Contacts of the strand formed by residues 46 - 51 (chain K) in PDB entry 5T0G
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 46 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40K ILE 3.5 14.8 - - - +
41K GLN* 4.7 4.0 - - - -
45K GLY* 1.3 78.1 - - - +
47K CYS* 1.3 62.3 + - - +
48K LEU* 5.4 4.5 - - + -
144K GLY* 4.4 7.9 - - - -
145K GLY 4.0 4.3 - - - +
151K PRO* 3.6 19.7 - - + -
152K GLN 3.4 28.0 - - - +
153K LEU* 4.2 25.1 - - + -
191K LEU* 4.7 0.8 - - - +
218K ALA 3.3 2.6 - - - +
219K THR* 3.2 4.9 - - - -
220K VAL* 2.9 42.5 + - + +
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Residues in contact with CYS 47 (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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39K GLY 3.6 0.2 - - - -
40K ILE* 2.7 53.9 + - - +
42K THR* 4.3 4.9 - - - -
45K GLY 4.2 0.4 - - - -
46K VAL* 1.3 74.4 - - - +
48K LEU* 1.3 59.3 + - - +
191K LEU* 4.3 9.4 - - + -
194K ALA* 3.7 38.6 - - - -
195K ILE* 4.3 9.6 - - + -
198K SER* 5.8 2.0 - - - -
217K LEU* 6.2 3.1 - - + -
218K ALA 3.2 3.8 - - - -
219K THR* 3.6 19.7 - - + -
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Residues in contact with LEU 48 (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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37K ALA* 4.4 7.0 - - + -
38K ILE 3.9 3.8 - - - +
39K GLY* 3.6 20.6 - - - +
46K VAL* 5.4 3.8 - - + -
47K CYS* 1.3 77.0 - - - +
49K ALA* 1.3 74.6 + - - +
67K ILE* 3.9 18.1 - - + +
76K CYS 5.4 1.3 - - - -
77K ALA* 3.7 35.2 - - + +
142K LEU* 4.1 20.0 - - + +
144K GLY* 5.6 2.7 - - - +
153K LEU* 4.4 12.6 - - + -
216K GLU 3.7 0.3 - - - +
217K LEU* 3.4 4.4 - - - +
218K ALA* 2.5 52.5 + - + +
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Residues in contact with ALA 49 (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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37K ALA* 3.3 6.4 - - - +
38K ILE* 3.0 35.6 + - + +
48K LEU* 1.3 78.8 - - - +
50K VAL* 1.3 60.1 + - - +
67K ILE* 4.8 0.7 - - - -
198K SER* 4.4 10.1 - - - -
202K LEU* 3.7 25.5 - - + +
215K ILE* 5.3 0.4 - - + -
216K GLU 3.2 7.6 - - - +
217K LEU* 3.6 24.7 - - + -
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Residues in contact with VAL 50 (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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35K SER* 4.6 2.7 - - - -
36K THR 3.4 18.4 - - - +
37K ALA* 3.6 9.9 - - + -
49K ALA* 1.3 76.3 - - - +
51K GLU* 1.3 79.0 + - - +
52K LYS* 4.7 4.5 - - + +
66K LYS* 3.6 36.3 - - + -
67K ILE* 3.6 26.5 - - + -
202K LEU* 4.7 4.7 - - - -
215K ILE* 3.1 29.2 - - - +
216K GLU* 3.4 19.0 + - + +
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Residues in contact with GLU 51 (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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35K SER* 3.6 23.0 + - - -
36K THR* 3.4 29.6 + - + +
50K VAL* 1.3 79.8 - - - +
52K LYS* 1.3 64.2 + - - +
53K ARG* 3.4 25.5 + - + +
66K LYS* 5.9 0.3 - - - +
202K LEU* 4.8 5.1 - - + +
205K VAL* 4.1 7.3 - - - +
206K MET* 3.2 48.3 + - + +
207K GLU* 4.0 15.6 - - - +
208K GLU* 5.1 3.1 + - - +
214K ASN* 3.7 8.7 - - + +
215K ILE* 4.0 6.3 - - + -
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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