Contacts of the strand formed by residues 18 - 23 (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 ILE 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D LEU* 1.4 82.6 + - - +
19D TRP* 1.3 61.6 + - - +
48D ARG* 5.4 2.5 - - + -
114D SER* 5.0 1.8 - - - -
115D GLY 3.5 18.6 - - - +
116D GLN* 4.0 14.3 - - + +
117D HIS* 5.1 1.9 + - - -
65E ILE* 4.1 37.2 - - + -
67E ASP* 4.2 19.7 - - + +
76E VAL* 4.2 28.0 - - + +
78E ILE* 5.0 5.6 - - + -
94E ILE* 4.8 8.3 - - + -
96E LEU* 4.6 14.6 - - + -
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Residues in contact with TRP 19 (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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17D LEU 4.4 0.9 - - - +
18D ILE* 1.3 75.3 - - - +
20D GLY* 1.3 71.9 + - - +
21D CYS* 3.9 21.5 - - - -
30D PHE* 4.2 27.0 - + - -
32D PHE* 3.9 20.2 - + - -
45D LEU* 3.9 24.2 - - + -
47D LEU* 4.3 2.7 - - + -
102D PHE* 3.8 25.4 - + - -
113D ILE* 4.1 20.0 - - + -
114D SER* 3.3 7.3 - - - -
115D GLY* 2.7 50.7 + - - +
116D GLN 4.6 0.7 - - - +
117D HIS* 4.3 26.2 - + - +
76E VAL* 3.5 13.4 - - - +
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Residues in contact with GLY 20 (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* 1.3 94.2 + - - +
21D CYS* 1.3 61.2 + - - +
30D PHE* 5.4 2.9 - - - -
113D ILE 3.2 14.4 - - - -
76E VAL* 3.8 16.9 - - - +
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Residues in contact with CYS 21 (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* 3.9 16.5 - - + -
20D GLY* 1.3 73.8 - - - +
22D GLU* 1.3 60.8 + - - +
23D LEU* 4.1 5.8 - - - -
30D PHE* 3.7 46.2 - - + -
102D PHE* 4.6 2.9 - - - -
112D TYR* 3.4 10.7 - - - +
113D ILE* 3.2 53.0 + - - +
77E PRO* 5.8 0.9 - - - +
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Residues in contact with GLU 22 (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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21D CYS* 1.3 75.0 - - - +
23D LEU* 1.3 75.2 + - - +
24D ASN* 3.1 25.4 + - - +
27D ASN* 4.4 9.9 - - - +
29D THR 5.4 0.7 - - - +
30D PHE* 5.3 3.5 - - - +
110D PRO* 3.7 18.6 - - + +
111D LEU 3.4 6.5 - - - +
112D TYR* 3.3 30.8 + - + -
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Residues in contact with LEU 23 (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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21D CYS* 4.1 8.7 - - - -
22D GLU* 1.3 79.7 - - - +
24D ASN* 1.3 62.7 - - - +
27D ASN 3.5 13.2 - - - +
28D LYS 3.9 0.4 - - - +
29D THR 4.2 1.1 - - - +
30D PHE* 3.8 32.1 - - + +
63D VAL* 4.7 3.1 - - + -
102D PHE* 3.8 20.4 - - + +
103D ARG 3.9 3.6 - - - -
104D LEU* 3.5 44.2 - - + +
109D GLY* 4.0 1.0 - - - -
110D PRO* 3.7 1.0 - - - +
111D LEU* 2.9 51.4 + - + +
113D ILE* 4.3 6.7 - - + -
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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