Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 5VT2
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 ARG 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 3.1 42.7 + - - -
14A CYS 3.2 10.5 - - - +
15A CYS* 1.3 74.8 - - - +
17A LEU* 1.3 73.2 + - - +
18A HIS* 3.2 38.6 + - + +
44A CYS* 3.5 2.8 - - - -
45A ILE 2.9 27.8 + - - +
109A CYS* 3.7 11.4 - - - -
203A EDO 5.7 1.1 - - - -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 1.3 86.9 + - - +
18A HIS* 1.3 63.5 + - - +
19A THR* 5.4 1.3 - - - +
42A THR* 3.8 28.7 - - + -
43A MET 3.3 7.4 - - - +
106A ALA* 3.4 33.7 - - + +
107A LYS* 3.7 23.3 - - - +
108A ASP* 5.4 1.1 - - - -
109A CYS* 3.7 21.3 - - - -
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 5.2 0.2 - - - -
14A CYS 5.1 0.7 - - - -
16A ARG* 3.2 48.1 + - + +
17A LEU* 1.3 75.6 - - - +
19A THR* 1.3 65.2 + - - +
20A VAL* 5.0 2.9 - - + -
41A VAL 3.6 0.7 - - - +
42A THR* 3.3 5.4 - - - -
43A MET* 2.8 35.2 + - + +
45A ILE* 3.5 60.4 - - + +
46A GLY* 5.5 0.7 - - - -
72B THR* 6.0 2.2 - - + -
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.4 0.9 - - - +
18A HIS* 1.3 75.0 - - - +
20A VAL* 1.3 69.2 + - - +
21A ARG 4.2 1.2 + - - +
40A GLN* 3.6 41.7 - - + +
41A VAL 3.5 6.1 - - - +
42A THR* 3.5 17.1 - - + +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 5.0 5.6 - - + -
19A THR* 1.3 80.9 - - - +
21A ARG* 1.3 74.8 + - - +
22A ALA* 3.4 1.4 + - - +
41A VAL* 2.8 38.6 + - - +
43A MET* 4.3 30.7 - - + -
45A ILE* 5.0 2.0 - - + -
65B LEU* 4.7 11.0 - - + -
69B LYS* 4.3 19.7 - - - -
72B THR* 4.4 20.9 - - + -
73B VAL* 4.5 14.6 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 4.0 4.0 + - - +
20A VAL* 1.3 81.2 - - - +
22A ALA* 1.3 62.4 - - - +
26A ASP* 4.6 2.4 - - - +
38A GLU* 2.9 38.8 + - + +
39A VAL 3.7 1.6 - - - -
40A GLN* 3.2 44.3 + - - +
69B LYS* 4.8 8.7 + - - -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.2 5.2 - - + +
21A ARG* 1.3 76.8 - - - +
23A SER* 1.3 61.3 - - - +
26A ASP* 3.6 11.0 - - + +
27A LEU* 3.7 29.8 - - + +
38A GLU* 3.4 6.3 - - - -
39A VAL* 2.8 42.3 + - - +
41A VAL* 4.3 2.2 - - + -
65B LEU* 4.1 16.8 - - + -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 1.3 75.6 - - - +
24A LEU* 1.3 63.3 + - - +
25A GLU* 3.3 11.2 + - - +
26A ASP* 3.0 37.4 + - - +
27A LEU* 3.0 25.1 + - - +
37A ARG 3.8 10.3 - - - -
38A GLU* 4.4 4.5 - - - +
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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