Contacts of the strand formed by residues 38 - 43 (chain B) 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 THR 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 1.3 81.3 + - - +
39B SER* 1.3 70.7 + - - +
40B VAL* 4.8 2.9 - - + -
52B THR* 3.8 0.2 - - - -
53B GLN* 2.8 42.9 + - - +
167B ALA* 5.2 0.7 - - + -
168B ALA 3.3 11.4 - - - +
170B VAL* 3.4 4.9 + - - +
171B LYS* 2.9 57.3 + - + +
175B SER* 5.2 0.2 - - - -
202B LEU* 3.6 23.5 - - + +
205B VAL* 5.2 0.4 - - + -
206B LEU* 4.7 0.6 - - - +
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.3 1.2 - - - +
38B THR* 1.3 74.9 + - - +
40B VAL* 1.3 64.0 + - - +
51B VAL 3.4 5.2 - - - -
52B THR* 3.0 31.7 + - - +
79B VAL* 3.7 17.5 - - - +
80B MET 4.3 1.2 + - - -
81B THR* 3.0 25.1 + - - +
139B ILE* 5.9 2.0 - - - -
167B ALA* 3.1 6.9 - - - +
168B ALA* 2.9 35.0 + - - -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 4.8 1.6 - - + -
39B SER* 1.3 80.3 - - - +
41B ALA* 1.3 65.0 + - - +
42B VAL* 4.1 13.9 - - + -
49B VAL 4.0 0.3 - - - +
50B ILE* 3.5 4.7 - - - +
51B VAL* 2.8 44.5 + - + +
79B VAL* 6.0 0.7 - - - -
139B ILE* 5.7 0.2 - - - -
166B THR 3.8 9.9 - - - +
167B ALA* 4.2 0.9 - - + -
175B SER* 3.9 14.4 - - - +
179B LEU* 4.0 19.7 - - + -
198B ALA* 4.2 10.0 - - - +
201B CYS* 4.1 8.5 - - - -
202B LEU* 3.8 39.3 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 1.3 75.7 - - - +
42B VAL* 1.3 65.9 + - - +
49B VAL 3.3 5.4 - - - -
50B ILE* 3.5 23.8 - - + -
139B ILE* 3.7 24.9 - - + -
141B ILE* 4.9 0.9 - - + -
151B VAL* 4.2 13.0 - - + +
165B ALA* 3.3 3.0 - - - +
166B THR* 2.9 38.0 + - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 4.1 3.1 - - + -
41B ALA* 1.3 82.4 - - - +
43B ARG* 1.3 67.5 + - - +
48B ALA* 3.5 2.1 - - - +
49B VAL 2.8 35.1 + - - +
151B VAL* 4.3 5.5 - - - +
164B LYS 4.0 2.9 - - - +
165B ALA* 4.2 11.4 - - + -
179B LEU* 4.1 20.4 - - + -
183B VAL* 6.0 0.9 - - + -
189B TRP* 4.4 20.4 - - + -
194B THR* 3.7 23.8 - - + +
197B THR* 4.8 2.7 - - + -
198B ALA* 3.8 32.3 - - + +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 1.3 81.6 - - - +
44B GLY* 1.3 71.1 + - - +
47B CYS 4.0 2.7 - - - -
48B ALA* 4.3 1.1 - - + +
149B PRO* 3.5 36.2 + - + +
150B GLN* 4.4 15.1 - - - +
151B VAL* 3.8 16.0 - - + +
163B PHE 3.5 17.8 + - - -
164B LYS* 2.9 55.3 + - - +
189B TRP* 4.7 9.9 - - - -
57C ASP* 2.3 32.5 + - - +
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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
------------------------------------------------------------
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