Contacts of the helix formed by residues 82 - 99 (chain C) in PDB entry 2VE7
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 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 4.1 9.6 - - + -
158A LEU* 3.3 37.0 + - + +
159A GLY* 4.5 1.2 + - - -
187A TRP* 4.2 5.6 - - + -
191A CYS* 3.4 63.7 - - + -
194A ILE* 4.0 24.2 - - + -
195A HIS* 4.4 4.5 - - + -
79C MET* 2.9 10.9 + - + +
81C GLY* 1.3 77.9 - - - +
83C LEU* 1.3 70.5 + - - +
84C PRO 3.2 1.9 - - - -
85C PHE* 3.2 56.3 + + + +
86C SER* 3.6 7.7 + - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 4.1 31.9 - - + -
198A MET* 4.2 5.6 - - + -
64C PHE 3.6 11.7 - - - +
65C TYR* 4.4 20.4 - - + -
66C MET 3.7 21.8 - - - +
67C MET* 3.7 27.1 - - + +
79C MET* 3.2 14.0 + - + +
80C GLU* 3.9 20.2 - - + +
82C PHE* 1.3 77.2 - - + +
84C PRO* 1.4 73.8 - - + +
86C SER* 3.2 10.3 + - - -
87C ASN* 3.4 14.9 - - - +
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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
----------------------------------------------------------
46C HIS* 4.4 15.0 - - + -
50C MET* 3.8 24.5 - - + -
64C PHE* 3.6 12.2 - - + +
65C TYR* 3.6 29.2 - - + +
80C GLU 3.2 16.6 - - - +
81C GLY 3.7 9.0 - - - +
82C PHE 3.4 4.0 - - - -
83C LEU* 1.4 91.5 - - + +
85C PHE* 1.3 65.0 + - - +
87C ASN* 2.9 13.9 + - - +
88C LEU* 2.9 15.8 + - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 4.3 28.7 - - + -
158A LEU* 4.8 1.8 - - + +
195A HIS* 4.1 19.7 - + - -
46C HIS* 5.2 4.6 - - - +
81C GLY 5.3 1.5 + - - +
82C PHE* 3.2 44.8 + + + +
84C PRO* 1.3 77.9 - - - +
86C SER* 1.3 68.1 + - - +
87C ASN 3.0 0.7 + - - -
88C LEU* 3.1 20.6 + - - +
89C VAL* 3.1 34.9 + - + +
106C THR* 4.3 8.5 - - - -
109C ILE* 4.5 11.7 - - + -
110C LEU* 3.4 48.2 - - + -
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 4.5 0.9 - - - -
195A HIS* 3.2 37.3 + - - -
198A MET* 3.8 23.5 + - - +
82C PHE* 3.6 18.9 + - - -
83C LEU 3.2 8.4 + - - -
84C PRO 3.1 0.4 + - - -
85C PHE* 1.3 88.3 - - - +
87C ASN* 1.3 70.8 + - - +
89C VAL* 3.9 6.9 + - - +
90C THR* 3.5 16.5 + - - -
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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
----------------------------------------------------------
198A MET* 3.2 32.9 - - - +
63C HIS 2.8 28.4 + - - +
64C PHE* 3.3 32.9 + - + +
66C MET* 4.5 5.9 + - - +
83C LEU* 3.4 13.0 + - - +
84C PRO 2.9 5.3 + - - +
86C SER* 1.3 78.9 - - - +
88C LEU* 1.3 69.0 + - - +
90C THR* 3.8 4.4 + - - -
91C HIS* 3.3 29.4 + - + +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 4.2 20.6 - - + +
49C TYR* 4.0 23.1 - - + -
50C MET* 3.8 29.8 - - + -
53C LEU* 4.0 18.4 - - + -
64C PHE* 4.1 11.2 - - + -
84C PRO 2.9 14.9 + - - +
85C PHE* 3.1 10.7 + - - +
87C ASN* 1.3 75.7 - - - +
89C VAL* 1.3 65.5 + - - +
91C HIS* 3.1 5.0 + - - +
92C LEU* 2.8 39.0 + - + +
109C ILE* 3.7 25.1 - - + -
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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
----------------------------------------------------------
195A HIS* 4.6 14.1 - - + +
85C PHE* 3.1 40.1 + - + +
86C SER 4.0 6.1 - - - +
87C ASN 3.5 0.2 - - - -
88C LEU* 1.3 76.4 - - - +
90C THR* 1.3 66.4 + - - +
92C LEU* 3.8 0.6 - - - -
93C ASP* 3.0 46.4 + - - +
106C THR* 3.9 20.6 - - + -
109C ILE* 3.8 25.1 - - + -
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 5.5 2.1 - - - -
198A MET 4.3 14.3 + - - +
199A LYS* 5.7 4.1 - - + +
202A SER* 5.5 7.2 - - - +
86C SER 3.5 13.9 + - - -
87C ASN* 3.8 6.2 + - - -
88C LEU 3.3 0.8 - - - -
89C VAL* 1.3 83.4 - - - +
91C HIS* 1.3 72.8 + - + +
93C ASP* 3.7 11.6 + - - +
94C SER* 3.8 10.9 + - - -
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Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.8 25.8 - - + -
57C TYR* 4.6 11.2 + + + -
59C ILE* 3.5 34.7 - - + +
64C PHE* 4.4 10.7 - + - -
87C ASN* 3.3 20.9 + - + -
88C LEU 3.1 4.2 + - - +
90C THR* 1.3 81.7 - - + +
92C LEU* 1.3 61.4 + - - +
94C SER* 3.0 8.7 + - - -
95C PHE* 2.8 30.7 + - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 3.9 39.9 - - + -
53C LEU* 4.5 12.1 - - + -
88C LEU* 2.8 31.0 + - + +
89C VAL 4.0 3.1 - - - +
91C HIS* 1.3 73.1 - - - +
93C ASP* 1.3 60.8 + - - +
95C PHE* 3.9 19.5 - - + +
96C LEU* 3.2 46.6 + - + +
97C PRO* 4.1 0.2 - - - +
104C PHE* 3.7 36.2 - - + +
109C ILE* 3.8 16.6 - - + -
124C ILE* 5.4 0.2 - - + -
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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
----------------------------------------------------------
115B LYS* 2.9 39.7 + - + +
89C VAL* 3.0 39.6 + - - +
90C THR* 3.9 8.0 - - - +
91C HIS 3.1 0.4 - - - -
92C LEU* 1.3 78.4 - - - +
94C SER* 1.3 57.8 + - - +
97C PRO* 3.1 22.4 - - - +
104C PHE* 4.6 8.0 - - - +
105C GLU* 5.7 0.9 - - - -
106C THR* 5.8 3.3 + - - +
109C ILE* 5.9 0.5 - - - +
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.3 15.3 + - - -
90C THR 3.8 8.7 + - - -
91C HIS* 3.0 9.3 + - - -
93C ASP* 1.3 81.0 - - - +
95C PHE* 1.3 62.5 + - - +
97C PRO* 3.3 11.3 - - - +
98C ILE* 3.7 18.2 - - - +
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 4.1 15.9 - - + -
53C LEU* 3.9 18.4 - - + -
56C VAL* 3.5 38.1 - - + -
57C TYR* 3.5 28.7 - + + +
91C HIS 2.8 16.7 + - - +
92C LEU* 4.3 14.4 - - + -
94C SER* 1.3 77.6 + - - +
96C LEU* 1.3 66.6 + - + +
98C ILE* 3.1 18.3 + - + +
99C CYS* 3.2 32.2 + - - -
124C ILE* 3.7 32.3 - - + -
127C PHE* 4.1 10.5 - + - -
128C ILE* 5.7 0.2 - - + -
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Residues in contact with LEU 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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49C TYR* 5.0 1.3 - - + -
92C LEU* 3.2 40.8 + - + +
95C PHE* 1.3 75.8 - - + +
97C PRO* 1.4 66.8 - - + +
99C CYS* 2.9 12.8 + - + +
100C ARG 3.1 0.2 + - - -
101C VAL* 2.8 48.1 + - + +
104C PHE* 3.3 45.3 - - + -
120C PHE* 4.2 20.2 - - + +
124C ILE* 4.0 28.5 - - + -
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Residues in contact with PRO 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU 4.1 0.2 - - - +
93C ASP* 3.1 29.4 - - - +
94C SER* 3.3 11.0 - - - +
96C LEU* 1.4 92.3 - - + +
98C ILE* 1.3 58.0 + - + +
100C ARG* 2.9 25.3 + - - -
101C VAL 3.0 14.3 - - - +
102C ASN* 3.8 17.9 + - - +
104C PHE* 6.1 0.9 - - + -
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Residues in contact with ILE 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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226A LEU* 5.4 2.7 - - + -
230A ILE* 3.6 42.2 - - + -
233A TYR* 3.4 20.8 - - + -
57C TYR* 3.8 20.4 - - + +
94C SER* 3.7 18.8 - - - +
95C PHE* 3.1 13.5 + - + +
97C PRO* 1.3 72.9 - - + +
99C CYS* 1.3 59.6 + - - +
100C ARG* 2.9 13.2 + - - +
127C PHE* 3.4 36.8 - - + -
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Residues in contact with CYS 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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233A TYR* 4.5 3.5 + - - -
6C PHE* 3.5 15.9 - - - -
95C PHE* 3.2 45.7 + - - -
96C LEU* 2.9 13.9 + - + +
98C ILE* 1.3 73.9 - - - +
100C ARG* 1.3 71.6 + - - +
101C VAL* 3.3 4.6 + - + +
123C GLY* 3.5 24.8 - - - +
124C ILE* 3.8 11.7 - - - +
127C PHE* 3.7 22.9 - - - -
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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