Contacts of the strand formed by residues 43 - 48 (chain j) in PDB entry 5GJQ
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 43 (chain j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37j ILE 3.5 15.0 - - - +
38j LEU* 3.9 20.9 - - + -
39j ALA* 4.5 0.9 - - - +
42j GLY* 1.3 77.2 - - - +
44j LEU* 1.3 69.2 + - - +
137j ILE* 3.6 32.0 - - + +
138j GLY 4.6 1.3 - - - +
145j PHE* 3.7 22.2 - - + -
146j GLN 4.3 5.4 - - - +
147j LEU* 4.3 11.4 - - + -
186j LEU* 4.7 2.9 - - - +
215j THR* 3.6 1.8 - - - -
216j LEU* 2.9 44.4 + - + +
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Residues in contact with LEU 44 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 5.4 2.2 - - + +
36j GLY* 3.0 24.6 - - - -
37j ILE* 3.0 54.6 + - + +
39j ALA* 6.2 0.2 - - + -
43j VAL* 1.3 81.7 - - - +
45j LEU* 1.3 75.6 + - - +
46j ALA* 4.3 3.4 - - + -
137j ILE* 4.7 1.3 - - - -
186j LEU* 4.9 4.5 - - + -
189j ALA* 3.8 21.8 - - + +
190j LEU* 4.8 8.5 - - + -
193j ALA* 4.1 22.7 - - + -
213j ILE* 4.1 11.4 - - + -
214j ALA 3.3 12.3 - - - +
215j THR* 3.6 18.4 - - + -
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Residues in contact with LEU 45 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34j CYS* 4.6 0.7 - - - -
35j LEU 3.4 11.7 - - - +
36j GLY* 4.3 5.2 - - - -
44j LEU* 1.3 73.4 - - - +
46j ALA* 1.3 62.9 + - - +
65j ILE* 4.0 23.3 - - + +
74j CYS* 3.9 6.3 - - - +
75j SER* 3.6 34.3 - - - +
135j LEU* 3.8 31.0 - - + +
137j ILE* 3.6 44.8 - - + +
147j LEU* 4.7 0.7 - - + -
212j GLU 4.5 0.2 - - - -
213j ILE* 3.5 3.5 - - - +
214j ALA* 2.8 37.6 + - + +
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Residues in contact with ALA 46 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33j THR 4.3 0.2 - - - +
34j CYS* 3.6 1.6 - - - -
35j LEU* 2.9 48.5 + - + +
44j LEU* 4.3 14.1 - - + -
45j LEU* 1.3 76.8 - - - +
47j ALA* 1.3 61.2 + - - +
193j ALA* 4.7 7.9 - - + +
197j LEU* 5.9 4.7 - - + -
211j VAL* 6.2 1.8 - - + -
212j GLU 3.2 9.6 - - - +
213j ILE* 4.4 16.8 - - + -
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Residues in contact with ALA 47 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33j THR 3.4 9.4 - - - +
34j CYS* 4.0 18.2 - - + -
46j ALA* 1.3 75.2 - - - +
48j GLU* 1.3 61.6 + - - +
49j ARG* 3.7 0.4 + - - -
64j LYS* 4.1 29.4 - - + -
65j ILE* 4.8 5.8 - - + +
75j SER* 4.2 2.7 - - - +
211j VAL* 3.5 5.2 - - - +
212j GLU* 2.9 39.2 + - + +
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Residues in contact with GLU 48 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32j GLY* 4.2 1.4 - - - -
33j THR* 2.7 46.6 + - - +
47j ALA* 1.3 70.5 - - - +
49j ARG* 1.3 70.0 + - - +
50j ARG* 2.5 40.5 + - - -
64j LYS* 3.4 26.5 + - - +
166j ASN* 5.1 2.4 + - - +
201j MET* 5.0 20.4 - - + -
202j ASP* 5.6 2.4 + - - +
210j LYS* 3.6 9.6 - - + +
211j VAL* 4.7 4.9 - - + +
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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