Contacts of the strand formed by residues 362 - 366 (chain B) in PDB entry 2DH3
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 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 2.4 34.1 + - - +
121B GLY 3.9 3.1 - - - +
123B LEU* 3.8 29.6 - - + -
298B LEU* 4.4 12.3 - - + -
329B TRP* 3.0 18.8 + - - +
330B CYS 3.0 7.9 + - - -
331B SER* 3.2 5.7 - - - -
332B TRP* 2.9 23.7 + - - -
361B GLY* 1.3 71.1 - - - -
363B PRO* 1.3 81.0 - - + +
364B VAL* 4.5 3.1 - - + -
429B ARG* 4.1 2.5 - - - +
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Residues in contact with PRO 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY 3.3 18.4 - - - +
122B ALA* 3.5 15.8 - - + +
123B LEU 3.1 23.0 + - - -
332B TRP* 3.5 9.6 - - + +
356B LEU* 3.4 27.8 - - + +
357B PHE* 4.4 14.6 - - + -
361B GLY 3.6 7.6 - - - +
362B THR* 1.3 86.9 - - - +
364B VAL* 1.3 60.9 + - - +
365B PHE* 4.1 15.7 - - + -
429B ARG* 4.1 10.3 - - - +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.8 23.3 - - + +
125B ARG* 3.2 43.0 + - + +
159B VAL* 5.4 2.2 - - + -
245B GLN* 5.8 1.3 - - - +
276B ILE* 6.1 4.7 - - + -
298B LEU* 5.4 2.7 - - + -
300B THR* 4.3 12.3 - - + -
331B SER* 4.3 16.2 - - - -
332B TRP 3.2 8.8 + - - +
333B SER* 3.7 20.6 - - - -
334B LEU 5.1 0.5 + - - -
340B LEU* 6.1 0.3 - - - +
356B LEU* 5.5 0.7 - - - +
362B THR* 4.2 16.8 - - + +
363B PRO* 1.3 78.3 - - - +
365B PHE* 1.3 71.0 + - - +
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Residues in contact with PHE 365 (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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122B ALA* 4.4 8.5 - - + -
123B LEU 3.0 16.7 + - - +
124B TYR* 3.6 6.9 - - + -
125B ARG* 2.7 41.3 + - - +
340B LEU* 4.3 14.8 - - + -
353B GLN* 4.6 8.5 - - + -
356B LEU* 3.9 39.0 - - + -
357B PHE* 3.8 36.3 - + - -
363B PRO* 4.1 16.4 - - + -
364B VAL* 1.3 78.2 - - - +
366B SER* 1.3 61.2 + - - +
369B ASP* 3.6 26.5 - - + +
422B PHE* 3.9 23.8 - + + -
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Residues in contact with SER 366 (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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124B TYR* 4.6 2.8 - - - -
125B ARG* 3.0 30.3 + - - +
337B ALA 2.6 28.5 + - - -
338B ARG 3.3 6.4 + - - -
339B LEU* 4.2 13.5 - - - -
365B PHE* 1.3 78.5 - - - +
367B TYR* 1.3 67.9 + - - +
368B GLY 3.6 0.2 + - - -
369B ASP* 3.1 28.7 + - - +
370B GLU* 4.4 1.4 - - - +
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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