Contacts of the strand formed by residues 44 - 52 (chain B) 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 GLN 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP* 5.4 5.9 - - - +
32B PHE* 6.0 0.4 - - - -
42B GLU 3.5 8.3 + - - +
43B HIS* 1.3 74.7 - - - +
45B LEU* 1.4 60.3 + - - +
46B ALA 3.9 0.2 - - - -
95B GLU* 3.4 44.9 + - + +
96B LEU 3.2 20.3 - - - +
97B ASP* 4.2 16.8 + - - +
98B PRO* 4.3 1.6 - - - -
117B HIS* 3.7 8.2 + - - -
118B VAL* 3.0 43.5 + - + +
119B ALA 5.0 6.6 + - - +
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Residues in contact with LEU 45 (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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19B TRP* 3.7 53.2 - - + -
32B PHE* 4.1 32.1 - - + -
44B GLN* 1.4 71.0 - - - +
46B ALA* 1.3 59.0 + - - +
47B LEU* 4.0 10.3 + - + -
94B ILE 3.9 0.7 - - - +
95B GLU* 3.5 1.1 - - - -
96B LEU* 2.8 41.3 + - + +
98B PRO* 4.7 1.2 - - - +
100B VAL* 4.9 5.4 - - + -
102B PHE* 4.2 16.4 - - + -
115B GLY* 4.3 1.1 - - - -
116B GLN 3.7 23.6 - - - +
117B HIS* 4.4 10.1 - - + -
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Residues in contact with ALA 46 (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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44B GLN 3.9 1.0 - - - -
45B LEU* 1.3 71.4 - - - +
47B LEU* 1.3 64.3 + - - +
48B ARG* 3.7 33.3 - - - +
94B ILE 3.4 7.0 - - - +
95B GLU* 3.7 22.2 - - - +
115B GLY* 3.1 2.3 - - - -
116B GLN 2.9 36.7 + - - +
118B VAL* 4.1 9.6 - - + -
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Residues in contact with LEU 47 (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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19B TRP* 4.5 1.6 - - + -
45B LEU* 4.0 15.0 + - + -
46B ALA* 1.3 75.8 - - - +
48B ARG* 1.3 71.6 + - - +
50B VAL* 5.4 0.7 - - + -
78B ILE* 3.8 28.3 - - + -
91B MET* 3.6 33.7 - - + +
92B VAL* 5.4 0.2 - - - -
93B GLY 5.5 0.9 + - - -
94B ILE* 3.1 39.7 + - + +
96B LEU* 4.5 7.6 - - + -
102B PHE* 4.0 31.4 - - + -
113B ILE* 4.0 20.9 - - + -
114B SER 3.6 4.3 - - - +
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Residues in contact with ARG 48 (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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18B ILE* 5.4 1.6 - - + -
46B ALA* 3.7 31.6 - - - +
47B LEU* 1.3 80.7 + - - +
49B THR* 1.3 66.8 + - - +
90B THR* 3.7 4.7 - - - +
91B MET* 2.9 28.1 + - - +
92B VAL* 6.3 0.2 - - - +
93B GLY 5.8 4.0 - - - +
95B GLU* 5.1 3.4 + - - -
114B SER* 2.7 22.4 + - - +
115B GLY* 4.0 15.0 - - - +
116B GLN* 2.7 35.9 + - + +
118B VAL* 4.1 12.1 - - - +
92C VAL 3.5 19.8 + - - +
93C GLY* 3.0 23.3 + - - -
94C ILE* 3.6 27.1 - - + -
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Residues in contact with THR 49 (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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48B ARG* 1.3 90.6 - - + +
50B VAL* 1.3 71.3 + - - +
51B CYS* 4.9 0.9 - - - -
88B MET* 4.4 8.5 - - + -
89B ALA 3.2 12.8 - - - +
90B THR* 4.6 4.3 - - + +
91B MET* 4.2 4.1 - - - +
112B TYR 5.2 0.2 + - - -
113B ILE* 3.7 0.7 - - - +
114B SER* 2.7 42.2 + - - +
77C PRO 4.2 1.2 + - - -
78C ILE* 3.4 33.9 + - + +
91C MET* 4.5 17.7 - - + -
92C VAL 6.3 0.2 - - - +
94C ILE* 4.6 6.3 - - + -
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Residues in contact with VAL 50 (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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47B LEU* 5.4 0.7 - - + -
49B THR* 1.3 79.3 - - - +
51B CYS* 1.3 69.9 + - - +
63B VAL* 4.3 7.9 - - + -
78B ILE* 5.4 5.2 - - + -
79B ALA* 4.2 19.7 - - + -
81B LEU* 3.4 22.7 - - + -
88B MET* 3.2 1.7 - - - +
89B ALA 3.0 32.8 + - - +
91B MET* 4.1 23.8 - - + -
111B LEU* 4.1 16.2 - - + -
112B TYR 3.2 8.7 - - - +
113B ILE* 4.3 20.4 - - + -
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Residues in contact with CYS 51 (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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49B THR* 4.9 1.1 - - - -
50B VAL* 1.3 80.7 - - - +
52B LEU* 1.3 62.6 + - - +
81B LEU* 4.2 1.8 - - - -
87B PRO 3.6 4.7 - - - -
88B MET* 3.6 13.7 - - + -
111B LEU* 3.6 1.3 - - - -
112B TYR* 2.7 52.6 + - - +
77C PRO* 4.2 13.5 - - - -
78C ILE 4.1 7.6 - - - +
79C ALA* 4.0 19.7 - - - -
80C THR* 3.3 21.5 - - - +
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Residues in contact with LEU 52 (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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51B CYS* 1.3 72.5 - - - +
53B GLY* 1.3 65.0 + - - +
56B ALA* 4.0 3.1 - - + -
61B HIS* 3.6 40.8 - - + +
81B LEU* 4.0 10.1 - - + -
82B LYS* 3.8 15.3 - - - +
83B PRO* 3.5 43.5 - - + -
87B PRO* 3.2 18.9 + - + +
110B PRO 3.5 9.2 - - - +
111B LEU* 4.0 14.8 - - + -
112B TYR* 4.3 2.6 - - - -
60C PHE* 6.5 0.2 - - + -
62C ILE* 3.8 1.9 - - - +
80C THR* 2.7 37.0 + - + +
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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