C LEU* 1.3 75.3 - - - +
88C GLU* 1.3 62.4 + - - +
90C SER* 2.8 21.4 + - - -
91C GLN* 2.7 40.7 + - - +
128C ARG* 3.7 4.3 - - - +
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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
----------------------------------------------------------
59C LYS* 4.6 11.2 - - - +
84C ARG* 2.8 56.5 + - + +
85C GLU* 4.0 12.3 - - - +
87C SER* 1.3 74.2 - - - +
89C ASN* 1.3 63.4 + - - +
91C GLN* 3.1 8.4 + - - +
92C GLN* 3.0 30.8 + - - +
203C THR* 3.9 37.4 - - + +
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TRP* 2.9 37.2 - - + +
85C GLU* 2.9 24.8 + - - +
86C LEU* 4.8 0.7 - - - -
88C GLU* 1.3 81.2 - - - +
90C SER* 1.3 56.4 + - - +
92C GLN* 3.4 23.4 - - - +
93C ALA* 3.1 20.4 + - - +
121C LEU* 3.9 23.9 - - + +
198C LEU* 3.7 11.0 - - + +
203C THR* 5.4 0.5 - - - +
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Residues in contact with SER 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU 3.0 16.1 + - - -
87C SER 2.8 15.1 + - - -
89C ASN* 1.3 74.3 - - - +
91C GLN* 1.3 59.6 - - - +
92C GLN 3.3 0.4 - - - -
93C ALA* 3.3 7.8 + - - +
94C ALA* 3.0 21.5 + - - +
121C LEU* 3.8 9.8 - - - +
124C LEU* 3.7 35.3 - - - +
125C GLY* 3.9 2.6 - - - -
128C ARG* 2.9 29.2 + - - -
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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
----------------------------------------------------------
52C ASP* 4.6 2.4 + - - -
59C LYS* 5.1 6.5 - - - +
87C SER* 2.7 41.3 + - - +
88C GLU* 3.4 6.7 - - - +
90C SER* 1.3 74.9 + - - +
92C GLN* 1.3 63.3 + - - +
94C ALA* 3.2 4.0 + - - +
95C ASN* 3.0 27.0 + - - -
128C ARG* 3.6 25.1 - - - +
202C SER 3.9 2.9 - - - -
203C THR 3.4 25.4 + - - +
204C THR* 3.6 5.7 - - - +
205C HIS* 3.0 44.2 + - + +
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Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLU 3.0 13.3 + - - +
89C ASN* 3.4 31.6 - - - +
90C SER 3.3 0.2 - - - -
91C GLN* 1.3 77.3 - - - +
93C ALA* 1.3 60.7 + - - +
95C ASN 3.3 0.9 + - - -
96C VAL* 3.1 26.9 + - - +
198C LEU* 3.1 34.7 + - + +
199C ASN* 4.1 11.7 + - - +
201C ALA* 2.9 24.2 + - + +
202C SER 3.3 20.4 - - - +
203C THR* 3.7 18.9 - - + +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASN 3.1 14.1 + - - +
90C SER 3.4 7.0 - - - +
91C GLN 3.2 0.2 - - - -
92C GLN* 1.3 76.2 - - - +
94C ALA* 1.3 62.1 + - - +
96C VAL* 3.1 7.5 + - - +
97C LEU* 3.0 27.2 + - + +
121C LEU* 3.4 31.6 - - + +
122C VAL* 4.7 2.2 - - - +
125C GLY* 4.1 5.6 - - - -
194C PHE* 4.4 11.3 - - + -
198C LEU* 3.6 13.6 - - + +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C SER 3.0 14.5 + - - +
91C GLN 3.6 3.8 - - - +
93C ALA* 1.3 75.2 - - - +
95C ASN* 1.3 58.6 + - - +
97C LEU* 3.8 2.6 - - - +
98C SER* 2.9 33.6 + - - -
125C GLY* 3.6 25.0 - - - +
128C ARG* 3.8 7.4 - - + -
129C ALA* 4.4 1.9 - - + +
205C HIS* 3.6 35.7 - - + +
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Residues in contact with ASN 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 GLN 3.0 14.9 + - - +
92C GLN 3.7 4.9 - - - +
94C ALA* 1.3 72.3 - - - +
96C VAL* 1.3 59.4 + - - +
98C SER* 4.4 3.2 + - - -
99C GLY* 2.7 34.3 + - - +
100C ALA* 3.2 2.5 + - - -
201C ALA* 3.9 11.4 - - + -
202C SER* 2.9 32.2 + - - +
204C THR 2.9 27.1 + - - +
205C HIS* 3.2 21.2 - - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLN 3.1 16.9 + - - +
93C ALA* 3.1 9.4 + - - +
95C ASN* 1.3 76.2 - - - +
97C LEU* 1.3 58.2 + - + +
100C ALA* 3.4 6.6 + - + -
101C CYS* 2.9 30.9 + - - -
181C LEU* 4.3 16.6 - - + -
194C PHE* 4.5 13.5 - - + +
197C LEU* 3.7 36.3 - - + +
198C LEU* 3.6 31.6 - - + +
201C ALA* 3.8 4.3 - - + -
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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 ALA* 3.0 17.8 + - + +
94C ALA* 3.8 3.1 - - - +
96C VAL* 1.3 79.3 - - + +
98C SER* 1.3 59.2 + - - +
101C CYS* 3.4 13.6 - - - +
103C LEU* 2.9 41.8 + - + +
109C VAL* 4.8 4.7 - - + -
122C VAL* 3.9 14.4 - - + +
125C GLY* 3.8 7.4 - - - -
126C CYS* 3.7 35.4 - - - +
131C LEU* 3.6 21.3 - - + -
158C VAL* 4.4 11.4 - - + -
181C LEU* 3.6 29.2 - - + -
194C PHE* 5.4 5.2 - - + -
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER* 3.2 20.1 - - - +
94C ALA 2.9 17.8 + - - -
95C ASN* 4.4 1.9 + - - -
97C LEU* 1.3 78.3 - - - +
99C GLY* 1.3 59.2 + - - +
102C GLY* 3.4 11.7 - - - -
103C LEU 3.4 18.6 - - - +
104C GLN* 4.6 0.7 + - - -
129C ALA* 4.1 19.7 - - - -
205C HIS* 3.8 16.8 + - - -
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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
----------------------------------------------------------
516A LEU* 3.1 26.2 - - - +
517A SER* 3.9 10.1 - - - -
95C ASN* 2.7 20.2 + - - -
97C LEU 3.5 0.2 - - - -
98C SER* 1.3 74.6 + - - +
100C ALA* 1.3 67.2 + - - +
101C CYS 3.3 0.4 - - - -
102C GLY* 3.3 5.2 + - - -
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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