Contacts of the strand formed by residues 393 - 399 (chain B) in PDB entry 2WNW
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 LEU 393 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1448A GOL 5.1 0.5 + - - -
34B ILE* 4.6 6.7 - - + -
388B SER* 3.1 25.6 + - - +
389B TYR* 3.4 41.3 - - + +
390B ASP* 2.8 13.0 + - + +
391B ASN* 4.0 3.0 - - - -
392B LEU* 1.3 76.8 - - - +
394B GLU* 1.3 63.9 + - - +
395B GLU* 3.7 2.5 + - - +
409B VAL* 4.6 11.0 - - + -
410B TYR 3.6 2.5 - - - +
411B ASN* 3.7 36.6 - - + +
417B ARG* 4.0 19.1 - - + +
418B ARG 3.7 9.6 - - - +
419B CYS* 3.9 11.4 - - + -
432B LEU* 5.0 6.7 - - + -
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Residues in contact with GLU 394 (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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1448A GOL 5.6 2.0 - - - -
315B HIS* 2.8 52.2 + - - +
318B ILE* 3.9 22.0 - - + +
319B GLY 5.4 0.2 + - - -
391B ASN* 3.6 16.8 - - - +
392B LEU 4.2 4.3 - - - +
393B LEU* 1.3 70.2 - - - +
395B GLU* 1.3 63.8 + - - +
409B VAL* 3.3 1.4 - - - +
410B TYR* 2.7 55.8 + - + +
412B ARG* 2.9 27.8 + - - +
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Residues in contact with GLU 395 (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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1448A GOL 3.1 31.6 + - - +
34B ILE* 4.0 17.6 - - + +
318B ILE* 3.7 8.3 - - - +
322B LYS* 3.1 23.4 + - - +
386B SER* 2.5 34.2 + - - -
387B SER* 3.8 4.7 - - - -
388B SER* 4.0 18.8 - - - -
393B LEU 4.1 1.6 - - - +
394B GLU* 1.3 79.1 - - - +
396B VAL* 1.3 63.0 + - - +
407B LEU* 3.7 10.4 - - + +
408B VAL 3.1 13.2 - - - +
409B VAL* 4.2 13.2 - - + -
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Residues in contact with VAL 396 (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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318B ILE* 4.1 12.6 - - + +
321B PHE* 4.0 9.6 - - + -
322B LYS* 3.6 37.5 - - + +
373B PHE* 3.7 35.9 - - + -
383B VAL* 4.1 15.3 - - + -
395B GLU* 1.3 78.9 - - - +
397B GLY* 1.3 63.9 + - - +
398B PHE* 3.9 7.6 - - + -
406B VAL 4.2 0.3 - - - +
407B LEU* 3.8 4.2 - - - -
408B VAL* 2.9 33.0 + - + +
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Residues in contact with GLY 397 (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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383B VAL* 3.3 11.3 - - - +
384B MET* 2.8 40.6 + - - -
386B SER* 4.2 6.7 + - - -
396B VAL* 1.3 76.7 - - - +
398B PHE* 1.3 62.0 + - - -
406B VAL 3.1 10.8 - - - -
407B LEU* 3.9 12.5 - - - +
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Residues in contact with PHE 398 (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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45B ILE* 4.3 11.2 - - + -
48B PHE* 4.7 2.2 - + - -
321B PHE* 3.9 26.5 - + + -
373B PHE* 3.8 38.1 - + - -
377B VAL* 3.7 42.6 - - + -
381B ALA* 4.5 3.6 - - + -
382B ARG 3.2 11.0 - - - +
383B VAL* 3.7 31.2 - - + -
384B MET* 3.2 9.9 - - - +
396B VAL* 3.9 14.8 - - + -
397B GLY* 1.3 75.8 - - - -
399B VAL* 1.3 65.0 + - - +
400B ASN* 4.1 0.9 - - - +
405B ARG* 3.5 1.0 - - - -
406B VAL* 2.7 43.7 + - + +
408B VAL* 4.7 2.9 - - + -
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Residues in contact with VAL 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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38B PRO* 4.1 24.0 - - + +
41B ALA* 6.1 4.0 - - + -
381B ALA* 3.4 2.6 - - - -
382B ARG* 2.8 34.8 + - + +
384B MET* 4.1 17.5 - - + -
398B PHE* 1.3 78.2 - - - +
400B ASN* 1.3 74.8 + - - +
403B GLY* 4.0 10.3 - - - +
404B GLU 3.3 2.9 - - - -
405B ARG* 3.7 29.2 - - + +
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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