Contacts of the helix formed by residues 93 - 105 (chain D) 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 LEU 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D VAL* 2.9 30.4 + - + +
92D LEU* 1.3 94.5 - - + +
94D VAL* 1.3 66.7 + - - +
96D PRO* 3.9 0.9 - - - -
97D PHE* 3.1 40.6 + - + +
117D TRP* 4.0 4.7 - - - -
120D LEU* 4.3 27.6 - - + -
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D VAL* 3.5 5.2 + - + +
90D VAL* 3.6 25.6 - - + +
93D LEU* 1.3 76.1 - - + +
95D VAL* 1.3 61.0 + - - +
98D GLY* 3.0 16.6 + - - -
117D TRP* 2.9 28.6 + - - +
120D LEU* 4.1 15.0 - - + +
121D ASP* 3.8 38.4 - - + +
124D CYS* 4.9 1.1 - - - -
333D TYR* 3.5 40.8 - - + +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 5.0 9.6 - - + -
52D VAL* 3.8 26.0 - - + +
55D ILE* 4.7 8.5 - - + -
90D VAL* 2.9 31.5 + - + +
91D GLY* 4.8 2.7 - - - -
94D VAL* 1.3 71.2 - - - +
96D PRO* 1.3 69.9 - - + +
98D GLY* 3.2 1.4 + - - +
99D ALA* 2.8 24.2 + - + +
330D TRP* 4.0 20.0 - - + -
333D TYR* 3.7 40.6 - - + -
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Residues in contact with PRO 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 4.6 14.8 - - + -
91D GLY 3.3 24.5 - - - +
92D LEU* 3.3 28.7 - - - +
93D LEU 3.9 0.4 - - - -
94D VAL 3.7 2.9 - - - -
95D VAL* 1.3 92.9 - - + +
97D PHE* 1.3 68.6 + - + +
99D ALA* 3.3 12.9 + - + +
100D THR* 3.3 17.4 + - - +
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Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU 4.8 4.3 - - - -
93D LEU* 3.1 39.0 + - + +
94D VAL 3.4 1.6 + - - -
95D VAL 3.3 0.4 - - - -
96D PRO* 1.3 84.9 - - + +
98D GLY* 1.3 63.1 + - - +
100D THR* 2.5 25.1 + - - -
101D LEU* 3.2 7.4 + - - +
107D TRP* 4.1 18.0 - + + -
109D TRP* 3.4 64.2 - + + -
113D LEU* 5.5 5.6 - - + -
117D TRP* 4.0 12.8 - + + +
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL 3.0 12.3 + - - -
95D VAL* 3.6 4.0 - - - -
97D PHE* 1.3 76.6 - - - +
99D ALA* 1.3 56.5 + - - +
101D LEU* 3.2 3.8 + - - +
102D VAL* 3.0 34.9 + - - +
117D TRP* 3.5 26.5 - - - -
330D TRP* 3.9 12.3 - - - -
333D TYR* 5.8 1.8 - - - -
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 6.1 2.0 - - + -
95D VAL* 2.8 14.7 + - + +
96D PRO* 3.4 13.2 - - + +
98D GLY* 1.3 73.7 - - - +
100D THR* 1.3 65.4 + - + +
102D VAL* 4.6 1.6 - - - +
103D VAL* 3.0 33.8 + - + +
330D TRP* 3.8 15.3 - - + -
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PRO 3.3 11.6 + - - +
97D PHE* 2.5 20.5 + - - -
99D ALA* 1.3 77.5 - - + +
101D LEU* 1.3 56.9 + - - +
103D VAL* 5.0 1.6 - - - -
104D ARG* 2.8 37.6 + - - +
106D THR 4.6 1.6 - - - -
107D TRP* 5.2 0.3 - - - -
108D LEU* 4.7 11.2 - - + +
109D TRP* 3.2 40.2 + - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D PHE 3.2 7.1 + - - +
98D GLY* 3.4 9.2 - - - +
99D ALA 3.1 0.8 - - - -
100D THR* 1.3 79.6 + - - +
102D VAL* 1.3 72.2 + - + +
105D GLY* 2.8 26.9 + - - +
106D THR* 3.3 35.8 + - - +
107D TRP* 3.4 25.8 - - + +
117D TRP* 4.0 28.0 - - + -
197D GLY 5.1 0.7 - - - +
199D CYS* 4.4 15.0 - - + +
200D ASP* 5.5 4.0 - - - +
400D P32 6.0 0.7 - - + -
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLY* 3.0 17.3 + - - +
99D ALA* 4.3 2.0 - - - +
101D LEU* 1.3 81.7 - - + +
103D VAL* 1.3 65.7 + - + +
105D GLY* 3.9 5.2 + - - -
326D VAL* 4.3 24.7 - - + -
330D TRP* 3.6 31.0 - - + +
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ALA* 3.0 21.6 + - + +
100D THR* 4.4 1.6 - - - +
102D VAL* 1.3 79.8 - - + +
104D ARG* 1.3 67.2 + - - +
105D GLY* 2.9 5.9 + - - -
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 2.8 24.4 + - - +
103D VAL* 1.3 78.0 - - + +
105D GLY* 1.3 57.0 + - - +
106D THR* 3.3 11.6 - - - +
108D LEU* 3.4 40.0 - - + +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 2.8 18.5 + - - +
102D VAL 4.3 4.3 - - - -
103D VAL 2.9 5.4 + - - -
104D ARG* 1.3 76.0 - - - +
106D THR* 1.3 63.8 + - - +
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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