Contacts of the helix formed by residues 74 - 93 (chain B) in PDB entry 2VT4
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 THR 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 6.0 0.2 - - - +
71B ARG 4.1 14.8 - - - +
72B LEU* 3.1 6.5 + - - +
73B GLN* 1.3 79.8 - - - +
75B LEU* 1.3 64.7 + - - +
76B THR* 3.5 8.3 + - - -
77B ASN* 3.1 30.0 + - - +
78B LEU* 3.4 22.2 + - - +
155B ARG* 5.0 6.9 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 1.3 72.2 - - - +
76B THR* 1.3 59.5 + - - +
77B ASN 3.1 1.3 - - - -
78B LEU* 2.8 31.0 + - + +
79B PHE* 3.3 15.9 + - + -
138B ASP* 5.3 1.3 - - - +
139B ARG* 5.7 1.3 - - - +
149B TYR* 3.6 19.1 - - + +
153B MET* 3.3 44.2 - - + +
154B THR 3.4 20.9 - - - +
155B ARG* 3.5 28.7 - - + +
158B ALA* 3.9 14.4 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.8 7.4 - - - -
75B LEU* 1.3 80.1 - - - +
77B ASN* 1.3 66.1 + - - +
79B PHE* 3.2 15.1 + - - +
80B ILE* 3.1 30.7 + - + +
135B ILE* 5.1 6.4 - - + +
138B ASP* 3.7 4.6 + - - +
139B ARG* 3.4 34.7 + - - +
292B LEU* 4.2 26.7 - - + -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.5 22.9 - - + +
72B LEU* 2.4 55.9 + - - +
74B THR* 3.1 22.1 + - - +
75B LEU 3.1 0.8 - - - -
76B THR* 1.3 83.8 - - - +
78B LEU* 1.3 61.6 + - - +
79B PHE 3.3 0.2 - - - -
80B ILE* 3.5 13.7 - - - +
81B THR* 3.0 30.7 + - - -
349B PHE* 4.2 12.3 - - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 5.5 3.4 - - + -
73B GLN* 5.4 15.7 - - + +
74B THR 3.4 13.1 + - - +
75B LEU* 2.8 18.7 + - + +
77B ASN* 1.3 79.3 - - - +
79B PHE* 1.3 59.3 + - - +
81B THR* 3.3 12.3 + - - +
82B SER 3.3 15.2 + - - -
155B ARG* 3.8 46.7 - - + +
158B ALA* 4.2 7.9 - - + -
159B LYS* 4.8 17.0 - - + -
162B ILE* 3.4 19.8 - - + +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.8 17.7 - - + -
76B THR* 3.2 13.9 + - - +
78B LEU* 1.3 73.8 - - - +
80B ILE* 1.3 61.2 + - - +
82B SER* 3.1 6.2 + - - -
83B LEU* 3.0 22.2 + - - +
131B THR* 3.6 15.0 - - + +
134B VAL* 3.9 31.9 - - + -
135B ILE* 3.8 23.6 - - + -
138B ASP* 4.3 24.7 - - + -
153B MET* 5.2 6.1 - - + -
158B ALA* 3.5 46.0 - - + -
161B ILE* 4.3 13.9 - - + -
162B ILE* 3.5 19.1 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.1 13.2 - - + -
66B ILE* 4.2 6.7 - - + -
76B THR* 3.1 19.8 + - + +
77B ASN* 3.5 21.8 - - - +
79B PHE* 1.3 74.3 - - - +
81B THR* 1.3 59.7 + - - +
83B LEU* 3.3 11.8 - - + +
84B ALA* 2.8 25.1 + - - +
135B ILE* 4.4 13.7 - - + -
292B LEU* 4.3 18.2 - - + -
295B ILE* 5.5 2.2 - - + -
343B TYR* 3.0 48.0 + - + +
349B PHE* 5.4 4.0 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 5.3 0.7 - - - -
63B ILE* 3.8 28.4 + - + +
66B ILE* 3.6 22.5 - - - +
77B ASN 3.0 14.5 + - - -
78B LEU* 3.5 15.9 - - - +
79B PHE 3.3 0.2 - - - -
80B ILE* 1.3 73.8 - - - +
82B SER* 1.3 61.2 + - - +
84B ALA* 3.1 6.8 + - - +
85B CYS* 2.9 37.2 + - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 3.3 3.1 + - - -
79B PHE* 3.1 10.9 + - - -
81B THR* 1.3 80.0 - - - +
83B LEU* 1.3 62.5 + - - +
85B CYS* 3.3 8.0 + - - +
86B ALA* 3.1 21.8 + - - +
131B THR* 3.8 14.7 + - - -
162B ILE* 3.5 34.1 - - - +
166B TRP* 3.1 28.1 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE 3.0 10.6 + - - +
80B ILE* 3.3 11.9 - - + +
82B SER* 1.3 77.3 - - - +
84B ALA* 1.3 62.0 + - - +
86B ALA* 3.3 6.4 + - + +
87B ASP* 3.0 28.4 + - - +
128B SER* 3.9 41.3 - - - +
131B THR* 4.1 10.5 - - + +
132B LEU* 3.6 29.4 - - + -
135B ILE* 4.1 13.0 - - + -
295B ILE* 4.2 8.1 - - + -
339B ASN* 3.9 23.8 - - - +
343B TYR* 4.4 6.5 - - - +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 3.5 27.7 - - - +
62B VAL* 4.1 12.1 - - + -
63B ILE* 3.7 25.6 - - + -
80B ILE 2.8 16.5 + - - +
81B THR* 3.1 9.4 + - - +
83B LEU* 1.3 72.0 - - - +
85B CYS* 1.3 58.4 + - - +
87B ASP* 2.9 6.7 + - - +
88B LEU* 2.8 26.9 + - - +
339B ASN* 5.6 0.8 - - - +
343B TYR* 6.3 0.2 - - + -
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Residues in contact with CYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.9 17.0 - - - -
81B THR* 2.9 24.2 + - - +
82B SER* 3.6 10.8 - - - +
84B ALA* 1.3 75.1 - - - +
86B ALA* 1.3 62.4 + - - +
88B LEU* 3.1 10.5 + - - +
89B VAL* 3.1 29.5 + - + +
166B TRP* 4.8 7.6 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER 3.1 9.8 + - - +
83B LEU* 3.8 9.2 - - - +
84B ALA 3.3 0.4 - - - -
85B CYS* 1.3 75.9 - - - +
87B ASP* 1.3 60.9 + - - +
89B VAL* 4.7 1.1 - - - -
90B VAL* 3.3 25.5 + - - +
124B CYS* 3.7 17.3 - - + +
127B ALA* 4.9 2.5 - - + -
128B SER* 4.2 18.8 - - - +
166B TRP* 3.5 32.7 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.3 11.1 - - - +
59B ASN* 3.5 25.4 - - - +
83B LEU* 3.0 17.1 + - - +
84B ALA 2.9 9.1 + - - +
86B ALA* 1.3 77.2 - - - +
88B LEU* 1.3 56.8 + - - +
90B VAL* 3.3 3.6 + - - +
91B GLY 3.0 23.4 + - - -
128B SER* 4.7 8.6 + - - -
335B ASN* 4.8 6.5 + - - -
336B SER* 2.6 40.4 + - - +
339B ASN* 3.6 23.6 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 4.4 1.3 - - - +
56B VAL* 3.8 26.2 - - + +
59B ASN* 3.9 15.0 - - + -
60B VAL* 3.7 33.0 - - + +
63B ILE* 4.2 17.3 - - + -
84B ALA 2.8 10.7 + - - +
85B CYS* 3.4 12.6 - - - +
87B ASP* 1.3 72.9 - - - +
89B VAL* 1.3 68.9 + - + +
91B GLY* 3.0 3.0 + - - +
92B LEU* 2.8 44.5 + - + +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B CYS* 3.1 16.1 + - + +
86B ALA* 4.0 1.3 - - - +
88B LEU* 1.3 75.0 - - + +
90B VAL* 1.3 54.2 + - - +
92B LEU* 4.6 5.1 - - - +
93B LEU* 2.6 43.6 + - + -
94B VAL* 3.4 3.0 + - + -
120B LEU* 4.5 27.4 - - + -
124B CYS* 3.7 27.6 - - - -
166B TRP* 5.3 6.7 - - + -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.8 0.7 - - + -
86B ALA 3.3 15.8 + - - +
87B ASP* 3.3 8.9 + - - +
88B LEU 3.1 1.0 - - - -
89B VAL* 1.3 77.0 - - - +
91B GLY* 1.3 60.8 + - - +
94B VAL* 3.2 25.2 + - + -
95B VAL* 2.8 48.5 + - + +
121B ASP* 5.8 0.7 - - - +
124B CYS* 3.8 21.3 - - + -
125B VAL* 6.4 0.9 - - + -
333B TYR* 4.4 16.4 - - + +
336B SER* 3.9 22.7 - - - +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 3.4 24.1 - - - +
55B ILE* 3.5 32.7 - - - +
56B VAL* 3.8 10.2 - - - +
87B ASP 3.0 12.1 + - - -
88B LEU 3.0 2.2 + - - -
90B VAL* 1.3 76.3 - - - +
92B LEU* 1.3 56.4 + - - +
95B VAL* 4.7 1.8 - - - -
96B PRO* 3.4 14.9 - - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 5.7 1.3 - - + -
56B VAL* 3.6 30.5 - - + -
88B LEU* 2.8 39.1 + - + +
89B VAL* 3.9 4.3 - - - +
91B GLY* 1.3 79.8 - - - +
93B LEU* 1.3 71.2 + - + +
96B PRO* 3.2 17.4 - - - +
97B PHE* 5.4 0.3 - - - -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 2.6 26.0 + - + +
92B LEU* 1.3 88.8 - - + +
94B VAL* 1.3 68.4 + - - +
95B VAL 3.5 0.9 - - - -
96B PRO* 3.7 1.0 - - - +
97B PHE* 3.1 47.3 + - + +
117B TRP* 4.3 2.6 - - + -
120B LEU* 3.6 31.6 - - + -
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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