Contacts of the strand formed by residues 45 - 52 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C TRP* 3.5 62.1 - - + -
32C PHE* 4.0 38.2 - - + -
44C GLN* 1.3 70.2 - - - +
46C ALA* 1.3 58.9 + - - +
47C LEU* 3.9 17.3 + - + -
94C ILE 3.7 1.2 - - - +
95C GLU* 3.2 3.5 - - - -
96C LEU* 2.6 49.1 + - + +
100C VAL* 5.4 0.4 - - + -
102C PHE* 4.1 11.2 - - + -
115C GLY 4.4 0.2 - - - -
116C GLN 3.6 22.4 - - - +
117C HIS* 4.6 3.6 - - + +
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Residues in contact with ALA 46 (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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44C GLN 3.9 1.8 + - - -
45C LEU* 1.3 70.6 - - - +
47C LEU* 1.3 61.8 + - - +
48C ARG* 3.7 32.6 - - - +
94C ILE 3.4 7.6 - - - +
95C GLU* 4.0 15.9 - - + +
115C GLY* 3.1 3.3 - - - -
116C GLN 2.8 43.4 + - - +
118C VAL* 4.0 13.1 - - + +
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Residues in contact with LEU 47 (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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19C TRP* 4.3 0.9 - - + -
45C LEU* 3.9 29.3 - - + -
46C ALA* 1.3 74.4 - - - +
48C ARG* 1.3 72.3 + - - +
50C VAL* 5.7 0.4 - - + -
65C ILE* 4.8 0.2 - - + -
78C ILE* 3.9 27.4 - - + -
91C MET* 3.7 28.8 - - + +
92C VAL* 5.5 0.2 - - - -
93C GLY 5.5 0.7 + - - -
94C ILE* 3.0 38.2 + - + +
96C LEU* 4.4 5.8 - - + -
102C PHE* 4.0 18.6 - - + -
113C ILE* 3.9 25.4 - - + -
114C SER 3.6 5.2 - - - +
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Residues in contact with ARG 48 (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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16C ASP 5.8 0.2 - - - +
18C ILE* 5.5 2.5 - - + -
46C ALA* 3.7 29.1 - - - +
47C LEU* 1.3 82.3 + - - +
49C THR* 1.3 67.3 + - - +
90C THR* 3.6 3.8 - - - +
91C MET* 2.8 30.7 + - - +
93C GLY 6.1 0.6 - - - +
95C GLU* 5.2 3.6 + - - -
114C SER* 2.8 19.8 + - - +
115C GLY* 3.7 19.7 - - - +
116C GLN* 2.8 32.2 + - + +
118C VAL* 3.9 11.9 - - - +
92D VAL 3.7 16.6 + - - +
93D GLY* 2.9 29.6 + - - -
94D ILE* 3.8 26.5 - - + -
95D GLU* 6.0 0.6 - - - +
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Residues in contact with THR 49 (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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48C ARG* 1.3 87.5 + - + +
50C VAL* 1.3 67.3 + - - +
51C CYS* 5.0 1.4 - - - -
88C MET* 3.9 16.2 - - + -
89C ALA 3.3 10.3 - - - +
90C THR* 4.4 7.2 - - + +
91C MET* 4.3 3.4 - - - +
112C TYR 4.5 0.2 - - - -
113C ILE* 3.5 4.2 - - - +
114C SER* 2.8 47.1 + - - +
77D PRO 4.3 0.9 + - - -
78D ILE* 3.1 31.6 + - - +
91D MET* 4.6 14.8 - - - -
94D ILE* 4.8 6.1 - - + -
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Residues in contact with VAL 50 (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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47C LEU* 5.7 0.2 - - + -
49C THR* 1.3 79.4 - - - +
51C CYS* 1.3 65.6 + - - +
63C VAL* 4.2 12.8 - - + -
78C ILE* 5.1 6.1 - - + -
79C ALA* 4.5 12.6 - - + -
81C LEU* 3.7 21.8 - - + -
88C MET* 3.3 1.9 - - - +
89C ALA 3.0 34.4 + - - +
91C MET* 4.4 21.7 - - + +
111C LEU* 3.8 24.5 - - + -
112C TYR 3.2 4.7 - - - -
113C ILE* 4.4 18.4 - - + -
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Residues in contact with CYS 51 (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 THR* 5.0 1.1 - - - -
50C VAL* 1.3 79.1 - - - +
52C LEU* 1.3 65.0 + - - +
81C LEU* 4.3 2.7 - - - -
87C PRO 3.4 5.4 - - - -
88C MET* 3.4 17.7 - - + +
111C LEU* 3.5 2.0 - - - +
112C TYR* 2.9 51.1 + - - -
77D PRO* 4.4 8.5 - - - -
78D ILE* 4.4 7.0 - - - +
79D ALA* 4.3 13.0 - - - -
80D THR* 3.5 24.2 - - - +
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Residues in contact with LEU 52 (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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51C CYS* 1.3 74.3 - - - +
53C GLY* 1.3 68.8 + - - +
56C ALA* 4.3 3.4 - - + -
61C HIS* 3.7 36.6 - - + +
81C LEU* 3.9 14.6 - - + -
82C LYS 3.9 13.7 - - - +
83C PRO* 3.6 42.2 - - + -
87C PRO* 3.0 23.2 + - + +
110C PRO 3.3 9.0 - - - +
111C LEU* 3.8 18.6 - - + -
112C TYR* 4.3 2.2 - - - -
62D ILE* 3.9 2.1 - - - +
80D THR* 2.7 30.5 + - + +
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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