Contacts of the strand formed by residues 100 - 106 (chain K) 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 VAL 100 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30K PHE 4.0 0.9 - - - +
31K GLU* 3.3 1.0 - - - -
32K PHE* 2.6 46.9 + - + +
45K LEU* 4.5 15.5 - - + -
65K ILE* 4.0 22.7 - - + -
66K VAL 5.1 2.2 - - - +
96K LEU* 4.1 40.2 - - + -
97K ASP 4.3 9.2 - - - +
98K PRO* 4.6 4.0 - - + -
99K PRO* 1.3 79.2 - - - +
101K THR* 1.3 65.2 + - - +
102K PHE* 4.2 16.6 - - + -
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Residues in contact with THR 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K THR* 3.2 35.0 - - + -
30K PHE 3.5 5.4 - - - +
31K GLU* 3.3 26.6 + - + +
65K ILE* 3.5 8.5 - - - +
66K VAL* 3.2 53.0 + - + +
99K PRO 5.3 0.5 - - - -
100K VAL* 1.3 77.3 - - - +
102K PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TRP* 4.0 25.1 - + - -
21K CYS* 4.7 3.6 - - - -
23K LEU* 4.1 11.3 - - + +
28K LYS 3.7 0.2 - - - +
29K THR* 3.0 8.2 - - - +
30K PHE* 2.7 47.1 + - + +
32K PHE* 4.8 2.5 - - + -
45K LEU* 4.5 3.6 - - + -
47K LEU* 3.8 37.9 - - + -
63K VAL* 4.7 4.3 - - + -
64K GLU 3.5 3.6 - - - +
65K ILE* 3.7 29.4 - - + -
78K ILE* 4.7 1.3 - - + -
96K LEU* 4.0 12.8 - - + -
100K VAL* 4.4 23.6 - - + -
101K THR* 1.3 74.0 - - - +
103K ARG* 1.3 61.4 + - - +
113K ILE* 3.6 30.1 - - + -
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Residues in contact with ARG 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LEU* 3.8 5.2 - - - -
28K LYS* 3.1 15.9 - - + +
29K THR* 3.4 21.4 + - + +
63K VAL* 3.5 2.1 - - - -
64K GLU* 2.8 60.2 + - + +
66K VAL* 4.1 24.9 - - + +
73K GLU* 5.6 3.0 - - - +
75K SER* 3.3 25.1 + - - -
102K PHE* 1.3 76.8 - - - +
104K LEU* 1.3 73.3 + - - +
105K LYS* 3.3 3.5 + - - +
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LEU* 3.7 27.1 - - + +
24K ASN* 3.9 22.7 - - - +
28K LYS* 2.7 34.5 + - + +
61K HIS* 4.3 4.0 - - + -
62K ILE 3.4 10.8 - - - +
63K VAL* 5.0 0.7 - - - -
103K ARG* 1.3 76.2 - - - +
105K LYS* 1.3 64.8 + - - +
106K ALA* 3.2 17.4 + - - +
107K GLY 3.4 24.0 - - - +
109K GLY 4.2 5.4 - - - +
111K LEU* 3.4 38.8 - - + -
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Residues in contact with LYS 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J GLU* 5.4 0.4 + - - -
112J TYR* 2.9 40.5 + - - +
28K LYS* 6.0 0.7 + - - -
62K ILE* 3.2 32.9 + - + +
64K GLU* 3.6 38.8 + - + +
77K PRO* 4.4 7.9 - - + +
103K ARG* 3.3 6.4 + - - +
104K LEU* 1.3 72.1 - - - +
106K ALA* 1.3 63.6 + - + +
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Residues in contact with ALA 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J ASP* 3.3 30.7 - - - +
60K PHE 3.6 9.9 - - - +
61K HIS* 3.0 3.5 - - - -
62K ILE* 2.9 35.1 + - + +
104K LEU* 3.2 11.6 - - - +
105K LYS* 1.3 84.0 - - + +
107K GLY* 1.3 63.2 + - - +
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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