Contacts of the strand formed by residues 45 - 52 (chain D) in PDB entry 2VTX
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D TRP* 3.9 39.0 - - + -
32D PHE* 3.8 37.0 - - + -
44D GLN* 1.3 74.8 - - - +
46D ALA* 1.3 66.4 + - - +
47D LEU* 3.9 22.8 + - + -
94D ILE 3.6 1.6 - - - +
95D GLU* 3.0 7.4 - - - -
96D LEU* 2.5 52.5 + - + +
100D VAL* 5.2 0.4 - - + -
102D PHE* 4.1 10.5 - - + -
115D GLY* 4.1 3.1 - - - -
116D GLN 3.7 24.9 - - - +
117D HIS* 4.5 3.6 - - - +
118D VAL* 5.2 0.2 - - - -
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Residues in contact with ALA 46 (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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45D LEU* 1.3 71.9 - - - +
47D LEU* 1.3 66.4 + - - +
48D ARG* 3.7 31.4 - - - +
94D ILE 3.4 7.4 - - - +
95D GLU* 4.2 18.2 - - + +
115D GLY* 3.0 2.2 - - - -
116D GLN 2.9 38.5 + - - +
118D VAL* 4.4 7.6 - - + +
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Residues in contact with LEU 47 (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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19D TRP* 4.3 2.9 - - + -
45D LEU* 3.9 17.7 - - + +
46D ALA* 1.3 75.9 - - - +
48D ARG* 1.3 72.1 + - - +
65D ILE* 4.5 0.7 - - + -
78D ILE* 4.0 25.4 - - + -
91D MET* 3.5 32.1 - - + +
92D VAL* 5.4 0.2 - - - -
93D GLY 5.5 0.7 + - - -
94D ILE* 2.9 44.0 + - + +
96D LEU* 4.3 4.9 - - + -
102D PHE* 3.8 34.3 - - + -
113D ILE* 4.0 20.4 - - + -
114D SER 3.6 5.4 - - - +
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Residues in contact with ARG 48 (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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18D ILE* 5.4 1.6 - - + -
46D ALA* 3.7 31.6 + - - +
47D LEU* 1.3 82.6 + - - +
49D THR* 1.3 69.3 + - - +
90D THR* 3.7 4.2 - - - +
91D MET* 2.8 27.0 + - - +
93D GLY 6.0 2.0 - - - +
95D GLU* 5.1 4.9 + - - -
114D SER* 3.0 21.3 + - - +
115D GLY* 4.1 10.5 - - - +
116D GLN* 2.8 31.0 + - + +
118D VAL* 5.8 2.0 - - - +
92E VAL* 3.8 16.8 + - - +
93E GLY* 3.0 31.2 + - - -
94E ILE* 3.6 26.9 - - + -
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Residues in contact with THR 49 (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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48D ARG* 1.3 92.8 - - + +
50D VAL* 1.3 66.7 + - - +
51D CYS* 4.2 1.4 - - - -
88D MET* 4.4 8.7 - - + -
89D ALA 3.3 14.1 - - - +
90D THR* 4.3 10.3 - - + +
91D MET* 4.2 4.2 - - - +
112D TYR 3.9 0.2 - - - +
113D ILE* 3.5 2.8 - - - +
114D SER* 2.9 43.2 + - - +
77E PRO 4.4 0.9 + - - -
78E ILE* 3.0 33.4 + - - +
91E MET* 4.6 9.6 - - + -
92E VAL 6.1 0.7 - - - +
94E ILE* 4.7 9.0 - - + -
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Residues in contact with VAL 50 (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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47D LEU* 5.9 0.4 - - + -
49D THR* 1.3 79.0 - - - +
51D CYS* 1.3 67.0 + - - +
63D VAL* 4.2 10.8 - - + -
78D ILE* 5.0 4.9 - - + -
79D ALA* 4.5 12.6 - - + -
81D LEU* 4.0 10.1 - - + +
88D MET* 3.4 1.7 - - - +
89D ALA* 3.0 31.0 + - + +
91D MET* 4.1 25.4 - - + -
111D LEU* 3.7 33.9 - - + -
112D TYR 3.2 11.4 - - - +
113D ILE* 4.3 17.5 - - + -
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Residues in contact with CYS 51 (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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49D THR* 4.8 1.8 - - - -
50D VAL* 1.3 77.9 - - - +
52D LEU* 1.3 63.9 + - - +
81D LEU* 4.4 2.2 - - - -
87D PRO 3.7 5.2 - - - -
88D MET* 3.5 14.6 - - + +
111D LEU* 3.6 1.6 - - - -
112D TYR* 2.8 45.7 + - - -
77E PRO* 4.1 24.5 - - - -
78E ILE 4.1 7.2 - - - +
79E ALA* 3.9 22.0 - - - -
80E THR* 3.4 20.6 - - - +
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Residues in contact with LEU 52 (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 CYS* 1.3 73.6 - - - +
53D GLY* 1.3 67.0 + - - +
56D ALA* 4.4 3.6 - - + -
61D HIS* 3.7 36.1 - - + +
81D LEU* 3.9 20.0 - - + -
82D LYS* 3.7 16.4 - - - +
83D PRO* 3.4 45.3 - - + -
87D PRO* 3.2 21.5 + - + +
110D PRO 3.6 3.8 - - - +
111D LEU* 4.1 12.1 - - + -
112D TYR* 4.2 2.6 - - - -
62E ILE* 3.6 2.4 - - - +
80E THR* 2.8 25.7 + - + +
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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