Contacts of the strand formed by residues 349 - 354 (chain B) in PDB entry 1D0N
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 GLN 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG 4.3 10.8 - - - +
121B GLU* 5.6 0.2 - - - +
125B PHE* 3.1 29.2 + - + +
126B GLU 3.2 4.6 + - - -
127B SER* 3.1 37.7 - - - +
128B ALA 4.7 0.4 + - - +
312B ASP 5.6 0.7 - - - +
313B GLY 3.1 19.1 + - - +
314B LYS* 3.1 24.2 + - + +
315B ILE* 3.0 26.9 + - - +
347B GLN 4.0 3.4 - - - +
348B THR* 1.3 72.7 - - - +
350B VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 350 (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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119B HIS* 3.3 3.8 - - - +
120B ARG* 2.8 56.6 + - + +
314B LYS* 4.5 0.4 - - - -
315B ILE* 3.5 13.9 - - + +
317B VAL* 4.4 5.6 - - + -
332B LEU* 5.0 4.9 - - + -
335B ALA* 3.6 26.2 - - + -
339B ILE* 3.6 31.6 - - + -
348B THR 3.6 4.4 + - - +
349B GLN* 1.3 80.5 - - - +
351B SER* 1.3 74.6 + - - +
352B VAL* 4.8 7.4 - - + +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 5.1 1.1 - - - -
118B GLN 3.2 8.3 - - - -
119B HIS* 2.9 27.9 + - - -
314B LYS* 3.3 29.0 + - - +
315B ILE 3.2 5.1 + - - -
316B PHE* 3.2 9.6 - - - -
317B VAL* 2.9 24.1 + - - +
350B VAL* 1.3 77.2 + - - +
352B VAL* 1.3 61.7 + - - +
353B LEU* 3.8 13.7 - - - +
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Residues in contact with VAL 352 (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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116B ALA 4.3 1.2 - - - +
117B VAL* 3.7 1.4 - - - -
118B GLN* 2.9 71.9 + - + +
317B VAL* 3.3 29.8 - - + -
319B LYS* 3.9 24.9 - - + -
331B ALA* 4.1 6.5 - - + -
332B LEU* 3.7 22.9 - - + -
350B VAL* 4.9 4.7 - - + +
351B SER* 1.3 74.1 - - - +
353B LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 353 (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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117B VAL* 4.3 13.9 - - + -
316B PHE* 4.3 14.8 - - + -
317B VAL 2.9 9.5 + - - +
318B TRP* 3.6 11.9 - - + -
319B LYS* 3.0 31.1 + - - +
351B SER* 3.8 26.0 - - - +
352B VAL* 1.3 79.3 - - - +
354B PRO* 1.3 71.0 - - + +
357B GLY 4.3 1.8 - - - +
358B GLU* 3.5 30.1 - - + -
359B THR* 3.5 23.8 - - + +
362B PHE* 4.0 16.4 - - + -
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Residues in contact with PRO 354 (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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114B GLY 3.8 22.9 - - - +
115B ARG* 4.2 10.8 - - - +
116B ALA 3.6 19.5 - - - +
117B VAL* 4.4 7.0 - - + -
318B TRP* 4.5 1.3 - - - -
319B LYS* 3.9 18.2 - - + +
353B LEU* 1.3 91.1 - - + +
355B GLU* 1.3 59.3 + - - +
356B GLY 3.2 0.2 + - - -
357B GLY* 2.7 44.2 + - - +
358B GLU* 3.7 3.8 + - - +
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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