Contacts of the strand formed by residues 18 - 23 (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 ILE 18 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ILE* 3.3 41.7 - - + +
67G ASP* 3.9 18.1 + - - +
74G LYS* 4.8 10.9 + - + +
76G VAL* 3.6 30.9 - - + +
78G ILE* 4.8 1.3 - - + -
94G ILE* 5.7 2.7 - - + -
96G LEU* 4.3 13.7 - - + +
17K LEU* 1.3 83.7 + - - +
19K TRP* 1.3 69.9 + - - +
48K ARG* 5.6 2.2 - - + -
114K SER* 4.5 4.3 - - - +
115K GLY 2.9 35.4 - - - +
116K GLN* 4.2 10.0 - - + +
117K HIS* 5.3 0.9 - - - -
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Residues in contact with TRP 19 (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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74G LYS* 4.5 8.3 - - - +
76G VAL* 3.5 6.3 - - - +
17K LEU 3.4 0.6 + - - -
18K ILE* 1.3 81.0 - - - +
20K GLY* 1.3 75.2 + - - +
21K CYS* 3.6 35.0 - - + -
30K PHE* 4.3 13.5 - + - -
32K PHE* 3.4 42.5 - + + -
45K LEU* 3.8 26.5 - - + -
47K LEU* 4.4 2.9 - - + -
102K PHE* 4.0 18.4 - + - -
113K ILE* 4.1 20.6 - - + -
114K SER* 3.5 1.8 - - - -
115K GLY 2.8 44.4 + - - +
116K GLN 5.0 0.2 - - - +
117K HIS* 4.1 19.7 - + + +
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Residues in contact with GLY 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LYS* 3.7 14.7 + - - +
76G VAL* 3.7 20.3 - - - +
77G PRO* 6.1 1.1 - - - -
19K TRP* 1.3 93.5 + - - +
21K CYS* 1.3 60.1 + - - +
30K PHE* 5.3 2.1 - - - -
113K ILE 3.1 14.4 - - - -
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Residues in contact with CYS 21 (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* 3.6 24.4 - - + -
20K GLY* 1.3 73.0 - - - +
22K GLU* 1.3 59.9 + - - +
23K LEU* 4.2 6.9 + - - -
30K PHE* 3.7 46.4 - - + -
102K PHE* 4.7 3.8 - - - -
111K LEU 3.5 0.9 - - - +
112K TYR* 3.3 7.6 - - - +
113K ILE* 2.9 47.3 + - - +
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Residues in contact with GLU 22 (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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21K CYS* 1.3 74.2 - - - +
23K LEU* 1.3 72.6 + - - +
24K ASN* 2.7 32.9 + - - +
27K ASN* 4.0 10.4 - - - +
30K PHE* 4.8 8.4 - - - +
110K PRO* 3.6 23.7 - - + +
111K LEU 3.3 7.4 - - - +
112K TYR* 3.3 26.2 + - + -
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Residues in contact with LEU 23 (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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21K CYS* 4.3 8.1 - - - -
22K GLU* 1.3 81.1 - - - +
24K ASN* 1.3 59.8 + - - +
27K ASN 3.3 11.7 - - - +
28K LYS 4.0 3.6 - - - +
30K PHE* 3.6 34.1 - - + +
63K VAL* 4.0 20.9 - - + -
102K PHE* 4.1 10.8 - - + +
103K ARG 3.8 7.2 - - - -
104K LEU* 3.7 42.1 - - + +
109K GLY* 3.8 2.4 - - - -
110K PRO* 3.5 3.1 - - - +
111K LEU* 2.8 46.7 + - + +
113K ILE* 4.2 6.1 - - + -
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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