Contacts of the strand formed by residues 402 - 407 (chain B) in PDB entry 2W8D
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 PHE 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ASN* 3.1 28.0 + - + -
247B VAL 3.0 25.5 + - - -
248B ILE* 3.9 22.2 - - + -
337B TYR* 3.2 11.2 - - - -
338B THR* 3.1 16.2 - - - +
395B LEU* 3.7 35.9 - - + -
396B GLU* 6.1 0.2 - - - -
398B LEU* 3.9 30.3 - - + -
399B PRO 4.3 4.5 - - - +
400B GLN* 3.7 27.1 - - + -
401B PRO* 1.3 74.2 - - - +
403B TYR* 1.3 59.8 + - - +
404B THR* 3.6 14.6 - - + -
460B LEU* 4.2 19.7 - - + -
464B SER* 4.8 0.2 - - - -
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Residues in contact with TYR 403 (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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247B VAL* 3.4 22.9 - - + -
249B TYR* 3.4 33.3 + + - -
304B MSE 4.5 2.3 + - - -
305B GLU* 2.5 31.1 + - - -
328B VAL* 3.3 36.6 - - + +
329B PRO* 3.7 29.4 - - + -
332B LEU* 4.0 11.2 - - + -
337B TYR* 4.2 13.0 - - + -
338B THR 2.9 9.3 + - - +
339B SER* 3.1 28.0 - - - -
340B ALA 3.2 3.5 + - - +
361B ILE* 4.8 0.9 - - + -
402B PHE* 1.3 74.8 - - - +
404B THR* 1.3 63.1 + - - +
405B LYS* 4.3 11.7 - - + -
530B ILE* 5.7 1.8 - - + -
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL 3.0 13.1 + - - +
248B ILE* 3.4 19.4 - - - +
249B TYR* 2.9 29.5 + - - +
340B ALA* 3.2 8.5 - - + +
342B PHE* 3.8 7.9 - - + -
395B LEU* 3.8 9.0 - - + -
398B LEU* 3.6 24.2 - - + -
402B PHE* 3.6 19.7 - - + -
403B TYR* 1.3 81.0 - - - +
405B LYS* 1.3 65.1 + - - +
406B PHE* 3.6 16.1 - - - -
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Residues in contact with LYS 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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249B TYR* 3.4 19.1 - - + -
301B GLU* 2.5 35.3 + - - +
304B MSE 5.5 2.2 - - - -
305B GLU* 2.8 43.2 + - - +
340B ALA 3.1 5.2 + - - +
341B THR* 3.5 24.7 - - + +
342B PHE* 2.9 29.1 + - - -
356B TYR* 3.3 19.8 + - - -
361B ILE* 4.4 6.7 - - + -
403B TYR* 4.3 10.8 - - + -
404B THR* 1.3 76.2 - - - +
406B PHE* 1.3 62.7 + - - +
407B ILE* 3.9 12.8 - - + +
469B TYR* 5.3 4.0 - - - -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.9 18.2 - - + -
249B TYR 2.8 18.2 + - - +
250B VAL* 3.4 11.9 - - + +
251B SER 3.1 21.8 + - - -
342B PHE* 3.5 40.4 - + + -
387B PHE* 4.1 9.6 - + + -
388B PHE* 3.8 28.7 - + + -
391B SER* 3.7 25.6 - - - -
395B LEU* 3.8 25.8 - - + -
404B THR* 3.6 20.9 - - - -
405B LYS* 1.3 76.2 - - - +
407B ILE* 1.3 61.7 + - - +
408B THR 3.8 0.7 - - - -
451B PHE* 3.9 14.6 - + - -
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Residues in contact with ILE 407 (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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251B SER* 4.0 21.1 - - - +
297B TPO 4.0 25.1 - - + -
301B GLU* 3.7 31.0 - - + +
341B THR* 3.9 21.8 - - + -
342B PHE 3.1 9.4 + - - +
343B HIS* 3.0 45.4 + - + +
344B GLY 4.6 0.5 + - - -
352B ARG* 4.1 6.1 - - - +
356B TYR* 4.4 1.3 - - - +
387B PHE* 4.3 6.5 - - - -
405B LYS* 4.5 16.2 - - + +
406B PHE* 1.3 71.9 - - - +
408B THR* 1.3 65.7 + - - +
409B LEU* 3.9 1.7 + - - +
469B TYR* 4.5 2.2 - - - +
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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