Contacts of the strand formed by residues 398 - 405 (chain B) in PDB entry 2W8B
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 GLY 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B SER* 3.5 6.2 - - - -
395B GLN* 2.9 31.6 + - - +
396B GLY 3.3 1.0 + - - -
397B MET* 1.3 80.2 - - - +
399B SER* 1.3 64.3 + - - -
400B VAL* 3.8 3.6 + - - +
420B GLN* 3.3 17.7 - - - -
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Residues in contact with SER 399 (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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378B GLU* 4.9 5.2 + - - -
392B SER* 3.9 5.5 + - - -
393B SER 3.3 8.0 + - - -
394B SER* 4.5 6.9 + - - +
398B GLY* 1.3 71.3 - - - -
400B VAL* 1.3 66.3 + - - +
420B GLN* 2.8 26.9 + - - -
421B VAL* 2.9 33.0 + - - +
422B LYS* 3.7 27.3 + - - +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 2.8 19.2 + - - -
393B SER* 2.9 41.5 + - - +
395B GLN* 3.8 42.0 - - + +
398B GLY 4.0 8.5 - - - +
399B SER* 1.3 80.8 - - - +
401B LEU* 1.3 64.4 + - - +
402B ASN* 3.8 6.7 - - - +
413B ARG* 5.8 1.3 - - + -
414B LEU 6.0 0.9 - - - +
415B PRO* 6.1 5.2 - - + -
421B VAL* 3.3 14.6 - - + +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 5.4 3.1 - - + -
167B ILE* 4.8 2.7 - - + -
169B TYR* 4.1 20.4 - - + -
390B ILE* 4.2 18.6 - - + -
391B TYR 3.3 5.6 - - - +
392B SER* 4.3 0.2 - - - -
400B VAL* 1.3 77.8 - - - +
402B ASN* 1.3 67.8 + - - +
413B ARG* 3.8 6.4 - - - +
414B LEU* 3.5 47.0 + - + +
421B VAL* 3.6 42.2 - - + +
422B LYS* 4.0 6.1 - - - -
424B PRO* 3.8 32.5 - - + -
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Residues in contact with ASN 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B THR* 3.7 18.5 - - - +
390B ILE* 3.4 7.7 - - - +
391B TYR* 2.8 62.6 + - + +
392B SER 4.0 0.2 - - - -
393B SER* 2.7 40.8 + - - +
395B GLN* 5.1 1.2 - - - +
400B VAL* 3.8 5.8 - - - +
401B LEU* 1.3 80.7 + - - +
403B LEU* 1.3 63.8 + - - +
412B ALA 3.5 5.7 - - - +
413B ARG* 3.8 17.5 - - - +
414B LEU* 4.7 0.4 - - - -
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.8 28.3 - - + -
187B TYR* 5.4 2.7 - - + +
388B MET* 4.4 5.2 - - + -
389B VAL 3.4 6.3 - - - +
390B ILE* 3.9 16.2 - - + -
391B TYR* 4.5 1.7 + - - -
402B ASN* 1.3 75.2 - - - +
404B VAL* 1.3 62.3 + - - +
410B PHE* 4.5 12.1 - - + -
411B LYS* 3.4 4.0 - - - +
412B ALA* 2.8 52.9 + - + +
413B ARG* 4.6 0.4 - - - +
414B LEU* 3.5 25.1 - - + -
426B TRP* 3.5 38.6 - - + -
1433B GOL 5.9 1.1 - - - +
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Residues in contact with VAL 404 (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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358B ILE* 5.1 2.0 - - + -
371B LEU* 3.7 39.0 - - + +
372B SER* 4.9 4.5 - - - -
388B MET* 3.8 4.0 - - - -
389B VAL* 2.8 45.8 + - + +
391B TYR* 3.9 23.6 - - + +
403B LEU* 1.3 75.8 - - - +
405B SER* 1.3 72.7 + - - +
408B GLY* 4.2 7.6 - - - -
410B PHE 3.2 13.2 - - - +
411B LYS* 4.1 13.0 - - + -
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Residues in contact with SER 405 (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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65B SER 5.2 2.2 - - - -
66B GLY* 5.7 0.4 - - - -
371B LEU* 3.9 4.7 - - - +
387B THR 3.4 13.9 - - - -
388B MET* 3.6 13.6 - - - -
404B VAL* 1.3 81.9 - - - +
406B THR* 1.3 60.2 + - - +
407B ASP* 2.6 28.1 + - - -
408B GLY* 3.0 16.8 + - - -
409B ARG 3.3 1.2 + - - -
410B PHE* 2.8 42.2 + - - +
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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