Contacts of the strand formed by residues 43 - 48 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE 3.4 17.3 - - - +
38D LEU* 4.0 19.5 - - + -
39D ALA* 4.3 0.9 - - - +
42D GLY* 1.3 78.1 - - - +
44D LEU* 1.3 69.1 + - - +
137D ILE* 3.6 33.6 - - + +
138D GLY 4.9 1.3 - - - +
145D PHE* 3.8 15.5 - - + -
146D GLN 4.8 4.7 - - - +
147D LEU* 4.7 8.7 - - + -
186D LEU* 4.4 5.9 - - - +
215D THR* 3.5 1.6 - - - -
216D LEU* 2.8 50.4 + - + +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 5.4 1.8 - - + -
36D GLY* 3.1 5.4 - - - -
37D ILE* 3.0 66.4 + - + +
43D VAL* 1.3 82.6 - - - +
45D LEU* 1.3 75.0 + - - +
46D ALA* 4.2 1.8 - - + +
137D ILE* 4.9 1.6 - - - -
186D LEU* 4.7 3.8 - - + -
189D ALA* 3.7 22.0 - - + +
190D LEU* 4.1 14.4 - - + -
193D ALA* 3.9 24.9 - - + -
213D ILE* 4.1 10.8 - - + -
214D ALA 3.2 13.9 - - - +
215D THR* 3.8 13.0 - - + +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D CYS* 4.9 0.4 - - - -
35D LEU 3.4 11.0 - - - +
36D GLY* 4.2 6.1 - - - -
44D LEU* 1.3 74.1 - - - +
46D ALA* 1.3 63.1 + - - +
65D ILE* 4.0 21.1 - - + -
74D CYS* 4.0 7.2 - - - +
75D SER* 3.7 33.2 - - - +
135D LEU* 3.7 31.9 - - + +
137D ILE* 3.6 46.8 - - + +
147D LEU* 4.7 0.7 - - + -
212D GLU 4.5 0.2 - - - -
213D ILE* 3.4 2.4 - - - +
214D ALA* 2.8 36.1 + - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D CYS* 3.6 0.8 - - - -
35D LEU* 2.9 44.0 + - + +
44D LEU* 4.2 10.1 - - + -
45D LEU* 1.3 77.5 - - - +
47D ALA* 1.3 61.0 + - - +
193D ALA* 4.3 4.5 - - + -
197D LEU* 3.5 24.7 - - + +
212D GLU 3.2 8.5 - - - +
213D ILE* 4.2 15.5 - - + -
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR 3.3 10.1 - - - +
34D CYS* 3.9 18.6 - - + -
46D ALA* 1.3 76.5 - - - +
48D GLU* 1.3 67.7 + - - +
49D ARG* 3.6 0.4 + - + -
64D LYS* 4.3 21.1 - - + +
65D ILE* 5.0 5.2 - - + -
75D SER* 4.4 2.0 - - - +
197D LEU* 4.4 5.3 - - - +
211D VAL* 3.5 3.7 - - - -
212D GLU* 2.9 40.2 + - + +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLY* 4.0 1.7 - - - -
33D THR* 2.7 48.9 + - - +
47D ALA* 1.3 70.9 - - - +
49D ARG* 1.3 70.0 + - - +
50D ARG* 2.5 41.9 + - - +
64D LYS* 3.3 28.2 + - - +
166D ASN* 4.8 4.0 + - - +
197D LEU* 4.7 8.3 - - + +
201D MET* 5.4 14.0 - - + -
210D LYS 3.7 8.7 - - - +
211D VAL* 4.9 1.8 - - - +
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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