Contacts of the strand formed by residues 17 - 23 (chain H) 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 17 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASP* 1.3 84.5 - - - +
18H ILE* 1.4 64.2 + - - +
116H GLN* 3.2 6.3 - - - -
117H HIS* 3.0 57.0 + - + +
67I ASP* 5.4 7.4 - - + +
68I GLN 5.0 1.6 - - - +
69I GLU* 4.0 27.4 - - + -
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Residues in contact with ILE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASP 3.6 1.1 + - - +
17H LEU* 1.4 76.5 - - - +
19H TRP* 1.3 62.2 + - - +
115H GLY 3.5 5.6 - - - +
116H GLN* 3.8 9.6 - - + +
117H HIS* 3.9 7.6 + - - -
65I ILE* 4.1 27.1 - - + +
67I ASP* 4.8 16.6 - - + +
69I GLU* 5.9 5.7 - - + +
74I LYS* 3.9 23.6 - - + +
76I VAL* 3.4 31.0 - - + -
94I ILE* 5.6 0.9 - - + -
96I LEU* 3.1 36.1 - - + -
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Residues in contact with TRP 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ILE* 1.3 81.3 - - - +
20H GLY* 1.3 65.5 + - - +
21H CYS* 3.7 24.2 - - + -
30H PHE* 3.7 31.9 - + - -
32H PHE* 3.4 21.7 - + + -
45H LEU* 3.6 34.3 - - + -
47H LEU* 4.2 2.9 - - + -
102H PHE* 4.0 11.7 - + - -
113H ILE* 3.9 25.8 - - + -
114H SER* 3.2 3.6 - - - -
115H GLY* 2.6 54.1 + - - +
117H HIS* 3.7 34.5 - + + +
76I VAL* 3.4 9.0 - - - +
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Residues in contact with GLY 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 1.3 94.4 + - - +
21H CYS* 1.3 62.8 + - - +
30H PHE* 5.3 1.7 - - - -
113H ILE 3.1 11.9 - - - -
76I VAL* 3.9 18.9 - - - +
77I PRO* 6.2 0.7 - - - -
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Residues in contact with CYS 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 3.7 22.0 - - + -
20H GLY* 1.3 74.5 - - - +
22H GLU* 1.3 59.7 + - - +
23H LEU* 4.6 6.7 - - - -
30H PHE* 3.8 47.1 - - + -
102H PHE* 4.7 2.2 - - - -
111H LEU 3.8 0.5 - - - +
112H TYR* 3.3 8.5 - - - +
113H ILE* 2.9 54.5 + - - +
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Residues in contact with GLU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H CYS* 1.3 76.2 - - - +
23H LEU* 1.3 77.2 + - - +
24H ASN* 2.8 27.7 + - - +
27H ASN* 4.3 7.4 - - - +
30H PHE* 5.0 4.0 - - - +
110H PRO* 3.4 22.8 - - + +
111H LEU 3.5 3.6 - - - +
112H TYR* 3.6 33.1 + - + -
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H CYS* 4.6 7.9 - - - -
22H GLU* 1.3 76.9 - - - +
24H ASN* 1.3 62.7 + - - +
27H ASN 3.4 3.8 - - - +
28H LYS 3.7 0.4 - - - -
29H THR 3.5 39.9 - - - +
30H PHE* 3.6 16.8 - - + +
63H VAL* 4.4 1.8 - - + -
102H PHE* 3.8 12.8 - - + +
103H ARG 4.0 3.6 - - - -
104H LEU* 3.8 32.0 - - + +
109H GLY* 4.0 1.7 - - - -
110H PRO* 3.6 1.4 - - - +
111H LEU* 3.0 58.7 + - + +
113H ILE* 4.2 9.9 - - + -
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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