Contacts of the strand formed by residues 41 - 45 (chain E) 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 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E VAL 3.6 4.0 - - - +
36E ARG* 3.8 31.4 - - + -
40E ILE* 1.3 78.7 - - - +
42E VAL* 1.3 60.7 + - - +
43E LEU* 4.3 3.0 + - - +
134E VAL* 3.6 30.3 - - + -
135E GLY 4.6 9.6 - - - +
136E PHE* 5.4 2.9 - - + +
142E PRO* 4.0 14.8 - - + -
143E ARG 4.5 9.0 - - - +
144E LEU* 5.7 1.1 - - + -
209E ALA 4.1 0.2 - - - +
210E VAL* 3.3 4.2 - - - -
211E MET* 2.9 48.7 + - + +
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLY* 3.3 2.6 - - - -
35E VAL* 2.9 39.3 + - + +
40E ILE* 6.2 0.4 - - + -
41E VAL* 1.3 74.7 - - - +
43E LEU* 1.3 61.7 + - - +
134E VAL* 5.4 1.6 - - - +
187E THR* 4.9 5.1 - - - -
188E ILE* 4.9 11.7 - - - +
191E VAL* 3.7 25.9 - - + +
208E LEU* 6.2 1.8 - - + -
209E ALA 3.5 4.9 - - - +
210E VAL* 3.8 18.2 - - + -
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL 3.4 11.4 - - - +
34E GLY* 4.3 4.5 - - - -
41E VAL 4.5 2.5 - - - +
42E VAL* 1.3 76.7 - - - +
44E GLY* 1.3 59.0 + - - +
62E ILE* 3.5 24.6 - - + +
70E CYS* 3.6 13.5 - - - -
71E MET* 3.8 11.0 - - - -
72E ALA* 3.6 41.3 - - + +
132E LEU* 4.3 4.0 - - + +
134E VAL* 3.6 42.4 - - + -
191E VAL* 4.6 2.5 - - - -
208E LEU* 3.6 1.2 - - - -
209E ALA* 2.9 39.9 + - + +
210E VAL* 5.5 0.7 - - - -
217E LEU* 5.6 0.2 - - + -
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Residues in contact with GLY 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E THR 4.2 0.2 - - - +
32E ALA* 3.5 2.4 - - - -
33E VAL* 2.9 38.4 + - - +
43E LEU* 1.3 75.9 - - - +
45E VAL* 1.3 60.6 + - - -
62E ILE* 4.4 1.8 - - - -
191E VAL* 4.0 15.3 - - - +
195E LEU* 5.5 5.5 - - - +
206E ILE* 5.7 1.6 - - - -
207E GLU 3.2 13.0 - - - -
208E LEU* 4.1 4.0 - - - -
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E SER* 4.3 4.3 - - - -
31E THR 3.3 11.2 - - - +
32E ALA* 4.2 11.2 - - + +
44E GLY* 1.3 74.2 - - - -
46E GLU* 1.3 74.6 + - - +
47E LYS 5.7 0.2 - - - +
61E LYS* 3.7 45.5 - - + +
62E ILE* 4.1 21.3 - - + -
72E ALA* 5.7 1.6 - - + -
73E PHE 4.7 1.1 - - - +
195E LEU* 6.0 2.2 - - - -
206E ILE* 4.0 5.3 - - - +
207E GLU* 3.0 43.1 + - + +
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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